1990–1998
PhD, Physical Chemistry
University of Pennsylvania, Philadelphia, Pennsylvania
Thesis: Role of solvent on chemical reaction dynamics of small molecules
Advisor: Robin M. Hochstrasser
01
Research Overview
- My research program spans a diverse set of projects unified by a common theme: use of mechanistic modeling, machine learning, and artificial intelligence to scientific challenges in health, biothreats, and energy.
- Funded projects covered membrane biology, host-pathogen interactions, antigen design, toxins, sepsis, immune receptors, dementia, processive enzymatic catalysis, and signaling in immune responses and cancer.
- All projects involve close collaborations with experimental partners, both within LANL and externally (University, Industry and National Lab), and rely on measurements to validate models and test predictions.
- The computational methods I use include molecular dynamics simulations, enhanced sampling, polymer theory, coarse-graining, network theory, sequence analysis, and electronic structure calculations.
- More recently, my research has focused on extending the applicability of large language models and integrating machine learning with mechanistic approaches for physics-based understanding of biology.
02
Education
1986–1989
BS, Chemistry
Virginia Commonwealth University, Richmond, Virginia
03
Positions & Honors
2005–Present
Staff Scientist
Los Alamos National Laboratory, Los Alamos, New Mexico
2013–2016
Research Scientist
New Mexico Consortium, Los Alamos, New Mexico
2001–2004
Postdoctoral Research Associate
Theoretical Biology and Biophysics Group, Los Alamos National Laboratory
Conformational dynamics, stability, and folding studies of short peptides. Advisor: Angel Garcia.
1999–2001
Postdoctoral Fellow
Department of Chemistry, University of Pennsylvania
Structure determination from vibrational-mode couplings deduced from 2D-IR. Advisor: Robin M. Hochstrasser.
04
Patent Applications
- Acute transmitted HIV envelope signatures (2008)
- Genetic signatures in envelope glycoprotein of HIV (2010)
- Mosaic HIV envelope immunogenic polypeptides (2015)
- Mosaic HIV envelopes to induce ADCC responses (Pending, 2021)
- Machine learning algorithm (Hunting Fox) for antibiotic design (2020)
- AI designed ligands for targeting ACE2 receptors for drug delivery (2024)
- SignalGen: Agentic AI molecular biology tool for enhanced expression of proteins (2026)
05
Professional Service
- Served as co-Lead, New Mexico State task force for Alzheimer’s state plan
- Served as Scientific advisory committee member - PEW Research Antibiotic Resistance Project
- Served as q-Bio board member – Governing body for q-Bio conference
- Executive Committee, Center for Nonlinear Studies (CNLS), Los Alamos National Laboratory
- Advisory Group, Southwestern Biofuels Association - involved in New Mexico State Plan for Biofuels
- Affiliate, NIH Spatial Temporal Systems Biology Modeling Center (STMC), University of New Mexico
- Member, New Mexico Alzheimer’s Medical Science Committee
- Recognition for contributions to the DOE National Virtual Biotechnology Laboratory Project -Covid19
- Served as T division chair of Physics-Theory colloquium Series, longest running colloquium series at LANL
Conference Organization
Proteins under Pressure, Energy for the 20 th Century, Antibiotic Resistance, CNLS Annual Conferences, and q-Bio conferences and summer school.
Tutorials & Seminars
A three-part series tutorial on Protein Physics for non-bio audience, a four-part course for Q-bio summer school on multi-scale modeling of biomolecules, and q-Bio Seminar Series at CNLS.
06
Mentoring
Contributes to recruitment of future talent and to enrichment of the LANL postdoc program.
Successful in bringing in top postdoc talent through the highly competitive Directors Fellowship Program. Four out the 16 postdocs mentored are Directors Fellows.
Almost half of the mentored postdocs hold faculty positions at academic institutions.
Current Postdocs
Ilona UnartaHIV immunogen and Glycosylation effects
Brandon PhanAgentic AI framework for antigen design
Past Postdocs
Tongye ShenFaculty, Univ. of Tennessee, Knoxville
Rath ParthasarthiFaculty, Indian Institute of Toxicology, Pune, India
Giovanni BellesiaLead Scientist, Roche Pharmaceuticals
Anurag SethiScientist, Calico / Google
Joshua PhillipsFaculty, Middle Tennessee State Univ.
Cesar LopezScientist, LANL, T-6
Jianhui TianSenior Data Scientist, Instacart
Jeevapani HettigeResearch Specialist, Stowers Institute
Animesh AgarwalFinancial industry, India
Tyler ReddyScientist, LANL, CAI-1
Tim TraversScientist, Pebble Labs
Rachael MansbachFaculty, Concordia Univ, Montreal
Srirupa ChakrabortyFaculty, Northeastern University, Boston
Kien NguyenScientist, Cresset, Oxford, UK
Pedro ManriqueFaculty, Florida Polytechnic University
Mingfei ZhaoFaculty, University of Alabama, Tuscaloosa
Hung DoScientist, NIH
Graduate Students
- Sarah Crotzer (NM Tech, Chemistry), 05/2024 - Current
- Harshita Sahni (UNM, Computer Science), 05/2023 - 09/25/2025
- Anju Yadav (UTEP, Chemistry), 05/2023 - 09/25/2025
- Justin Lindsay (U Tennessee, Chemistry)
- Marc Duchatelier (underprivilege university - LANL program)
- Bruininks, Bart (Univ of Groningen)
- Michael Earsmus (UNM), currently Chief Scientific Officer, Specifica
- Julie Phillips (Merced) Currently, professor at Cumberland University
- Zhuoyun Zhuang (UCSB)
- Parimal Kar (Michigan State) currently Professor IIT, Indor, India
- Andrea Asztalos (Notre Dame)
- Shared grad students with UC Santa Barbara campus on two different joint LANL/UC projects
LANL Work Contributing to PhD Theses
- Megan Murphy (Emory)
- Andrea Asztalos (Notre Dame)
- Frank Erasmus (UNM)
- Justin Lindsay (Tennessee)
- Harshita Sahni (UNM)
Undergraduate Students
- Prasi Desi (Rice), 05/2025 – Current (LANL work contributed to Barry Goldwater fellowship)
- Joe McKenzie (Kansas) 05/2025 – Current
- Connor Brown (Princeton) 05/2025 - 8/2025
- Liam Herndon (MIT): currently at Stanford Grad school
- Celeste Bean (UCSB), currently a ML/engineer at Playstation
- Martin Loncaric, currently a software developer
- Allison Poehler -currently a consultant
- Sundar Subramanian
- Ray Romero, currently a financial analyst, LANL
- Agate Sutton
High School Students
- Amandeep Prasantkumar (currently at UNM BS/MD) 05/2025 – 08/2025
- Aditya Koushik (currently at Stanford). 05/2024 – 08/2025
- Katherine J. Wang (attended Princeton)
07
Scientific Leadership
- Maintains an active research program with a team of postdocs and students on a wide range of topics from machine learning to large language models to molecular simulations to statistical physics.
- LANL PI on two ongoing multi-PI NIH grants with the University of Washington on HIV assembly and the effect of glycosylation on immunogens.
- Co-lead the computational Biology Core of the NIH funded Duke Center for HIV Structural Biology that is responsible developing new approaches and tools to characterize viral fusion and B-cell receptors.
- Co-lead a project on neuronal mimics for toxins funded by DTRA/Dept. of War. Previous toxins projects were funded IARPA.
- Led a team of senior scientists, early career staff, postdocs and students in a multi-million multi-DOE lab -NCI Pilot project on RAS-mediated cancer.
- LANL PI for a team of scientists and postdocs on a NIH-funded multi-institution grant on antibiotic discovery where new approaches were developed that combined simulations with machine learning.
- Served a key role as a computational structural biologist in a large multi-institutional team of scientists and immunologists as part of the NIH funded HIV project (CHAVD) for over 15 years.
- Led a six million-dollar project involving more than seven LANL staff scientists and senior fellows on antibiotic resistance mediated by efflux pumps as part of the LANL LDRD program.
- Led/co-led past LDRD projects on sepsis, biomass deconstruction, intrinsically disordered proteins, pH responsive protein switches and mechanisms of biological transport.
- Served as a co-chair for research in the New Mexico State Plan for Alzheimer’s disease. As part of this effort, brought together researchers from across New Mexico for two annual conferences.
08
Current Research Support
Demonstrated the ability to secure and maintain self-supported funding on a yearly basis since 2005.
Breadth of sponsors: LDRD-DR, LDRD-ER, DOE, NIH, GATES, DTRA and IARPA.
Computational Design of Enhanced Antigen Binding Domains in Nanobodies Used for Intracellular Immuno-Therapeutics
SponsorCRADA / TRGR
Exploiting Glycan Holes and Sequence Diversity of HIV Envelope for Vaccine Immunogen Design
SponsorNIH
RAPTER – Rapid Assessment of Platform Technologies to Expedite Response
SponsorDTRA / DoW
Rationally Designed Neuronal Mimics for Broad-Spectrum Anti-Toxin Countermeasures
SponsorDTRA / DoW
CAPSIID: Computational Approaches for Predicting Shared Interactions of Infectious Diseases
SponsorSNL LDRD Grand Challenge
Interplay of the HIV-1 Env Cytoplasmic Tail, Gag-MA, and Membrane
SponsorNIH
Duke Center for HIV Structural Biology (DCHSB)
SponsorNIH
09
Past Research Support
National Institutes of Health, NIAID
Center for HIV/AIDS Vaccine Immunology and Discovery (CHAVI-ID)
The major goals of this project are to provide project oversight, vaccine design, and statistical analysis of vaccine response data. Genetic sequence statistical analysis, and phylogenetically corrected signature analysis of immunological/sequence data to define critical mutational patterns associated with antibody resistance and susceptibility.
National Institutes of Health, NIAID
Optimization of Efflux Avoidance and Inhibition for Antibiotic Development
Failures of antibiotic therapy occur with increasing frequency in clinics due to the spread of multidrug resistant bacterial pathogens. The goal of the project is to develop a new technology for optimization of efflux avoidance and inhibition in clinical and investigational antibacterial agents that will be effective against Gram-negative bacteria by simultaneously targeting the multidrug efflux mechanism and the outer membrane barrier.
National Institutes of Health, NIGMS
New Mexico Spatiotemporal Modeling Center
The major goals of this project are to understand cell membrane spatial organization and dynamics and to determine how the spatial proximity, dynamics, interactions and biochemical modifications of membrane receptors and signaling proteins together determine the outcome of complex, interacting cell signaling networks important in immune system diseases and cancer.
National Cancer Institute (NCI) – DOE Joint Program
Joint Design of Advanced Computing Solutions for Cancer
The major goal of this project to establish DOE-NCI partnership to advance exascale development through cancer research designed to synergize investments by the NCI and the DOE. Our efforts are focused specifically on Pilot #2 - producing an unprecedented scale of adaptive simulations for the RAS oncogene to facilitate new drug discovery and development.
Office of the Director of National Intelligence, IARPA
Functional Genomic and Computational Assessment of Threats (Fun GCAT)
Evaluating the evolutionarily optimized combinatorial peptide libraries of cone snails
Explore the chemical diversity of conopeptides from a structural perspective while establishing the relationship to sequence and function. Evaluate how the chemical diversity of conopeptides enables exquisite specificity and potency for specific receptors.
DOE/LANL – LDRD Exploratory Research
Nanotherapeutic Adjuvants for Sepsis
Lipopolysaccharide, a component of the cell wall of Gram-negative bacteria, is one of the most potent immune activators and causes of severe sepsis. Humans produce lipoproteins that have been shown to interact with LPS. We are exploring how to rationally design nanoparticles that mimic human lipoproteins for use as therapeutics for sepsis.
DOE/LANL – LDRD Directed Research
Tensor Networks: Robust Unsupervised Machine Learning for Big-Data Analytics
Development of machine learning (ML) techniques for efficient and robust data analyses. The objective of this project is to address this need by development of a novel ML methodology and a unique high-performance computing toolbox to perform data analyses by extracting meaningful and interpretable features from high-dimensional extra-large datasets.
DOE/LANL – LDRD Exploratory Research
Understanding Glycan Dynamics and Heterogeneity for Effective Human Immunodeficiency Virus (HIV) Vaccine Development
Glycans are ubiquitous biomolecules that play important roles in many biological problems, however, their study is complicated by their dynamics and the distinct heterogenous forms that can exist at a protein site. Here, we use novel molecular dynamics simulation strategies to characterize molecular details of glycan dynamics, and machine learning to predict the dominant type of glycan form at a site given the protein sequence.
Defense Threat Reduction Agency, DTRA
Multiplex Diagnosis of Toxins for Biosecurity Applications
DOE/LANL – LDRD Covid-19 Response
Strategies for Coronavirus Vaccines to Protect against the Current Pandemic Strains and Emergent Epidemics
Apply our combined expertise in viral evolution, structural modeling, and immunology to: i ) design a vaccine for the current COVID-19 pandemic; ii) provide ongoing analyses of emerging diversity in the of SARS-CoV-2 Spike protein, a key vaccine target, to support global COVID-19 vaccine efforts; and iii) concurrently design vaccines intended to combat future coronavirus zoonotic outbreaks.
10
Contributions to Science & Publications
Over 100 publications covering at least eight diverse scientific topics with the unique ability to manage, produce and excel in multiple and diverse research topics.
20267 entries
Do HN, Kubicek-Sutherland JZ, Negrete OA, Gnanakaran S. Agentic AI platforms for autonomous training and rule induction of human-human and virus-human protein-protein interactions. arXiv. 2026; arXiv:2604.23924. doi: 10.48550/arXiv.2604.23924.
Do HN, Kubicek-Sutherland JZ, Gnanakaran S. Knowledge database development by large language models for countermeasures against viruses and marine toxins. arXiv. 2026;arXiv:2603.29149. doi: 10.48550/arXiv.2603.29149.
Croft JT, Do HN, Leaman DP, Lovendahl KN, Ralli-Jain P, Chase KJ, Derdeyn CA, Zwick MB, Gnanakaran S, Lee KK. Reconstructing a Missing Link of HIV-1 Assembly: HIV-1 Envelope-Matrix Interactions in a Native Viral Context. bioRxiv. 2026 Jan 16; doi: 10.64898/2026.01.15.699503.
Croft JT, Do HN, Leaman DP, Lovendahl KN, Ralli-Jain P, Chase KJ, Chen C, Prasad VM, Derdeyn CA, Zwick MB, Gnanakaran S, Lee KK. Structure of HIV-1 Env glycoprotein on virions reveals an alternative fusion subunit organization and native membrane coupling. bioRxiv. 2026 Jan 10; doi: 10.64898/2026.01.09.698652.
Do HN, McKenzie J, Gnanakaran S. Challenges of Conventional Iterative All-Atom and Coarse-Grained Multiscale Molecular Dynamics. Sci Rep. 2026 (https://doi.org/10.1038/s41598-026-50650-8).
Carpenter TS, Aydin F, Neale C, Van QN, Zhang X, Bhatia H, Sidabras JW, Frank PH, Georgouli K, Tempkin JOB, Casamayor VB, Gulten G, Shrestha R, Goswami D, Di Natale F, Chavez JR, Moody A, Moon JY, Oppelstrup T, Glosli JN, Dharuman G, Wong S, Liu S, Hengartner NW, López CA, Nguyen K, Stanley CB, Stanton LG, Patel L, Reddy T, Turbyville TJ, Van Essen B, Bremer PT, Lightstone FC, Stephen AG, Gnanakaran S, McCormick F, Nissley DV, Streitz FH, Ingólfsson HI. Dynamics and lipid membrane coupling of the RAS-RAF complex revealed via multiscale simulations. Biophys J. 2026 Jan 20; 125(2):485-501. doi: 10.1016/j.bpj.2025.08.020. Epub 2025 Aug 22.
Unarta IC, Crotzer S, Gnanakaran S. Tracking the protein conformational motions driving HIV-1 membrane fusion. Sci Rep. 2026 Jan 6; 16(1):3387. doi: 10.1038/s41598-025-33350-7.
20258 entries
Sahni H, Crotzer SM, Moore J, Branda SS, Estrada T, Gnanakaran S. Challenges in predicting protein-protein interactions of understudied viruses: Arenavirus-human interactions. Comput Struct Biotechnol J. 2025; 27:5401-5412. doi: 10.1016/j.csbj.2025.11.037. eCollection 2025.
McKenzie JN, Do H, Shanker A, Kubicek-Sutherland J, Gnanakaran S, inventors. SignalGen: A Protein Language Model Based AI Agent For Optimal Signal Peptide Prediction. US patent application Provisional Patent, S number: IDF-000145. 2025 November.
Do HN, Zhao M, Alam SM, Gnanakaran S. Dynamics and Activation of Membrane-Bound B Cell Receptor Assembly. Commun Biol. 2025; 8:226. doi: 10.1038/s42003-025-07618-3.
Do HN, Shanker A, Kidner RQ, Montoya MM, Kubicek-Sutherland JZ, Gnanakaran S. Structure-Based Optimization of Pathogen Signal Sequences for Enhanced Antigen Expression in Humans for Vaccine Designs. bioRxiv. 2025 November. doi: 10.1101/2025.11.25.690495.
Do HN, Kubicek-Sutherland JZ, Gnanakaran S. Prediction of Specificity of α-Conotoxins to Subtypes of Human Nicotinic Acetylcholine Receptors with Semi-supervised Machine Learning. ACS Chem Neurosci. 2025 Jun 18; 16(12):2196-2207. doi: 10.1021/acschemneuro.4c00760. Epub 2025 May 29.
Do HN, Kubicek-Sutherland JZ, Gnanakaran S. Diverse toxins exhibit a common binding mode to the nicotinic acetylcholine receptors. Biophys J. 2025 Apr 15; 124(8):1195-1207. doi: 10.1016/j.bpj.2025.02.022. Epub 2025 Feb 26.
Do HN, Gnanakaran S, inventors. PEPTIDES FOR USE IN MEMBRANE- ANCHORED LIGANDS. US patent application 19/283,058. 2025 July.
Chakraborty S, Nguyen KN, Zhao M, Gnanakaran S. Allosteric Control and Glycan Shielding Adaptations in the SARS-CoV-2 Spike from Early to Peak Virulence. bioRxiv. 2025 Mar 12; doi: 10.1101/2025.03.11.642723.
20247 entries
Zhao M, Lopes LJS, Sahni H, Yadav A, Do HN, Reddy T, López CA, Neale C, Gnanakaran S. Insertion and Anchoring of the HIV-1 Fusion Peptide into a Complex Membrane Mimicking the Human T-Cell. J Phys Chem B. 2024 Dec 26; 128(51):12710-12727. doi: 10.1021/acs.jpcb.4c05018. Epub 2024 Dec 13.
Thakur B, Alam J, Cronin K, Patel P, Anasti K, Kane AP, Hossain A, Do H, Mansouri K, Spence TN, Edwards RJ, Janowska K, Lella M, Cook A, Saunders K, Gnanakaran S, Haynes BF, Acharya P, Alam SM. Anti-HIV-1 B cell antigen receptor signaling and structure. bioRxiv. 2024 Nov 15; doi: 10.1101/2024.11.15.623645.
Shrestha R, Carpenter TS, Van QN, Agamasu C, Tonelli M, Aydin F, Chen D, Gulten G, Glosli JN, López CA, Oppelstrup T, Neale C, Gnanakaran S, Gillette WK, Ingólfsson HI, Lightstone FC, Stephen AG, Streitz FH, Nissley DV, Turbyville TJ. Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane. Commun Biol. 2024 Feb 28; 7(1):242. doi: 10.1038/s42003-024-05916-0.
Manrique PD, Leus IV, López CA, Mehla J, Malloci G, Gervasoni S, Vargiu AV, Kinthada RK, Herndon L, Hengartner NW, Walker JK, Rybenkov VV, Ruggerone P, Zgurskaya HI, Gnanakaran S. Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors. Commun Chem. 2024 Apr 12; 7(1):84. doi: 10.1038/s42004-024-01161-y.
López CA, Alam SM, Derdeyn CA, Haynes BF, Gnanakaran S. Influence of membrane on the antigen presentation of the HIV-1 envelope membrane proximal external region (MPER). Curr Opin Struct Biol. 2024 Oct; 88:102897. doi: 10.1016/j.sbi.2024.102897. Epub 2024 Aug 21. Review.
Gorfe AA, Gnanakaran S. Editorial. Curr Opin Struct Biol. 2024 Dec; 89:102938. doi: 10.1016/j.sbi.2024.102938. Epub 2024 Oct 4.
Do HN, Gnanakaran S. Multiscale Molecular Dynamics Simulations: Accelerating Conformational Sampling of Biomolecular Systems by Iterating All-Atom and Coarse-Grained Simulations. Los Alamos, NM: acknowledged by NNSA for open-source release (O4782); 2024 October.
20236 entries
Trettel DS, Neale C, Zhao M, Gnanakaran S, Gonzalez-Esquer CR. Monatomic ions influence substrate permeation across bacterial microcompartment shells. Sci Rep. 2023 Sep 21; 13(1):15738. doi: 10.1038/s41598-023-42688-9.
Mopuri R, Welbourn S, Charles T, Ralli-Jain P, Rosales D, Burton S, Aftab A, Karunakaran K, Pellegrini K, Kilembe W, Karita E, Gnanakaran S, Upadhyay AA, Bosinger SE, Derdeyn CA. High throughput analysis of B cell dynamics and neutralizing antibody development during immunization with a novel clade C HIV-1 envelope. PLoS Pathog. 2023 Oct; 19(10): e1011717. doi: 10.1371/journal.ppat.1011717. eCollection 2023 Oct.
Mansbach RA, Patel LA, Watson NA, Kubicek-Sutherland JZ, Gnanakaran S. Inferring Pathways of Oxidative Folding from Prefolding Free Energy Landscapes of Disulfide-Rich Toxins. J Phys Chem B. 2023 Mar 2; 127(8):1689-1703. doi: 10.1021/acs.jpcb.2c07124. Epub 2023 Feb 15.
Manrique PD, López CA, Gnanakaran S, Rybenkov VV, Zgurskaya HI. New understanding of multidrug efflux and permeation in antibiotic resistance, persistence, and heteroresistance. Ann N Y Acad Sci. 2023 Jan; 1519(1):46-62. doi: 10.1111/nyas.14921. Epub 2022 Nov 7. Review.
Manrique PD, Chakraborty S, Henderson R, Edwards RJ, Mansbach R, Nguyen K, Stalls V, Saunders C, Mansouri K, Acharya P, Korber B, Gnanakaran S. Network analysis uncovers the communication structure of SARS-CoV-2 spike protein identifying sites for immunogen design. iScience. 2023 Jan 20; 26(1):105855. doi: 10.1016/j.isci.2022.105855. Epub 2022 Dec 26.
Ingólfsson HI, Bhatia H, Aydin F, Oppelstrup T, López CA, Stanton LG, Carpenter TS, Wong S, Di Natale F, Zhang X, Moon JY, Stanley CB, Chavez JR, Nguyen K, Dharuman G, Burns V, Shrestha R, Goswami D, Gulten G, Van QN, Ramanathan A, Van Essen B, Hengartner NW, Stephen AG, Turbyville T, Bremer PT, Gnanakaran S, Glosli JN, Lightstone FC, Nissley DV, Streitz FH. Machine Learning-Driven Multiscale Modeling: Bridging the Scales with a Next-Generation Simulation Infrastructure. J Chem Theory Comput. 2023 May 9; 19(9):2658-2675. doi: 10.1021/acs.jctc.2c01018. Epub 2023 Apr 19.
20226 entries
Zhao F, Berndsen ZT, Pedreño -Lopez N, Burns A, Allen JD, Barman S, Lee WH, Chakraborty S, Gnanakaran S, Sewall LM, Ozorowski G, Limbo O, Song G, Yong P, Callaghan S, Coppola J, Weisgrau KL, Lifson JD, Nedellec R, Voigt TB, Laurino F, Louw J, Rosen BC, Ricciardi M, Crispin M, Desrosiers RC, Rakasz EG, Watkins DI, Andrabi R, Ward AB, Burton DR, Sok D. Molecular insights into antibody-mediated protection against the prototypic simian immunodeficiency virus. Nat Commun. 2022 Sep 6; 13(1):5236. doi: 10.1038/s41467-022-32783-2.
Welbourn S, Chakraborty S, Yang JE, Gleinich AS, Gangadhara S, Khan S, Ferrebee C, Yagnik B, Burton S, Charles T, Smith SA, Williams D, Mopuri R, Upadhyay AA, Thompson J, Price MA, Wang S, Qin Z, Shen X, Williams LD, Eisel N, Peters T, Zhang L, Kilembe W, Karita E, Tomaras GD, Bosinger SE, Amara RR, Azadi P, Wright ER, Gnanakaran S, Derdeyn CA. A neutralizing antibody target in early HIV-1 infection was recapitulated in rhesus macaques immunized with the transmitted/founder envelope sequence. PLoS Pathog. 2022 May; 18(5): e1010488. doi: 10.1371/journal.ppat.1010488. eCollection 2022 May.
Nguyen K, López CA, Neale C, Van QN, Carpenter TS, Di Natale F, Travers T, Tran TH, Chan AH, Bhatia H, Frank PH, Tonelli M, Zhang X, Gulten G, Reddy T, Burns V, Oppelstrup T, Hengartner N, Simanshu DK, Bremer PT, Chen D, Glosli JN, Shrestha R, Turbyville T, Streitz FH, Nissley DV, Ingólfsson HI, Stephen AG, Lightstone FC, Gnanakaran S. Exploring CRD mobility during RAS/RAF engagement at the membrane. Biophys J. 2022 Oct 4; 121(19):3630-3650. doi: 10.1016/j.bpj.2022.06.035. Epub 2022 Jul 1.
López CA, Zhang X, Aydin F, Shrestha R, Van QN, Stanley CB, Carpenter TS, Nguyen K, Patel LA, Chen D, Burns V, Hengartner NW, Reddy TJE, Bhatia H, Di Natale F, Tran TH, Chan AH, Simanshu DK, Nissley DV, Streitz FH, Stephen AG, Turbyville TJ, Lightstone FC, Gnanakaran S, Ingólfsson HI, Neale C. Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework. J Chem Theory Comput. 2022 Aug 9; 18(8):5025-5045. doi: 10.1021/acs.jctc.2c00168. Epub 2022 Jul 22.
Ingólfsson HI, Neale C, Carpenter TS, Shrestha R, López CA, Tran TH, Oppelstrup T, Bhatia H, Stanton LG, Zhang X, Sundram S, Di Natale F, Agarwal A, Dharuman G, Kokkila Schumacher SIL, Turbyville T, Gulten G, Van QN, Goswami D, Jean-Francois F, Agamasu C, Chen D, Hettige JJ, Travers T, Sarkar S, Surh MP, Yang Y, Moody A, Liu S, Van Essen BC, Voter AF, Ramanathan A, Hengartner NW, Simanshu DK, Stephen AG, Bremer PT, Gnanakaran S, Glosli JN, Lightstone FC, McCormick F, Nissley DV, Streitz FH. Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins. Proc Natl Acad Sci U S A. 2022 Jan 4; 119(1). doi: 10.1073/pnas.2113297119.
Hackl M, Contrada EV, Ash JE, Kulkarni A, Yoon J, Cho HY, Lee KB, Yarbrough JM, López CA, Gnanakaran S, Chundawat SPS. Acoustic force spectroscopy reveals subtle differences in cellulose unbinding behavior of carbohydrate-binding modules. Proc Natl Acad Sci U S A. 2022 Oct 18; 119(42): e2117467119. doi: 10.1073/pnas.2117467119. Epub 2022 Oct 10.
202111 entries
[11 6 ] Shen X, Tang H, McDanal C, Wagh K, Fischer W, Theiler J, Yoon H, Li D, Haynes BF, Sanders KO, Gnanakaran S, Hengartner N, Pajon R, Smith G, Glenn GM, Korber B, Montefiori DC. SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines. Cell Host Microbe. 2021 Apr 14; 29(4):529-539.e3. doi: 10.1016/j.chom.2021.03.002. Epub 2021 Mar 5.
[11 5 ] Nguyen K, Chakraborty S, Mansbach RA, Korber B, Gnanakaran S. Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. Viruses. 2021 May 17; 13(5). doi: 10.3390/v13050927.
[11 4 ] Mehla J, Malloci G, Mansbach R, López CA, Tsivkovski R, Haynes K, Leus IV, Grindstaff SB, Cascella RH, D'Cunha N, Herndon L, Hengartner NW, Margiotta E, Atzori A, Vargiu AV, Manrique PD, Walker JK, Lomovskaya O, Ruggerone P, Gnanakaran S, Rybenkov VV, Zgurskaya HI. Predictive Rules of Efflux Inhibition and Avoidance in Pseudomonas aeruginosa. mBio. 2021 Jan 19; 12(1). doi: 10.1128/mBio.02785-20.
[11 3 ] Mansbach RA, Chakraborty S, Nguyen K, Montefiori DC, Korber B, Gnanakaran S. The SARS-CoV-2 Spike variant D614G favors an open conformational state. Sci Adv. 2021 Apr; 7(16). doi: 10.1126/sciadv.abf3671. Print 2021 Apr.
[11 2 ] Manrique PD, Gnanakaran S. Microscopic Approach to Intrinsic Antibiotic Resistance. J Phys Chem B. 2021 Apr 1; 125(12):3114-3118. doi: 10.1021/acs.jpcb.1c00607. Epub 2021 Mar 23.
[11 1 ] López CA, Agarwal A, Van QN, Stephen AG, Gnanakaran S. Unveiling the Dynamics of KRAS4b on Lipid Model Membranes. J Membr Biol. 2021 Apr; 254(2):201-216. doi: 10.1007/s00232-021-00176-z. Epub 2021 Apr 7.
[11 0 ] Patent filed on Hunting of FoX, ML based antibiotic discovery approach. 2021.
Lindsay RJ, Mansbach RA, Gnanakaran S, Shen T. Effects of pH on an IDP conformational ensemble explored by molecular dynamics simulation. Biophys Chem. 2021 Apr; 271:106552. doi: 10.1016/j.bpc.2021.106552. Epub 2021 Jan 26.
Korber BT, Gnanakaran S, Ferrari G, Haynes B, Henderson R, inventors. Mosaic HIV-1 Envelopes To Induce ADCC Responses. US patent application PCT/US 2021 /039598 (International). 2021 June.
Fischer W, Giorgi EE, Chakraborty S, Nguyen K, Bhattacharya T, Theiler J, Goloboff PA, Yoon H, Abfalterer W, Foley BT, Tegally H, San JE, de Oliveira T, Gnanakaran S, Korber B. HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens. Cell Host Microbe. 2021 Jul 14; 29(7):1093-1110. doi: 10.1016/j.chom.2021.05.012. Epub 2021 Jun 3. Review.
Chundawat SPS, Nemmaru B, Hackl M, Brady SK, Hilton MA, Johnson MM, Chang S, Lang MJ, Huh H, Lee SH, Yarbrough JM, López CA, Gnanakaran S. Molecular origins of reduced activity and binding commitment of processive cellulases and associated carbohydrate-binding proteins to cellulose III. J Biol Chem. 2021 Jan-Jun; 296:100431. doi: 10.1016/j.jbc.2021.100431. Epub 2021 Feb 19.. Chakraborty S, Wagh K, Gnanakaran S, López CA. Development of Martini 2.2 parameters for N-glycans: a case study of the HIV-1 Env glycoprotein dynamics. Glycobiology. 2021 Aug 7; 31(7):787-799. doi: 10.1093/ glycob /cwab017.
20209 entries
Van QN, López CA, Tonelli M, Taylor T, Niu B, Stanley CB, Bhowmik D, Tran TH, Frank PH, Messing S, Alexander P, Scott D, Ye X, Drew M, Chertov O, Lösche M, Ramanathan A, Gross ML, Hengartner NW, Westler WM, Markley JL, Simanshu DK, Nissley DV, Gillette WK, Esposito D, McCormick F, Gnanakaran S, Heinrich F, Stephen AG. Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane. Proc Natl Acad Sci U S A. 2020 Sep 29; 117(39):24258-24268. doi: 10.1073/pnas.2006504117. Epub 2020 Sep 10.
Travers T, López CA, Agamasu C, Hettige JJ, Messing S, García AE, Stephen AG, Gnanakaran S. Anionic Lipids Impact RAS-Binding Site Accessibility and Membrane Binding Affinity of CRAF RBD-CRD. Biophys J. 2020 Aug 4; 119(3):525-538. doi: 10.1016/j.bpj.2020.06.021. Epub 2020 Jun 27.
Mansbach RA, Leus IV, Mehla J, Lopez CA, Walker JK, Rybenkov VV, Hengartner NW, Zgurskaya HI, Gnanakaran S. Machine Learning Algorithm Identifies an Antibiotic Vocabulary for Permeating Gram-Negative Bacteria. J Chem Inf Model. 2020 Jun 22; 60(6):2838-2847. doi: 10.1021/acs.jcim.0c00352. Epub 2020 Jun 9.
Mansbach RA, Chakraborty S, Travers T, Gnanakaran S. Graph-Directed Approach for Downselecting Toxins for Experimental Structure Determination. Mar Drugs. 2020 May 14; 18(5). doi: 10.3390/md18050256.
López CA, Zgurskaya H, Gnanakaran S. Molecular characterization of the outer membrane of Pseudomonas aeruginosa. Biochim Biophys Acta Biomembr. 2020 Mar 1; 1862(3):183151. doi: 10.1016/j.bbamem.2019.183151. Epub 2019 Dec 14.
Li X, Giorgi EE, Marichannegowda MH, Foley B, Xiao C, Kong XP, Chen Y, Gnanakaran S, Korber B, Gao F. Emergence of SARS-CoV-2 through recombination and strong purifying selection. Sci Adv. 2020 Jul; 6(27). doi: 10.1126/ sciadv.abb 9153. Print 2020 Jul.
Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell. 2020 Aug 20; 182(4):812-827.e19. doi: 10.1016/j.cell.2020.06.043. Epub 2020 Jul 3.
Chakraborty S, Berndsen ZT, Hengartner NW, Korber BT, Ward AB, Gnanakaran S. Quantification of the Resilience and Vulnerability of HIV-1 Native Glycan Shield at Atomistic Detail. iScience. 2020 Dec 18; 23(12):101836. doi: 10.1016/j.isci.2020.101836. eCollection 2020 Dec 18.
Berndsen ZT, Chakraborty S, Wang X, Cottrell CA, Torres JL, Diedrich JK, López CA, Yates JR 3rd, van Gils MJ, Paulson JC, Gnanakaran S, Ward AB. Visualization of the HIV-1 Env glycan shield across scales. Proc Natl Acad Sci U S A. 2020 Nov 10; 117(45):28014-28025. doi: 10.1073/pnas.2000260117. Epub 2020 Oct 22.
20196 entries
Travers T, Kanagy WK, Mansbach RA, Jhamba E, Cleyrat C, Goldstein B, Lidke DS, Wilson BS, Gnanakaran S. Combinatorial diversity of Syk recruitment driven by its multivalent engagement with FcεRIγ. Mol Biol Cell. 2019 Aug 1; 30(17):2331-2347. doi: 10.1091/ mbc.E 18-11-0722. Epub 2019 Jun 19.
Mansbach RA, Travers T, McMahon BH, Fair JM, Gnanakaran S. Snails in Silico: A Review of Computational Studies on the Conopeptides. Mar Drugs. 2019 Mar 1; 17(3). doi: 10.3390/md17030145. Review.
Löpez CA, Vesselinov VV, Gnanakaran S, Alexandrov BS. Unsupervised Machine Learning for Analysis of Phase Separation in Ternary Lipid Mixture. J Chem Theory Comput. 2019 Nov 12; 15(11):6343-6357. doi: 10.1021/acs.jctc.9b00074. Epub 2019 Oct 7.
López CA, Swift MF, Xu XP, Hanein D, Volkmann N, Gnanakaran S. Biophysical Characterization of a Nanodisc with and without BAX: An Integrative Study Using Molecular Dynamics Simulations and Cryo-EM. Structure. 2019 Jun 4; 27(6):988-999.e4. doi: 10.1016/j.str.2019.03.013. Epub 2019 Apr 11.
Bricault CA, Yusim K, Seaman MS, Yoon H, Theiler J, Giorgi EE, Wagh K, Theiler M, Hraber P, Macke JP, Kreider EF, Learn GH, Hahn BH, Scheid JF, Kovacs JM, Shields JL, Lavine CL, Ghantous F, Rist M, Bayne MG, Neubauer GH, McMahan K, Peng H, Chéneau C, Jones JJ, Zeng J, Ochsenbauer C, Nkolola JP, Stephenson KE, Chen B, Gnanakaran S, Bonsignori M, Williams LD, Haynes BF, Doria-Rose N, Mascola JR, Montefiori DC, Barouch DH, Korber B. HIV-1 Neutralizing Antibody Signatures and Application to Epitope-Targeted Vaccine Design. Cell Host Microbe. 2019 Aug 14; 26(2):296. doi: 10.1016/j.chom.2019.07.016.
Agarwal A, Hengartner NW, Gnanakaran S, Voter AF. Computing long time scale biomolecular dynamics using quasi-stationary distribution kinetic Monte Carlo (QSD-KMC). J Chem Phys. 2019 Aug 21; 151(7):074109. doi: 10.1063/1.5094457.
20185 entries
Travers T, Wang KJ, López CA, Gnanakaran S. Sequence- and structure-based computational analyses of Gram-negative tripartite efflux pumps in the context of bacterial membranes. Res Microbiol. 2018;169(7-8):414-424. doi: 10.1016/j.resmic.2018.01.002.
Travers T, López CA, Van QN, Neale C, Tonelli M, Stephen AG, Gnanakaran S. Molecular recognition of RAS/RAF complex at the membrane: Role of RAF cysteine-rich domain. Sci Rep. 2018 May 31; 8(1):8461. doi: 10.1038/s41598-018-26832-4.
López CA, Unkefer CJ, Swanson BI, Swanson JMJ, Gnanakaran S. Membrane perturbing properties of toxin mycolactone from Mycobacterium ulcerans. PLoS Comput Biol. 2018;14(2): e1005972. doi: 10.1371/journal.pcbi.1005972.
Korber BTM, Gnanakaran S, Perkins S, Sodroski J, Haynes B, inventors. Mosaic HIV envelope immunogenic polypeptides. US Patent 9,855,329. 2018 Jan 2.
Carpenter TS, López CA, Neale C, Montour C, Ingólfsson HI, Di Natale F, Lightstone FC, Gnanakaran S. Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field. J Chem Theory Comput. 2018;14(11):6050-6062. doi: 10.1021/acs.jctc.8b00496.
20172 entries
Müller RT, Travers T, Cha H, Phillips JL, Gnanakaran S, Pos KM. Switch loop flexibility affects substrate transport of the AcrB efflux pump. J Mol Biol. 2017;429(24):3863-3874. doi: 10.1016/j.jmb.2017.09.018.
López CA, Travers T, Pos KM, Zgurskaya HI, Gnanakaran S. Dynamics of Intact MexAB-OprM Efflux Pump: Focusing on the MexA-OprM Interface. Sci Rep. 2017; 7(1):16521. doi: 10.1038/s41598-017-16497-w.
20165 entries
Tian J, López CA, Derdeyn CA, Jones MS, Pinter A, Korber B, Gnanakaran S. Effect of Glycosylation on an Immunodominant Region in the V1V2 Variable Domain of the HIV-1 Envelope gp120 Protein. PLoS Comput Biol. 2016;12(10): e1005094. doi: 10.1371/journal.pcbi.1005094.
Sanchez-Merino V, Fabra-Garcia A, Gonzalez N, Nicolas D, Merino-Mansilla A, Manzardo C, Ambrosioni J, Schultz A, Meyerhans A, Mascola JR, Gatell JM, Alcami J, Miro JM, Yuste E. Detection of Broadly Neutralizing Activity within the First Months of HIV-1 Infection. J Virol. 2016;90(11):5231-5245. doi: 10.1128/JVI.00049-16.
Merkli M, Berman GP, Sayre RT, Gnanakaran S, Könenberg M, Nesterov AI, Song H. Dynamics of a chlorophyll dimer in collective and local thermal environments. J Math Chem. 2016;54(4):866-917. doi: 10.1007/s10910-016-0593-z.
Hansen SG, Wu HL, Burwitz BJ, Hughes CM, Hammond KB, Ventura AB, et al. Broadly targeted CD8+ T cell responses restricted by major histocompatibility complex E. Science. 2016;351(6274):714-720. doi: 10.1126/science.aac9475.
Arkin A, Bader DC, Coffey R, Antypas K, Bard D, Dart E, Dosanjh S, et al. Biological and Environmental Research Exascale Requirements Review. Washington, DC: US Department of Energy; 2016.
20154 entries
Zgurskaya HI, López CA, Gnanakaran S. Permeability Barrier of Gram-Negative Cell Envelopes and Approaches to Bypass It. ACS Infect Dis. 2015; 1(11):512-522. doi: 10.1021/acsinfecdis.5b00097.
López CA, Sethi A, Goldstein B, Wilson BS, Gnanakaran S. Membrane-Mediated Regulation of the Intrinsically Disordered CD3ϵ Cytoplasmic Tail of the TCR. Biophys J. 2015;108(10):2481-2491. doi: 10.1016/j.bpj.2015.04.009.
López CA, Bellesia G, Redondo A, Langan P, Chundawat SPS, Dale BE, Marrink SJ, Gnanakaran S. MARTINI Coarse-Grained Model for Crystalline Cellulose Microfibers. J Phys Chem B. 2015;119(2):465-473. doi: 10.1021/jp5105938.
Hraber P, Korber B, Wagh K, Giorgi EE, Bhattacharya T, Gnanakaran S, et al. Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV Variants. Viruses. 2015;7(10):5443-5475. doi: 10.3390/v7102881.
20144 entries
Russell CA, Kasson PM, Donis RO, Riley S, Dunbar J, Rambaut A, et al. Improving pandemic influenza risk assessment. eLife. 2014;3: e03883.
Phillips JL and S. Gnanakaran. A Data-driven Approach to Modeling the Tripartite Structure of Multidrug Resistance Efflux Pumps. Proteins. 2014. 10.1002/prot.24632.
Mayes HB, Tian J, Nolte MW, Shanks BH, Beckham GT, Gnanakaran S, Broadbelt LJ. Sodium Ion Interactions with Aqueous Glucose: Insights from Quantum Mechanics, Molecular Dynamics, and Experiment. J Phys Chem B. 2014;118(8):1990-2000.
Langan P, Petridis L, O'Neill HM, Pingali SV, Foston M, Nishiyama Y, Schulz R, Lindner B, Hanson BL, Harton S, Heller WT, Urban V, Evans BR, Gnanakaran S, Ragauskas AJ, Smith JC, Davison BH. Common processes drive the thermochemical pretreatment of lignocellulosic biomass. Green Chem. 2014;16(1):63-68.
201313 entries
Tian J, Sethi A, Swanson BI, Goldstein B, Gnanakaran S. Taste of Sugar at the Membrane: Thermodynamics and Kinetics of the Interaction of a Disaccharide with Lipid Bilayers. Biophys J. 2013;104(3):622-632.
Stieh DJ, Phillips JL, Rogers PM, King DF, Cianci GC, Jeffs SA, Gnanakaran S, Shattock RJ. Dynamic electrophoretic fingerprinting of the HIV-1 envelope glycoprotein. Retrovirology. 2013; 10:33.
Singh S, Junghans A, Tian J, Dubey M, Gnanakaran S, Chlistunoff J, Majewski J. Polyelectrolyte multilayers as a platform for pH-responsive lipid bilayers. Soft Matter. 2013; 9:8938-8948.
Sethi A, Tian J, Derdeyn CA, Korber B, Gnanakaran S. A mechanistic understanding of allosteric immune escape pathways in the HIV-1 envelope protein. PLoS Comput Biol. 2013; 9(5): e1003046.
Sethi A, Anunciado D, Tian J, Vu DM, Gnanakaran S. Deducing conformational variability of intrinsically disordered proteins from infrared spectroscopy with Bayesian statistics. Chem Phys. 2013; 422:143-155.
Nemenman I, Gnanakaran S, Munsky B, Wall ME, Jiang Y, Hlavacek WS, Faeder JR. Special section dedicated to the Sixth q- bio Conference: meeting report and preface. Phys Biol. 2013;10(3):030301.
Murphy MK, Yue L, Pan R, Boliar S, Sethi A, Tian J, Pfafferot K, Karita E, Allen SA, Cormier E, Goepfert PA, Borrow P, Robinson JE, Gnanakaran S, Hunter E, Kong XP, Derdeyn CA. Viral Escape From Neutralizing Antibodies in Early Subtype A HIV-1 Infection. PLoS Pathog. 2013; 9(2): e1003173.
Liao HX, Lynch R, Zhou T, Gao F, Alam SM, Boyd SD, et al. Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature. 2013; 496(7446):469-476.
Jung J, Sethi A, Gaiotto T, Han JJ, Jeoh T, Gnanakaran S, Goodwin PM. Binding and Movement of Individual Cel7A on Cellulose Surfaces Revealed by Single-Molecule Fluorescence Imaging. J Biol Chem. 2013; 288(33):24164-24172.
Gottardo R, Bailer RT, Korber BT, Gnanakaran S, et al. Plasma IgG to linear epitopes in the V2 and V3 regions of HIV-1 gp120 correlate with a reduced risk of infection in the RV144 vaccine efficacy trial. PLoS One. 2013; 8(9): e75665.
Gao D, Chundawat SPS, Sethi A, Balan V, Gnanakaran S, Dale BE. Increased enzyme binding to substrate is not necessary for more efficient cellulose hydrolysis. Proc Natl Acad Sci U S A. 2013;110(27):10922-10927.
D. Sawada, Y. Nishiyama, L. Petridis, R. Parthasarathi, S. Gnanakaran, T. Forsyth, M. Wada, P. Langan. Structure and dynamics of a complex of cellulose with EDA: the action of amines on cellulose. Cellulose. 2013. 20:1563.
Bellesia G, Gnanakaran S. Sodium chloride interaction with solvated and crystalline cellulose: sodium ion affects the cellotetraose molecule and the cellulose fibril in aqueous solution. Cellulose. 2013; 20:2695-2702.
20126 entries
Tian J, Sethi A, Anunciado D, Vu DM, Gnanakaran S. Characterization of a disordered protein during micellation: interactions of alpha-synuclein with sodium dodecyl sulfate. J Phys Chem B. 2012; 116(15):4417-4424.
Sethi A, Tian J, Vu DM, Gnanakaran S. Identification of minimally interacting modules in an intrinsically disordered protein. Biophys J. 2012; 103(4):748-757.
Mukundan H, Price DN, Goertz M, Parthasarathi R, Montaño GA, Kumar S, Scholfield MR, Anderson AS, Gnanakaran S, Iyer S, Schmidt J, Swanson BI. Understanding the interaction of Lipoarabinomannan with membrane mimetic architectures. Tuberculosis (Edinb). 2012 Jan;92(1):38-47.
Brewer SH, Tang Y, Vu DM, Gnanakaran S, Raleigh DP, Dyer RB. Temperature dependence of water interactions with the amide carbonyls of alpha-helices. Biochemistry. 2012; 51(26):5293-5299.
Bellesia G, Chundawat SPS, Langan P, Redondo A, Dale BE, Gnanakaran S. Coarse-Grained Model for the Interconversion between Native and Liquid Ammonia-Treated Crystalline Cellulose. J Phys Chem B. 2012; 116(28):8031-8037.
Asztalos A, Daniels M, Sethi A, Shen T, Langan P, Redondo A, Gnanakaran S. A coarse-grained model for synergistic action of multiple enzymes on cellulose. Biotechnol Biofuels. 2012 Aug 1;5(1):55. doi: 10.1186/1754-6834-5-55.
201116 entries
Zhuang Z, Jewett AI, Kuttimalai S, Bellesia G, Gnanakaran S, Shea JE. Assisted peptide folding by surface pattern recognition. Biophys J. 2011; 100(5):1306-15.
Wada M, Nishiyama Y, Bellesia G, Forsyth T, Gnanakaran S, Langan P. Neutron crystallographic and molecular dynamics studies of the structure of ammonia-cellulose I: rearrangement of hydrogen bonding during treatment of cellulose with ammonia. Cellulose. 2011; 18:191-206.
Sethi A, Goldstein B, Gnanakaran S. Quantifying intramolecular binding in multivalent interactions: A structure-based synergistic study on Grb2:Sos1 complex. PLoS Comput Biol. 2011;7(10 ):e 1002192.
Parthasarathi R, Tian J, Redondo A, Gnanakaran S. A quantum chemical study of carbohydrate-phospholipid interactions. J Phys Chem A. 2011;115(45):12826-12840.
Parthasarathi R, Romero RA, Redondo A, Gnanakaran S. Theoretical study of the remarkably diverse linkages in lignin. J Phys Chem Lett. 2011; 2(20):2660-2666.
Parthasarathi R, Bellesia G, Chundawat SP, Dale BE, Langan P, Gnanakaran S. Insights into hydrogen bonding and stacking interactions in cellulose. J Phys Chem A. 2011 Dec 15;115(49):14191-202.
Lynch RM, Rong R, Boliar S, Sethi A, Li B, Mulenga J, Allen S, Robinson JE, Gnanakaran S, Derdeyn CA. The B cell response is redundant and highly focused on V1V2 during early subtype C infection in a Zambian seroconvertor. J Virol. 2011; 85(2):905-915.
Langan P, Gnanakaran S, Rector KD, Pawley N, Fox D, Cho DW, Hammel KE. Exploring new strategies for cellulosic biofuels production. Energy Environ Sci. 2011; 4:3820-3833. doi: 10.1039/c1ee01268a.
Korber B, Gnanakaran S. AIDS/HIV. Converging on an HIV vaccine. Science. 2011;333(6049):1589-1590.
Kirchherr JL, Hamilton J, Lu X, Gnanakaran S, Muldoon M, Daniels M, Kasongo W, Chalwe V, Mulenga C, Mwananyanda L, Musonda RM, Yuan X, Montefiori DC, Korber BT, Haynes BF, Gao F. Identification of amino acid substitutions associated with neutralization phenotype in the human immunodeficiency virus type-1 subtype C gp120. Virology. 2011;409(2):163-74.
Haili Tang, James E. Robinson, S. Gnanakaran, Ming Li, Eric S. Rosenberg, Barton F. Haynes, Celia C. LaBranche, Bette T. Korber, and David C. Montefiori. Epitopes Adjacent to the Base of the V3 Loop of gp120 as Targets for the Initial Autologous Neutralizing Antibody Response in Two HIV-1 Subtype B-Infected Individuals. J Virol. 2011. Sep;85(18):9286-99.
Gnanakaran S, Bhattacharya T, Daniels M, Keele BF, Hraber PT, Lapedes AS, Shen T, Gaschen B, Krishnamoorthy M, Li H, Decker JM, Salazar-Gonzalez JF, Wang S, Jiang C, Gao F, Swanstrom R, Anderson JA, Ping LH, Cohen MS, Markowitz M, Goepfert PA, Saag MS, Eron JJ, Hicks CB, Blattner WA, Tomaras GD, Asmal M, Letvin NL, Gilbert PB, Decamp AC, Magaret CA, Schief WR, Ban YE, Zhang M, Soderberg KA, Sodroski JG, Haynes BF, Shaw GM, Hahn BH, Korber B. Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. PLoS Pathog. 2011 Sep;7(9): e1002209.
Gnanakaran S, Bhattacharya T, Daniels M, Keele BF, Hraber P, Lapedes AS, Shen T, Zhang M, Gaschen B, Li H, Decker JM, Salazar-Gonzalez JF, Wang S, Gao F, Swanstrom R, et al. Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. PLoS Pathog. 2011;7(9 ):e 1002209.
Chundawat, Shishir P.S.; Bellesia, Giovanni; Uppugundla, Nirmal; Sousa, Leonardo; Gao, Dahai; Cheh, Albert; Agarwal, Umesh; Bianchetti, Christopher; Phillips, George; Langan, Paul; Balan, Venkatesh; Gnanakaran, S; Dale, Bruce. Restructuring crystalline cellulose hydrogen bond network enhances its depolymerization rate. J. Am. Chem. Soc. 2011 133(29), 11163-11174.
Bellesia, Giovanni; Chundawat, Shishir P.S., Langan, Paul; Dale, Bruce; Gnanakaran, S. Probing the Early Events Associated with Liquid Ammonia Pretreatment of Native Crystalline Cellulose. J. Phys. Chem. B. 2011 115(32), 9782-9788 (2011).
Asmal M, Hellmann I, Liu W, Keele BF, Perelson AS, Bhattacharya T, Gnanakaran S, Daniels M, Haynes BF, Korber BT, Hahn BH, Shaw GM, Letvin NL. A Signature in HIV-1 Envelope Leader Peptide Associated with Transition from Acute to Chronic Infection Impacts Envelope Processing and Infectivity. PLoS One. 2011;6(8): e23673.
20103 entries
Lynch RM, Shen T, Rong R, Li B, Honnen W, Mulenga J, Allen S, Zolla- Pazner S, Pinter A, Gnanakaran S, Derdeyn CA. Subtype-specific conservation of isoleucine 309 in the Env V3 domain is linked to immune evasion in subtype C HIV-1 infection. Virology. 2010;404(1):59-70.
Gnanakaran S, Daniels M, Bhattacharya T, Lapedes AS, Sethi A, Li M, Tang H, Greene K, Gao H, Haynes BF, Cohen MS, Shaw GM, Seaman MS, Kumar A, Gao F, Montefiori DC, Korber B. Genetic signatures in the envelope glycoproteins of HIV-1 that are associated with broadly neutralizing antibodies. PLoS Comput Biol. 2010;6(10): e1000955.
Cho DW, Parthasarathi R, Pimentel AS, Maestas GD, Park HJ, Yoon UC, Dunaway-Mariano D, Gnanakaran S, Langan P, Mariano PS. 2010. Nature and Kinetic Analysis of Carbon-Carbon Bond Fragmentation Reactions of Cation Radicals Derived from SET-Oxidation of Lignin Model Compounds. J Org Chem. 75, 6549-6562.
20095 entries
Tongye Shen, Paul Langan, Alfred D. French, Glenn P. Johnson and S. Gnanakaran. Conformational flexibility of soluble cellulose oligomers: Chain Length and temperature dependence. J. Am. Chem. Soc., 2009; 131: 14786-14794.
Smita S. Kulkarni, Alan Lapedes, Haili Tang, S. Gnanakaran, Marcus G. Daniels, Ming Zhang, Tanmoy Bhattacharya, Ming Li, Victoria R. Polonis, Francine E. McCutchan, Lynn Morris, Dennis Ellenberger, Salvatore T. Butera, Robert C. Bollinger, Bette T. Korber, Ramesh S. Paranjape, and David C. Montefiori. Highly complex neutralization determinants on a monophyletic lineage of newly transmitted subtype C HIV-1 Env clones from India. Virology 2009; 385, 505-20.
Rong Rong, Bing Li, Rebecca M. Lynch, Richard E. Haaland, Megan K. Murphy, Joseph Mulenga, Susan A. Allen, Jerry L. Blackwell, Abraham Pinter, George M. Shaw, Eric Hunter, James E. Robinson, S. Gnanakaran, and Cynthia A. Derdeyn. Escape from Autologous Neutralizing Antibodies in Acute/Early Subtype C HIV-1 Infection Requires Multiple Pathways. PLoS Pathogens. 2009; 5(9): e1000594.
Rebecca M., Tongye Shen, S. Gnanakaran and Cynthia A. Derdeyn. Appreciating HIV-1 Diversity: Subtypic Differences in Env. AIDS Res. and Hum. Retroviruses 2009; 25, 237-248.
B. Korber and S. Gnanakaran. The implications of patterns in HIV Diversity for neutralizing antibody induction and susceptibility. Curr Opin in HIV and AIDS. 2009; 4(5):408-17.
2008–199427 entries
M.Vuyisich, S. Gnanakaran, JA. Lovchik, Rick Lyons, G. Gupta. A dual-purpose protein ligand for effective therapy and sensitive diagnosis of anthrax. Protein J. 2008; 27, 292-302.
Gnanakaran S, Scott B, McCleskey TM, Garcia AE. Perturbation of local solvent structure by a small dication: structural, spectroscopic and reactive properties of beryllium ion in water. J Phys Chem B. 2008;112(10):2958-2963.
Erzsebet Ravasz, S. Gnanakaran, Zoltan Toroczkai, Network Structure of Protein Folding Pathways. 2008. available at arXiv:0705.0912v1 [q-bio.BM].
D. Paschek, M. Puhse, A. Perez-Goicochea, S. Gnanakaran, A.E. Garcia, S. Decatur, A. Geiger and R. Winter. 2008. The solvent dependent shift of the amide-I band of a fully solvated peptide in Methanol/ Water mixture as a local probe for the solvent composition in the peptide/solvent interface. Chemphyschem. 2008; 9, 2742-50.
Brian L. Scott, T. Mark McCleskey, Anu Chaudhary, Elizabeth Hong-Geller, and S. Gnanakaran. The bioinorganic chemistry and associated immunology of Chronic Beryllium Disease, Chem. Comm. 2008; 25, 2837-2847.
S. Gnanakaran, Dorothy Lang, Marcus Daniels, Tanmoy Bhattacharya, Cynthia A. Derdeyn, and Bette Korber. Clade Specific Differences in HIV-1: Diversity and Correlations in C3-V4 Regions of gp120. J. Virol. 2007; 81:4886-4891.
Rong, R., S. Gnanakaran, J.M. Decker, F. Bibollet -Ruche, J. Taylor, J.N. Sfakianos, J.L. Mokili, M. Muldoon, J. Mulenga, S. Allen, B.H. Hahn, G.M. Shaw, J.L. Blackwell, B.T. Korber, E. Hunter, and C.A. Derdeyn. Unique Mutational patterns in the envelope-2 amphipathic helix and acquisition of length in gp120 hypervariable domains are associated with resistance to autologous neutralization of subtype C HIV type 1. J. Virol. 2007; 81:5658-5668.
M. Vuyisich, S. Gnanakaran, J.A. Lovchik, CR. Lyons, K.L. DeBord, and G. Gupta. Novel therapy for anthrax. J. Biomol. Struct. Dyn. 2007; 24:727-728.
M. Kunkel, M. Vuyisich, S. Gnanakaran, G.E. Bruening, A.M. Dandekar, E. Civerolo, J.J. Marchalonis and G. Gupta. Rapid clearance of bacteria and their toxins: Development of therapeutic proteins. Crit. Rev. Immuno. 2007; 27, 233-245.
W. Blay, S. Gnanakaran, B. Foley, N. Doria-Rose, B.T. Korber, and N.L. Haigwood. Consistent Patterns of Change During Divergence of Human Immunodeficiency Virus Type 1 Envelope in SHIV-Infected Macaques. J. Virol. 2006; 80:999-1014.
S. Gnanakaran, R. Nussinov, and A.E. Garcia. Atomic level description of amyloid beta dimer formation. J. Am. Chem. Soc. 2006; 128:2158-2159.
S. Gnanakaran and A.E. Garcia. Helix-coil transition of alanine peptides in water: Force field dependence on the folded and unfolded structures. Proteins-Structure Function and Genetics. 2005; 59:773-782.
D. Paschek, S. Gnanakaran, and A.E. Garcia. Simulations of the pressure and temperature unfolding of an alpha-helical peptide. Proc. Natl. Acad. Sci. USA. 2005; 102:6765-6770.
S. Gnanakaran, R.M. Hochstrasser, and A.E. Garcia. Nature of structural inhomogeneities on folding a helix and their influence on spectral measurements. Proc. Natl. Acad. Sci. USA. 2004; 101:9229-9234.
H. Nymeyer, S. Gnanakaran, and A.E. Garcia. Atomic simulations of protein folding, using the replica exchange algorithm. Methods Enzymol. 2004; 383:119-149.
S. Gnanakaran, H. Nymeyer, J. Portman, K. Sanbonmatsu, and A.E. Garcia. Peptide folding simulations. Curr. Opin. Struct. Biol. 2003; 13:168-174.
R.M. Hochstrasser, N. Ge, S. Gnanakaran, and M. Zanni. Two-dimensional infrared spectroscopy: Studies of the dynamics of structures with femtosecond pulse Fourier transform correlation spectroscopy. Bull. Chem. Soc. Japan. 2002; 75:1103.
S. Gnanakaran and R.M. Hochstrasser. Conformational preferences of short peptides in relation to multidimensional IR spectroscopy. J. Am. Chem. Soc. 2001; 123:12886-12898.
M.T. Zanni, S. Gnanakaran, J. Stenger, and R.M. Hochstrasser. Two-dimensional infrared spectroscopy of solvent dependent conformations of acetylproline-NH2. J. Phys. Chem. 2001; 105:6520-6535.
S. Gnanakaran, G. Haran, R. Kumble, and R.M. Hochstrasser. 1999. Energy transfer and localization: Applications to photosynthetic systems. Chapter in book titled “Resonance Energy Transfer”. J. Wiley Publishing Co.
S. Gnanakaran, M. Lim, M. Volk, E. Gooding, Y. Kholodenko, and R.M. Hochstrasser. Chemical reaction dynamics of some simple molecules in solution. Phil. Trans. R. Soc. Lond. A. 1998; 356:377-388.
M. Volk, S. Gnanakaran, M. Lim, E. Gooding, Y. Kholodenko, and R.M. Hochstrasser. Anisotropy measurements of the solvated HgI2; Transition state and fragment rotational dynamics. J. Phys. Chem. A. 1997; 101:638-643.
M. Lim, S. Gnanakaran, and R.M. Hochstrasser. Charge shifting in the ultrafast photoreactions of ClO - in water. J. Chem. Phys. 1997; 106:3485-3493.
N. Pugliano, S. Gnanakaran, and R.M. Hochstrasser. The dynamics of photo-dissociation reaction. J. Photochem. & Photobiol. A. 1996; 102:21-28.
N. Pugliano, A. Szarka, S. Gnanakaran, and R.M. Hochstrasser. Vibrational populational dynamics of the HgI photofragment in ethanol solution. J. Chem. Phys. 1995; 103:6498-6511.
Smith PG, Gnanakaran S, Kaszinska AG, Motyka AL, Hong SM, Hochstrasser RM, Topp M. Electronic coupling and conformational barrier crossing of 9,9'-bifluorenyl studied in a supersonic jet. J Chem Phys. 1994; 100:3384-3393.
K. Wynne, S. Gnanakaran, C. Galli, F. Zhu, and R.M. Hochstrasser. Luminescence studies of ultrafast energy transfer oscillations in dimmers. J. Lumin. 1994; 60-1:735-738.