Research Topics
Genomes and Genes | Jorge L BarredaSummaryAffiliation: University of California Country: USA Publications
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Publications
A solvable model for the diffusion and reaction of neurotransmitters in a synaptic junctionJorge L Barreda
Department of Physics and Institute of Molecular Biophysics, Tallahassee, Florida 32306, USA
BMC Biophys 4:5. 2011..abstract:..- Molecular dynamics simulations and drug discoveryJacob D Durrant
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
BMC Biol 9:71. 2011..With constant improvements in both computer power and algorithm design, the future of computer-aided drug design is promising; molecular dynamics simulations are likely to play an increasingly important role... 
Theory of biomolecular recognitionJ A McCammon
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093 0365, USA
Curr Opin Struct Biol 8:245-9. 1998..Computational techniques for both particle-based and continuum models continue to improve and to yield useful insights into an ever wider range of biomolecular systems...- Target flexibility in molecular recognitionJ Andrew McCammon
Howard Hughes Medical Institute, La Jolla, CA 92093 0365, USA
Biochim Biophys Acta 1754:221-4. 2005..Early applications of this method have suggested a new approach to the development of inhibitors of HIV-1 Integrase... - Gated Diffusion-controlled ReactionsJ Andrew McCammon
Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093 0365, USA
BMC Biophys 4:4. 2011..This mini-review describes recent work in this area and some of the biological implications... - Exploring global motions and correlations in the ribosomeJoanna Trylska
Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California, USA
Biophys J 89:1455-63. 2005..Our model provides an efficient and reliable way to study the dynamics of large biomolecular systems composed of both proteins and nucleic acids... - Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidaseLily S Cheng
National Biomedical Computation Resource, University of California, San Diego, La Jolla, California 92093, USA
J Med Chem 51:3878-94. 2008..This ensemble-based VS and RCS approach may offer improvement over existing strategies for structure-based drug discovery... - Dependency map of proteins in the small ribosomal subunitKay Hamacher
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA. hamacher_at_ctbp.ucsd.edu
PLoS Comput Biol 2:e10. 2006..We could additionally determine the binding dependency of THX--a peptide not present in the ribosome of E. coli--and suggest its assembly path... 
(Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand bindingRiccardo Baron
Department of Chemistry and Biochemistry and Center for Theoretical and Biological Physics, University of California at San Diego, La Jolla, CA 92093 0365, USA
Chemphyschem 9:983-8. 2008..We find that receptor flexibility plays a generally underestimated role in protein-ligand binding (thermo)dynamics and that changes of receptor motional correlation determine such large entropy contributions...- Molecular dynamics simulations of metalloproteinases types 2 and 3 reveal differences in the dynamic behavior of the S1' binding pocketCesar Augusto F de Oliveira
Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA
Curr Pharm Des 13:3471-5. 2007.... - Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation studyBenzhuo Lu
Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093-0365, USA
Protein Sci 14:159-68. 2005..The largest conformational change of the protein was observed at about the first quarter time point along the release pathway. Two prominent intermediate states were observed in the release process... - Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug designAlexander L Perryman
Howard Hughes Medical Institute, Center for Theoretical Biological Physics, and Department of Pharmacology, University of California at San Diego, La Jolla, 92093 0365, USA
Biopolymers 82:272-84. 2006..These simulations supported our hypothesis of the mechanism governing flap motion, and they are the first step towards validating that peripheral surface as a new target for drug design... - Molecular docking of balanol to dynamics snapshots of protein kinase AChung F Wong
Department of Chemistry and Biochemistry, University of Missouri St Louis, Missouri 63121, USA
Proteins 61:850-8. 2005..We found that a useful way to identify the correctly docked structure was to locate the structure that appeared most frequently as the lowest energy structure in the docking experiments to different snapshots... - Toward understanding the conformational dynamics of RNA ligationRobert V Swift
Department of Chemistry and Biochemistry, NSF Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California 92093 0365, USA
Biochemistry 48:709-19. 2009..Important features of RNA binding and specificity are revealed for kinetoplastid ligases and the broader nucleotidyltransferase superfamily... - Brownian dynamics simulations of ion atmospheres around polyalanine and B-DNA: effects of biomolecular dielectricDavid S Cerutti
Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0365, USA
Biopolymers 70:391-402. 2003.... - Elasticity of peptide omega bondsTongye Shen
Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093-0365, USA
Phys Rev E Stat Nonlin Soft Matter Phys 73:041908. 2006..These results give mechanical properties of polyproline elasticity of a local nature and provide guidance for future experimental designs... - Molecular dynamics of acetylcholinesteraseTongye Shen
Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, Department of Pharmacology, and Department of Physics, University of California San Diego, La Jolla, California 92093 0365, USA
Acc Chem Res 35:332-40. 2002..The most recent work points to the complex and spatially extensive nature of such motions and suggests possible modes of regulation of the activity of the enzyme... - A simple electrostatic switch important in the activation of type I protein kinase A by cyclic AMPDominico Vigil
Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA 92037, USA
Protein Sci 15:113-21. 2006.... - H-ras protein in a bilayer: interaction and structure perturbationAlemayehu A Gorfe
Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, and Department of Pharmacology, University of California at San Diego, La Jolla, California 92093 0365, USA
J Am Chem Soc 129:12280-6. 2007..The results provide structural arguments in support of the proposed participation of ras in the organization of membrane nanoclusters... - Discovery of a novel binding trench in HIV integraseJulie R Schames
Department of Pharmacology, Howard Hughes Medical Institute, University of California-San Diego, La Jolla, CA 92093-0365, USA
J Med Chem 47:1879-81. 2004..Our ranking of ligands is open to experimental testing, and our approach suggests a new target for HIV-1 therapeutics... - Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitorsJacob D Durrant
Biomedical Sciences Program, University of California San Diego, La Jolla, California 92093 0365, USA
J Mol Recognit 23:173-82. 2010..Our strategy identifies molecular fragments predicted to target multiple MMP-2 binding pockets... - A dynamic model of HIV integrase inhibition and drug resistanceAlex L Perryman
Department of Molecular Biology, The Scripps Research Institute, MB5, 10550 N Torrey Pines Road, La Jolla, CA 92037, USA
J Mol Biol 397:600-15. 2010.... - SR protein kinase 1 is resilient to inactivationJacky Chi Ki Ngo
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
Structure 15:123-33. 2007.... - Mechanism of acetylcholinesterase inhibition by fasciculin: a 5-ns molecular dynamics simulationKaihsu Tai
Howard Hughes Medical Institute and Department of Chemistry, University of California, San Diego, La Jolla, California 92093-0365, USA
J Am Chem Soc 124:6153-61. 2002..Additional data from these simulations can be found at http://mccammon.ucsd.edu/... - Molecular dynamics: survey of methods for simulating the activity of proteinsStewart A Adcock
NSF Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0365, USA
Chem Rev 106:1589-615. 2006 - Charge optimization of the interface between protein kinases and their ligandsPeter A Sims
Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0365
J Comput Chem 25:1416-29. 2004..For the study of the PKA-PKI and CDK2-cyclin A interfaces, we identified residues whose charge distributions are already close to optimal and those whose charge distributions could be refined to further improve binding... - Protein flexibility and computer-aided drug designChung F Wong
Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0365, USA
Annu Rev Pharmacol Toxicol 43:31-45. 2003.... - Acetylcholinesterase: pivotal roles of its long omega loop (Cys69-Cys96) in regulating substrate bindingJennifer M Bui
Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0365, USA
Chem Biol Interact 157:357-9. 2005..The increased level of ACh in lung cancers, resulting from the fall of AChE activity, may collaborate to lung cancer growth... - Functional dynamics of the folded ankyrin repeats of I kappa B alpha revealed by nuclear magnetic resonanceCarla F Cervantes
Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093 0378, USA
Biochemistry 48:8023-31. 2009..The regions showing micro- to millisecond motions in the free protein are the ends of the beta-hairpins that directly interact with NF-kappaB in the complex... - Nanosecond dynamics of the mouse acetylcholinesterase cys69-cys96 omega loopJianxin Shi
Department of Pharmacology, University of California, San Diego, La Jolla, California 92093 0636, USA
J Biol Chem 278:30905-11. 2003.... - Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approachJoanna Trylska
Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0365, USA
J Am Chem Soc 127:11125-33. 2005..Our computed assembly map resembles that of E. coli; however, the central domain path is more similar to that of A. aeolicus, a hyperthermophilic bacteria... - Electrostatic interactionsNathan A Baker
University of California, San Diego, La Jolla, CA, USA
Methods Biochem Anal 44:427-40. 2003 - Finite concentration effects on diffusion-controlled reactionsSanjib Senapati
Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093-0365, USA
J Chem Phys 121:7896-900. 2004.... - From model complexes to metalloprotein inhibition: a synergistic approach to structure-based drug discoveryDavid T Puerta
Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
Angew Chem Int Ed Engl 42:3772-4. 2003 - Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case studyCesar Augusto F de Oliveira
Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, and Department of Pharmacology, University of California at San Diego, La Jolla, California 92093, USA
J Chem Phys 127:175105. 2007..Surprisingly, even for such a low barrier transition, it is difficult to obtain enough transitions to accurately estimate the rate constant when one uses normal MD... - An improved relaxed complex scheme for receptor flexibility in computer-aided drug designRommie E Amaro
Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093 0365, USA
J Comput Aided Mol Des 22:693-705. 2008..Finally, we outline potential methodological improvements that we anticipate will assist future development... - Accelerated entropy estimates with accelerated dynamicsDavid D L Minh
Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA
J Chem Phys 127:154105. 2007..Accelerated dynamics is applied to entropy calculations on a set of toy and molecular systems and is found to enhance the rate of convergence... - Computer-aided drug-discovery techniques that account for receptor flexibilityJacob D Durrant
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
Curr Opin Pharmacol 10:770-4. 2010.... - Generalized gradient-augmented harmonic Fourier beads method with multiple atomic and/or center-of-mass positional restraintsIlja V Khavrutskii
Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093 0365, USA
J Chem Phys 127:124901. 2007..78 A and length of 16.0 A. We provide a simple rationale as to why water enters the hydrophobic nanotube and why it does so in pulses and in wire assembly... - Calculating pKa values in enzyme active sitesJens Erik Nielsen
Departments of Pharmacology, Chemistry, and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
Protein Sci 12:1894-901. 2003..The work presented here has implications for the understanding of enzymes in general and for the design of novel biocatalysts... - Hot-spot residues at the E9/Im9 interface help binding via different mechanismsSergio E Wong
Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093 0365, USA
Biopolymers 89:916-20. 2008..This type of model may be helpful in engineering hot-spot clusters at protein-protein interfaces and, consequently, the design of specificity... - E9-Im9 colicin DNase-immunity protein biomolecular association in water: a multiple-copy and accelerated molecular dynamics simulation studyRiccardo Baron
Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, Department of Pharmacology, Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093 0365, USA
J Phys Chem B 112:16802-14. 2008..The description of key transient biological interactions can be significantly enriched by the dynamic and atomic-level information provided by computer simulations... - Catalytically requisite conformational dynamics in the mRNA-capping enzyme probed by targeted molecular dynamicsRobert V Swift
Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, 92039 0365, USA
Biochemistry 47:4102-11. 2008.... - Similar membrane affinity of mono- and Di-S-acylated ras membrane anchors: a new twist in the role of protein lipidationAlemayehu A Gorfe
Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California 92093 0365, USA
J Am Chem Soc 130:12624-5. 2008..The data further suggest that while Cys181-palmitate and Cys186-farnesyl together provide sufficient hydrophobic force for tight membrane binding, the palmitoyl at Cys184 is likely designed to serve another, presumably functional, role... - NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexesJacob D Durrant
Department of Chemistry and Biochemistry, NSF Center for Theoretical Biological Physics, National Biomedical Computation Resource, Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093, USA
J Chem Inf Model 50:1865-71. 2010..The scoring function presented here, used either on its own or in conjunction with other more traditional functions, could prove useful in future drug-discovery efforts... - Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma bruceiRommie E Amaro
Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093 0365, USA
Proc Natl Acad Sci U S A 105:17278-83. 2008..These compounds are promising scaffolds for future drug design and discovery efforts against these important pathogens... - Computational identification of uncharacterized cruzain binding sitesJacob D Durrant
Biomedical Sciences Program, University of California San Diego, La Jolla, California, United States of America
PLoS Negl Trop Dis 4:e676. 2010..The two sites identified may serve as targets for future pharmacological intervention... - Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug designJacob D Durrant
Biomedical Sciences Program, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0365, United States
Comput Biol Chem 34:97-105. 2010..Several potential inhibitors are identified that are predicted to bind to neuraminidase better than currently approved drugs... - A transition path ensemble study reveals a linchpin role for Mg(2+) during rate-limiting ADP release from protein kinase AIlja V Khavrutskii
Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093 0365, USA
Biochemistry 48:11532-45. 2009..The results of the present study enhance understanding of Mg(2+)-dependent association of nucleotides with protein kinases... - Dynamic binding of PKA regulatory subunit RI alphaJustin Gullingsrud
Department of Chemistry and Biochemistry, University of California, San Diego, California 92093, USA
Structure 14:141-9. 2006..The model structure is consistent with available experimental data... - Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approachDeqiang Zhang
Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093 0365, USA
Biopolymers 75:325-37. 2004..The overall icosahedral shape of the net overlaps with the capsid subunit icosahedral organization. Medium density of RNA is found under the pentamers of the capsid. These findings are consistent with experimental observations... - Accelerated molecular dynamics: a promising and efficient simulation method for biomoleculesDonald Hamelberg
NSF Center for Theoretical Biological Physics and Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093 0365, USA
J Chem Phys 120:11919-29. 2004..We have shown that our approach, which can be extended to biomolecules, samples the conformational space more efficiently than normal molecular dynamics simulations, and converges to the correct canonical distribution... - Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 proteaseDonald Hamelberg
Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA
J Am Chem Soc 127:13778-9. 2005..After loop formation of a linear peptide containing the Gly-Gly motif, the rate of isomerization is shown to increase by many orders of magnitude... - Channel opening motion of alpha7 nicotinic acetylcholine receptor as suggested by normal mode analysisXiaolin Cheng
Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093 0365, USA
J Mol Biol 355:310-24. 2006..Finally, as a further goal of the present study, an approximate open channel model, consistent with many experimental findings, has been produced... - Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamicsIvaylo Ivanov
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
J Am Chem Soc 128:1778-9. 2006..Our results indicate sensitive dependence of the overall shape on the sequence, suggesting that experimentally observed changes in activity can be correlated with particular sequences, providing an avenue for rational design... - Increased membrane affinity of the C1 domain of protein kinase Cdelta compensates for the lack of involvement of its C2 domain in membrane recruitmentJennifer R Giorgione
Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0721, USA
J Biol Chem 281:1660-9. 2006.... - Acetylcholinesterase: enhanced fluctuations and alternative routes to the active site in the complex with fasciculin-2Jennifer M Bui
Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093 0365, USA
J Am Chem Soc 126:7198-205. 2004..Fluctuations of part of the long omega loop (residues 69-96) are particularly enhanced. This loop forms one wall of the active site, and the enhanced fluctuations lead to additional routes of access to the active site... - Bio3d: an R package for the comparative analysis of protein structuresBarry J Grant
Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
Bioinformatics 22:2695-6. 2006..AVAILABILITY: The bio3d package is distributed with full source code as a platform-independent R package under a GPL2 license from: http://mccammon.ucsd.edu/~bgrant/bio3d/.. - Constant pH molecular dynamics in generalized Born implicit solventJohn Mongan
The Center for Theoretical Biological Physics, University of California at San Diego, 9500 Gilman Dr, La Jolla, California 92093 0365, USA
J Comput Chem 25:2038-48. 2004..A strong correlation between conformation and protonation state is noted and quantitatively analyzed, emphasizing the importance of sampling protonation states in conjunction with dynamics... - Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptorsXiaolin Cheng
Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, United States of America
PLoS Comput Biol 2:e134. 2006.... - Finite element simulations of acetylcholine diffusion in neuromuscular junctionsKaihsu Tai
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
Biophys J 84:2234-41. 2003..Ultimately, such models may provide useful insight on the functional implications of controlled changes in processes, suggesting therapies for neuromuscular diseases... - Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanismJennifer M Bui
Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0365, USA
Proc Natl Acad Sci U S A 103:15451-6. 2006.... - In-situ synthesis of a tacrine-triazole-based inhibitor of acetylcholinesterase: configurational selection imposed by steric interactionsSanjib Senapati
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 0365, USA
J Med Chem 49:6222-30. 2006..The architecture of the gorge plays an important role in this selective formation of 1... - Binding pathways of ligands to HIV-1 protease: coarse-grained and atomistic simulationsChia en A Chang
Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA
Chem Biol Drug Des 69:5-13. 2007..Simulations allow us to efficiently study the ligand binding processes and may help those who study drug discovery to find optimal association pathways and to design those ligands with the best binding kinetics... - Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction modelsYuhui Cheng
Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, National Biomedical Computation Resource, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0365, USA
Biophys Chem 127:129-39. 2007..The finite element method has demonstrated its flexibility and robustness in modeling large biological systems... - Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculationsYuhui Cheng
Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California, USA
Biophys J 92:3397-406. 2007.... - PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculationsTodd J Dolinsky
Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St Louis, 700 S. Euclid Avenue, Campus Box 8036, St Louis, MO 63110, USA
Nucleic Acids Res 32:W665-7. 2004.... - The physical basis of microtubule structure and stabilityDavid Sept
Department of Biomedical Engineering and Center for Computational Biology, Washington University, St Louis, Missouri 63130, USA
Protein Sci 12:2257-61. 2003..This explains observations of microtubule disassembly and may serve as another step toward understanding the basis for dynamic instability... - Studying the roles of W86, E202, and Y337 in binding of acetylcholine to acetylcholinesterase using a combined molecular dynamics and multiple docking approachJeremy Kua
Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA
Protein Sci 12:2675-84. 2003..We also find that all perturbations result in a significant reduction in binding of extended ACh in the catalytically productive orientation. This effect is primarily caused by a small shift in preferred position of the quaternary tail... - Agonist-mediated conformational changes in acetylcholine-binding protein revealed by simulation and intrinsic tryptophan fluorescenceFan Gao
Receptor Biology Laboratory, Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
J Biol Chem 280:8443-51. 2005..The collective findings showed that ACh initially establishes close register of conserved Trps from adjacent subunits and then draws the C-loop inward to occlude the entrance to the binding cavity... - Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systemsPeter A Sims
Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
J Comput Chem 26:668-81. 2005..As a result, the binding affinity of these two systems do not or only barely benefit from electrostatics contributions... - The entropic cost of protein-protein association: a case study on acetylcholinesterase binding to fasciculin-2David D L Minh
Biophys J 89:L25-7. 2005 - Comparative MD analysis of the stability of transthyretin providing insight into the fibrillation mechanismJesper Sørensen
Department of Chemistry, Aarhus University, Aarhus C, 8000, Denmark
Biopolymers 86:73-82. 2007..In addition to the energetic calculations, we have also investigated the dominant motions of the TTR and found that only the dimeric form of the protein could undergo the initial fibril formation... - Limitations of atom-centered dielectric functions in implicit solvent modelsJessica M J Swanson
J Phys Chem B 109:14769-72. 2005..These results suggest that implicit solvent dielectric functions must exclude interstitial high dielectric regions in order to yield physically meaningful results... - Control of cation permeation through the nicotinic receptor channelHai Long Wang
Receptor Biology Laboratory, Department of Physiology, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
PLoS Comput Biol 4:e41. 2008.... - Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensembleMelissa R Landon
Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
Chem Biol Drug Des 71:106-16. 2008..Our hot spot analysis provides further support for the feasibility of developing high-affinity inhibitors capable of binding these regions, which appear to be unique to the N1 strain... - HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamicsJoanna Trylska
Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Warsaw, Poland
Biophys J 92:4179-87. 2007..Moreover, the active site residues and the flap tips move in phase with the peptide. We suggest some mechanistic principles for how the flexibility of the protein may be involved in ligand binding and release... - Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approachJeremy Kua
Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093 0365, USA
J Am Chem Soc 124:8260-7. 2002..Substituting each tail methyl group with hydrogen results in both an incremental loss in docking energy and also a decrease in the percentage of structures docked in the active site correctly set up for catalysis...
Research Grants
- THEORY OF BIOMOLECULAR DIFFUSIONJAMES MCCAMMON; Fiscal Year: 2009..Training of undergraduate, graduate and postdoctoral students for careers in public health will continue to be a key aspect of the project. ..
- THEORY OF BIOMOLECULAR DIFFUSIONJAMES MCCAMMON; Fiscal Year: 2007..Training of undergraduate, graduate and postdoctoral students for careers in public health will continue to be a key aspect of the project. ..
- THEORY OF BIOMOLECULAR DIFFUSIONJAMES MCCAMMON; Fiscal Year: 2006..Training of undergraduate, graduate and postdoctoral students will continue to be a key aspect of this project. ..
- THEORY OF BIOMOLECULAR DIFFUSIONJAMES MCCAMMON; Fiscal Year: 2002..Training of undergraduate, graduate, and postdoctoral students will continue to be a key aspect of this project. ..
- THEORY OF BIOMOLECULAR DIFFUSIONJAMES A MCCAMMON; Fiscal Year: 2010..Training of undergraduate, graduate and postdoctoral students for careers in public health will continue to be a key aspect of the project. ..