Jorge L Barreda

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc A solvable model for the diffusion and reaction of neurotransmitters in a synaptic junction
    Jorge L Barreda
    Department of Physics and Institute of Molecular Biophysics, Tallahassee, Florida 32306, USA
    BMC Biophys 4:5. 2011
  2. pmc Molecular dynamics simulations and drug discovery
    Jacob D Durrant
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
    BMC Biol 9:71. 2011
  3. ncbi Theory of biomolecular recognition
    J 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
  4. ncbi Target flexibility in molecular recognition
    J Andrew McCammon
    Howard Hughes Medical Institute, La Jolla, CA 92093 0365, USA
    Biochim Biophys Acta 1754:221-4. 2005
  5. pmc Gated Diffusion-controlled Reactions
    J 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
  6. pmc Exploring global motions and correlations in the ribosome
    Joanna 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
  7. pmc Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase
    Lily S Cheng
    National Biomedical Computation Resource, University of California, San Diego, La Jolla, California 92093, USA
    J Med Chem 51:3878-94. 2008
  8. pmc Dependency map of proteins in the small ribosomal subunit
    Kay 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
  9. doi (Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding
    Riccardo 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
  10. ncbi Molecular dynamics simulations of metalloproteinases types 2 and 3 reveal differences in the dynamic behavior of the S1' binding pocket
    Cesar 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

Research Grants

  1. THEORY OF BIOMOLECULAR DIFFUSION
    JAMES MCCAMMON; Fiscal Year: 2009
  2. THEORY OF BIOMOLECULAR DIFFUSION
    JAMES MCCAMMON; Fiscal Year: 2007
  3. THEORY OF BIOMOLECULAR DIFFUSION
    JAMES MCCAMMON; Fiscal Year: 2006
  4. THEORY OF BIOMOLECULAR DIFFUSION
    JAMES MCCAMMON; Fiscal Year: 2002
  5. THEORY OF BIOMOLECULAR DIFFUSION
    JAMES A MCCAMMON; Fiscal Year: 2010

Collaborators

Detail Information

Publications78

  1. pmc A solvable model for the diffusion and reaction of neurotransmitters in a synaptic junction
    Jorge L Barreda
    Department of Physics and Institute of Molecular Biophysics, Tallahassee, Florida 32306, USA
    BMC Biophys 4:5. 2011
    ..abstract:..
  2. pmc Molecular dynamics simulations and drug discovery
    Jacob 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...
  3. ncbi Theory of biomolecular recognition
    J 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...
  4. ncbi Target flexibility in molecular recognition
    J 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...
  5. pmc Gated Diffusion-controlled Reactions
    J 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...
  6. pmc Exploring global motions and correlations in the ribosome
    Joanna 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...
  7. pmc Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase
    Lily 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...
  8. pmc Dependency map of proteins in the small ribosomal subunit
    Kay 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...
  9. doi (Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding
    Riccardo 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...
  10. ncbi Molecular dynamics simulations of metalloproteinases types 2 and 3 reveal differences in the dynamic behavior of the S1' binding pocket
    Cesar 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
    ....
  11. pmc Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation study
    Benzhuo 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...
  12. ncbi Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug design
    Alexander 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...
  13. ncbi Molecular docking of balanol to dynamics snapshots of protein kinase A
    Chung 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...
  14. pmc Toward understanding the conformational dynamics of RNA ligation
    Robert 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...
  15. ncbi Brownian dynamics simulations of ion atmospheres around polyalanine and B-DNA: effects of biomolecular dielectric
    David 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
    ....
  16. ncbi Elasticity of peptide omega bonds
    Tongye 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...
  17. ncbi Molecular dynamics of acetylcholinesterase
    Tongye 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...
  18. pmc A simple electrostatic switch important in the activation of type I protein kinase A by cyclic AMP
    Dominico Vigil
    Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA 92037, USA
    Protein Sci 15:113-21. 2006
    ....
  19. pmc H-ras protein in a bilayer: interaction and structure perturbation
    Alemayehu 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...
  20. ncbi Discovery of a novel binding trench in HIV integrase
    Julie 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...
  21. pmc Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitors
    Jacob 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...
  22. pmc A dynamic model of HIV integrase inhibition and drug resistance
    Alex 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
    ....
  23. ncbi SR protein kinase 1 is resilient to inactivation
    Jacky Chi Ki Ngo
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
    Structure 15:123-33. 2007
    ....
  24. ncbi Mechanism of acetylcholinesterase inhibition by fasciculin: a 5-ns molecular dynamics simulation
    Kaihsu 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/...
  25. pmc Molecular dynamics: survey of methods for simulating the activity of proteins
    Stewart 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
  26. ncbi Charge optimization of the interface between protein kinases and their ligands
    Peter 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...
  27. ncbi Protein flexibility and computer-aided drug design
    Chung 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
    ....
  28. ncbi Acetylcholinesterase: pivotal roles of its long omega loop (Cys69-Cys96) in regulating substrate binding
    Jennifer 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...
  29. pmc Functional dynamics of the folded ankyrin repeats of I kappa B alpha revealed by nuclear magnetic resonance
    Carla 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...
  30. ncbi Nanosecond dynamics of the mouse acetylcholinesterase cys69-cys96 omega loop
    Jianxin Shi
    Department of Pharmacology, University of California, San Diego, La Jolla, California 92093 0636, USA
    J Biol Chem 278:30905-11. 2003
    ....
  31. ncbi Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach
    Joanna 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...
  32. ncbi Electrostatic interactions
    Nathan A Baker
    University of California, San Diego, La Jolla, CA, USA
    Methods Biochem Anal 44:427-40. 2003
  33. ncbi Finite concentration effects on diffusion-controlled reactions
    Sanjib Senapati
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093 0365, USA
    J Chem Phys 121:7896-900. 2004
    ....
  34. ncbi From model complexes to metalloprotein inhibition: a synergistic approach to structure-based drug discovery
    David 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
  35. ncbi Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study
    Cesar 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...
  36. pmc An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
    Rommie 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...
  37. ncbi Accelerated entropy estimates with accelerated dynamics
    David 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...
  38. pmc Computer-aided drug-discovery techniques that account for receptor flexibility
    Jacob D Durrant
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
    Curr Opin Pharmacol 10:770-4. 2010
    ....
  39. ncbi Generalized gradient-augmented harmonic Fourier beads method with multiple atomic and/or center-of-mass positional restraints
    Ilja 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...
  40. pmc Calculating pKa values in enzyme active sites
    Jens 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...
  41. pmc Hot-spot residues at the E9/Im9 interface help binding via different mechanisms
    Sergio 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...
  42. pmc E9-Im9 colicin DNase-immunity protein biomolecular association in water: a multiple-copy and accelerated molecular dynamics simulation study
    Riccardo 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...
  43. doi Catalytically requisite conformational dynamics in the mRNA-capping enzyme probed by targeted molecular dynamics
    Robert V Swift
    Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, 92039 0365, USA
    Biochemistry 47:4102-11. 2008
    ....
  44. pmc Similar membrane affinity of mono- and Di-S-acylated ras membrane anchors: a new twist in the role of protein lipidation
    Alemayehu 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...
  45. pmc NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexes
    Jacob 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...
  46. pmc Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei
    Rommie 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...
  47. pmc Computational identification of uncharacterized cruzain binding sites
    Jacob 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...
  48. pmc Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug design
    Jacob 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...
  49. pmc A transition path ensemble study reveals a linchpin role for Mg(2+) during rate-limiting ADP release from protein kinase A
    Ilja 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...
  50. ncbi Dynamic binding of PKA regulatory subunit RI alpha
    Justin 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...
  51. pmc Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach
    Deqiang 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...
  52. ncbi Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules
    Donald 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...
  53. ncbi Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease
    Donald 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...
  54. ncbi Channel opening motion of alpha7 nicotinic acetylcholine receptor as suggested by normal mode analysis
    Xiaolin 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...
  55. ncbi Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamics
    Ivaylo 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...
  56. pmc Increased membrane affinity of the C1 domain of protein kinase Cdelta compensates for the lack of involvement of its C2 domain in membrane recruitment
    Jennifer R Giorgione
    Department of Pharmacology, University of California at San Diego, La Jolla, California 92093 0721, USA
    J Biol Chem 281:1660-9. 2006
    ....
  57. ncbi Acetylcholinesterase: enhanced fluctuations and alternative routes to the active site in the complex with fasciculin-2
    Jennifer 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...
  58. ncbi Bio3d: an R package for the comparative analysis of protein structures
    Barry J Grant
    Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
    Bioinformatics 22:2695-6. 2006
    ..The method is implemented in bio3d, an R package for the exploratory analysis of structure and sequence data...
  59. ncbi Constant pH molecular dynamics in generalized Born implicit solvent
    John 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...
  60. pmc Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors
    Xiaolin Cheng
    Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 2:e134. 2006
    ....
  61. pmc Finite element simulations of acetylcholine diffusion in neuromuscular junctions
    Kaihsu 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...
  62. pmc Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanism
    Jennifer 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
    ....
  63. ncbi In-situ synthesis of a tacrine-triazole-based inhibitor of acetylcholinesterase: configurational selection imposed by steric interactions
    Sanjib 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...
  64. ncbi Binding pathways of ligands to HIV-1 protease: coarse-grained and atomistic simulations
    Chia 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...
  65. pmc Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction models
    Yuhui 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...
  66. pmc Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations
    Yuhui Cheng
    Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California, USA
    Biophys J 92:3397-406. 2007
    ....
  67. pmc PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
    Todd 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
    ....
  68. pmc The physical basis of microtubule structure and stability
    David 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...
  69. pmc Studying the roles of W86, E202, and Y337 in binding of acetylcholine to acetylcholinesterase using a combined molecular dynamics and multiple docking approach
    Jeremy 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...
  70. ncbi Agonist-mediated conformational changes in acetylcholine-binding protein revealed by simulation and intrinsic tryptophan fluorescence
    Fan 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...
  71. ncbi Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems
    Peter 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...
  72. pmc The entropic cost of protein-protein association: a case study on acetylcholinesterase binding to fasciculin-2
    David D L Minh
    Biophys J 89:L25-7. 2005
  73. ncbi Comparative MD analysis of the stability of transthyretin providing insight into the fibrillation mechanism
    Jesper 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...
  74. ncbi Limitations of atom-centered dielectric functions in implicit solvent models
    Jessica 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...
  75. pmc Control of cation permeation through the nicotinic receptor channel
    Hai Long Wang
    Receptor Biology Laboratory, Department of Physiology, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
    PLoS Comput Biol 4:e41. 2008
    ....
  76. pmc Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble
    Melissa 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...
  77. pmc HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics
    Joanna 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...
  78. ncbi Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach
    Jeremy 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 Grants17

  1. THEORY OF BIOMOLECULAR DIFFUSION
    JAMES 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. ..
  2. THEORY OF BIOMOLECULAR DIFFUSION
    JAMES 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. ..
  3. THEORY OF BIOMOLECULAR DIFFUSION
    JAMES MCCAMMON; Fiscal Year: 2006
    ..Training of undergraduate, graduate and postdoctoral students will continue to be a key aspect of this project. ..
  4. THEORY OF BIOMOLECULAR DIFFUSION
    JAMES MCCAMMON; Fiscal Year: 2002
    ..Training of undergraduate, graduate, and postdoctoral students will continue to be a key aspect of this project. ..
  5. THEORY OF BIOMOLECULAR DIFFUSION
    JAMES 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. ..