研究领域

Biophysical Chemistry Chemical Biology Computational/Theoretical Chemistry Environmental Chemistry Nano Chemistry Physical Chemistry RNA BioChemistry Surface Chemistry Ultrafast Dynamics

Understanding the forces that determine the structure of proteins, peptides, nucleic acids, and complexes containing these molecules and the processes by which the structures are adopted is essential to extend our knowledge of the molecular nature of structure and function. To address such questions, we use statistical mechanics, molecular simulations, statistical modeling, and quantum chemistry. Creating atomic-level models to simulate biophysical processes (e.g., folding of a protein or binding of a ligand to a biological receptor) requires (1) the development of potential energy functions that accurately represent the atomic interactions and (2) the use of quantum chemistry to aid in parameterizing these models. Calculation of thermodynamic properties requires the development and implementation of new theoretical and computational approaches that connect averages over atomistic descriptions to experimentally measurable thermodynamic and kinetic properties. Interpreting experimental results at more microscopic levels is fueled by the development and investigation of theoretical models for the processes of interest that range form atomic level detail to more coarse-grained molecular representations. Massive computational resources are needed to realize these objectives, and this need motivates our efforts aimed at the efficient use of new computer architectures, including large supercomputers, Linux Beowulf clusters, and computational grids. Each of the objectives and techniques mentioned represents an ongoing area of development within our research program.

近期论文

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LS Ahlstrom, SM Law, A Dickson and CL Brooks III. Multiscale Modeling of a Conditionally Disordered pH-Sensing Chaperone. J Mol Biol, 2015, in the press. X Zeng, S Mukhopadhyay and CL Brooks III. Residue level resolution of alphavirus envelope protein interactions in pH dependent fusion. Proc Natl Acad Sci U S A, 2015, in the press. AM Mustoe, CL Brooks III and HM Al-Hashimi. Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity. Nucleic Acids Res, 2015, 42:11792-804. PubMed A Frank, SM Law, LS Ahlstrom and CL Brooks III. Predicting Protein Backbone Chemical Shifts From Cα Coordinates: Extracting High Resolution Experimental Observables from Low Resolution Models. J Chem Theor Comp, 2014, in the press. J Yesselman, S Horowitz, CL Brooks III and R Trievel. Frequent Side Chain Methyl Carbon-Oxygen Hydrogen Bonding in Proteins Revealed by Computational and Stereochemical Analysis of Neutron Structures. Proteins, 2014, in the press. EJ Arthur, JT King, KJ Kubarych and CL Brooks III. Heterogeneous preferential solvation of water and trifluoroethanol in homologous lysozymes. J Phys Chem B, 2014, 118:8118-27. PMCID: 4216199. PubMed A Dickson and CL Brooks III. WExplore: Hierarchical Exploration of High-Dimensional Spaces Using the Weighted Ensemble Algorithm. J Phys Chem B, 2014, 118:3532-42. PMCID: 24490961. PubMed A Dickson, AM Mustoe, L Salmon and CL Brooks III. Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore. Nucleic Acids Res, 2014, 42:12126-37. PMCID: 4231733. PubMed AT Frank, SM Law and CL Brooks III. A simple and fast approach for predicting (1)h and (13)c chemical shifts: toward chemical shift-guided simulations of RNA. J Phys Chem B, 2014, 118:12168-75. PMCID: 4207130. PubMed GB Goh, BS Hulbert, H Zhou and CL Brooks III. Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism. Proteins, 2014, 82:1319-31. PubMed GB Goh, EN Laricheva and CL Brooks III. Uncovering pH-dependent transient states of proteins with buried ionizable residues. J Am Chem Soc, 2014, 136:8496-9. PMCID: 4227812. PubMed X Han, Y Liu, FG Wu, J Jansensky, T Kim, Z Wang, CL Brooks III, J Wu, C Xi, CM Mello and Z Chen. Different interfacial behaviors of peptides chemically immobilized on surfaces with different linker lengths and via different termini. J Phys Chem B, 2014, 118:2904-12. PubMed JT King, EJ Arthur, CL Brooks III and KJ Kubarych. Crowding Induced Collective Hydration of Biological Macromolecules over Extended Distances. J Am Chem Soc, 2014, 136:188-94. PMCID: 3983708. PubMed SM Law, LS Ahlstrom, A Panahi and CL Brooks III. Hamiltonian Mapping Revisited: Calibrating Minimalist Models to Capture Molecular Recognition by Intrinsically Disordered Proteins. J Phys Chem Lett, 2014, 5:3441-3444. PMCID: 4183358. PubMed SM Law, AT Frank and CL Brooks III. PCASSO: A fast and efficient Calpha-based method for accurately assigning protein secondary structure elements. J Comput Chem, 2014, 35:1757-61. PMCID: 4127665. PubMed SM Law, JK Gagnon, AK Mapp and CL Brooks III. Prepaying the entropic cost for allosteric regulation in KIX. Proc Natl Acad Sci U S A, 2014, 111:12067-72. PMCID: 4143015. PubMed ER May, K Arora and CL Brooks III. pH-Induced Stability Switching of the Bacteriophage HK97 Maturation Pathway. J Am Chem Soc, 2014, 136:3097-3107. PMCID: 3985869. PubMed AM Mustoe, HM Al-Hashimi and CL Brooks III. Coarse Grained Models Reveal Essential Contributions of Topological Constraints to the Conformational Free Energy of RNA Bulges. J Phys Chem B, 2014, 118:2615-2627. PMCID: 3983386. PubMed AM Mustoe, CL Brooks III and HM Al-Hashimi. Hierarchy of RNA functional dynamics. Annu Rev Biochem, 2014, 83:441-66. PMCID: 4048628. PubMed RP Nobrega, K Arora, SV Kathuria, R Graceffa, RA Barrea, L Guo, S Chakravarthy, O Bilsel, TC Irving, CL Brooks III and CR Matthews. Modulation of frustration in folding by sequence permutation. Proc Natl Acad Sci U S A, 2014, 111:10562-7. PMCID: 4115504. PubMed