Research Topics
| Xiongwu WuSummaryAffiliation: National Institutes of Health Country: USA Publications
| Collaborators
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Detail Information
Publications
Chemoreceptors in Caulobacter crescentus: trimers of receptor dimers in a partially ordered hexagonally packed arrayCezar M Khursigara
Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
J Bacteriol 190:6805-10. 2008....- Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational samplingXiongwu Wu
Laboratory of Computational Biology, National Heart, Lung, and Blood Institute NHLBI, National Institutes of Health NIH, Bethesda, Maryland 20892, USA
J Chem Phys 137:044106. 2012..Especially for large systems, RXSGLD has remarkable advantages in terms of replica exchange efficiency, conformational searching ability, and system size extensiveness... - Force-momentum-based self-guided Langevin dynamics: a rapid sampling method that approaches the canonical ensembleXiongwu Wu
Laboratory of Computational Biology, National Heart, Lung, and Blood Institute NHLBI, National Institutes of Health NIH, Bethesda, Maryland 20892, USA
J Chem Phys 135:204101. 2011..For studies where preserving accessible conformational space is critical, such as free energy calculations and protein folding studies, SGLDfp is an efficient approach to search and sample the conformational space... - Isotropic periodic sum of electrostatic interactions for polar systemsXiongwu Wu
Laboratory of Computational Biology, NHLBI, NIH, Bethesda, Maryland 20892, USA
J Chem Phys 131:024107. 2009..For both homogeneous and heterogeneous systems, the 3D-IPS/discrete fast Fourier transform method using either the nonpolar or the polar electrostatic 3D-IPS potentials results in very similar simulation results... - Toward canonical ensemble distribution from self-guided Langevin dynamics simulationXiongwu Wu
Laboratory of Computational Biology, National Heart, Lung, and Blood Institute NHLBI, National Institutes of Health NIH, Bethesda, Maryland 20892, USA
J Chem Phys 134:134108. 2011..This development makes SGLD not only an efficient approach for conformational searching, but also an accurate means for conformational sampling... 
Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulationXiongwu Wu
Laboratory of Biophysical Chemistry, NHLBI, NIH, Building 50, Room 3308, Bethesda, Maryland 20892, USA
J Am Chem Soc 124:5282-3. 2002..Energetic analysis indicates that the driving force of the folding is the intrapeptide interaction, while the solvent interaction opposes the folding...- Beta-hairpin folding mechanism of a nine-residue peptide revealed from molecular dynamics simulations in explicit waterXiongwu Wu
Laboratory of Biophysical Chemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
Biophys J 86:1946-58. 2004..Comparing unfolding simulations using MD and SGMD methods demonstrate that SGMD simulations can qualitatively reproduce the kinetics of the peptide system... - A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopyXiongwu Wu
Laboratory of Biophysical Chemistry, NHLBI, National Institutes of Health, Building 50, Room 3308, 50 South Drive, Bethesda, MD 20892, USA
J Struct Biol 141:63-76. 2003.... - Using the isotropic periodic sum method to calculate long-range interactions of heterogeneous systemsXiongwu Wu
Laboratory of Computational Biology, NHLBI, NIH, Bethesda, Maryland 20892, USA
J Chem Phys 129:154115. 2008..Example simulations demonstrate that this method can accurately and efficiently calculate long-range interactions for molecular simulation... 
Extended polypeptide linkers establish the spatial architecture of a pyruvate dehydrogenase multienzyme complexJeffrey S Lengyel
Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
Structure 16:93-103. 2008....- Lateral density of receptor arrays in the membrane plane influences sensitivity of the E. coli chemotaxis responseCezar M Khursigara
Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
EMBO J 30:1719-29. 2011.... - Molecular structure of a 9-MDa icosahedral pyruvate dehydrogenase subcomplex containing the E2 and E3 enzymes using cryoelectron microscopyJacqueline L S Milne
Laboratory of Cell Biology, NCI, National Institutes of Health, Bethesda, MD 20892, USA
J Biol Chem 281:4364-70. 2006.... - Maintain rigid structures in Verlet based cartesian molecular dynamics simulationsPeng Tao
Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
J Chem Phys 137:134110. 2012..Numerical tests with four model systems including two proteins demonstrate that the accuracy and reliability of the SHAPE method are comparable to the SHAKE method, but with much more applicability and efficiency... - Role of HAMP domains in chemotaxis signaling by bacterial chemoreceptorsCezar M Khursigara
Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
Proc Natl Acad Sci U S A 105:16555-60. 2008..Based on these results, we propose that the compact and expanded conformations represent the "kinase-on" and "kinase-off" states of chemoreceptor trimers, respectively... - Mutagenesis and modeling of the peroxiredoxin (Prx) complex with the NMR structure of ATP-bound human sulfiredoxin implicate aspartate 187 of Prx I as the catalytic residue in ATP hydrolysisDuck Yeon Lee
Laboratory of Cell Signaling, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892 0301, USA
Biochemistry 45:15301-9. 2006..The modeling and mutagenesis analyses strongly implicate Asp187 of Prx I as the catalytic residue responsible for ATP hydrolysis in the cysteinesulfinic acid reduction of Prx by hSrx... - Molecular architecture and mechanism of an icosahedral pyruvate dehydrogenase complex: a multifunctional catalytic machineJacqueline L S Milne
Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
EMBO J 21:5587-98. 2002.... - Molecular dynamics simulations of perylene and tetracene librations: comparison with femtosecond upconversion dataTilman Rosales
Optical Spectroscopy Section, Laboratory of Molecular Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Building 10 Magnuson CC, 5D14, 10 Center Dr, Bethesda, Maryland 20892, USA
J Phys Chem A 112:5593-7. 2008..Sarkar, N.; Takeuchi, S.; Tahara, T. J. Phys. Chem. A 1999, 103, 4808]... - Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum methodJeffery B Klauda
Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
J Phys Chem B 111:4393-400. 2007.... - A common molecular basis for exogenous and endogenous cannabinoid potentiation of glycine receptorsWei Xiong
Laboratory for Integrative Neuroscience, National Institute on Alcohol Abuse and Alcoholism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
J Neurosci 32:5200-8. 2012..Such a specific interaction likely stems from a common molecular basis involving the S296 residue in the TM3 of the α1 and α3 subunits... - Accurate high-throughput structure mapping and prediction with transition metal ion FRETXiaozhen Yu
Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
Structure 21:9-19. 2013..Our results open the door to rapid, accurate mapping and prediction of protein structures at low concentrations, in large complex systems, and in living cells...