Xiongwu Wu

Xiongwu Wu

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Xiongwu Wu

Publications by authors named "Xiongwu Wu"

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Protonation state of the selectivity filter of bacterial voltage-gated sodium channels is modulated by ions.

Proteins 2019 Oct 7. Epub 2019 Oct 7.

Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD.

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http://dx.doi.org/10.1002/prot.25831DOI Listing
October 2019

The homogeneity condition: A simple way to derive isotropic periodic sum potentials for efficient calculation of long-range interactions in molecular simulation.

J Chem Phys 2019 Jun;150(21):214109

Laboratory of Computational Biology, NHLBI, NIH, 12 South Dr., Bldg. 12A, Room 3053K, Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1063/1.5097560DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6551215PMC
June 2019

A double exponential potential for van der Waals interaction.

AIP Adv 2019 Jun 7;9(6):065304. Epub 2019 Jun 7.

Laboratory of Computational Biology, NHLBI, NIH, 12 South Dr., Bldg. 12A, Room 3053K, Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1063/1.5107505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6555761PMC
June 2019

Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges.

J Comput Aided Mol Des 2018 10 15;32(10):1075-1086. Epub 2018 Oct 15.

Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.

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http://dx.doi.org/10.1007/s10822-018-0166-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6413509PMC
October 2018

Atomic Resolution Cryo-EM Structure of β-Galactosidase.

Structure 2018 06 10;26(6):848-856.e3. Epub 2018 May 10.

Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09692126183012
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http://dx.doi.org/10.1016/j.str.2018.04.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129192PMC
June 2018

Hydronium Ions Accompanying Buried Acidic Residues Lead to High Apparent Dielectric Constants in the Interior of Proteins.

J Phys Chem B 2018 06 1;122(23):6215-6223. Epub 2018 Jun 1.

Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI) , National Institutes of Health (NIH) , Bethesda , Maryland 20892 , United States.

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http://dx.doi.org/10.1021/acs.jpcb.8b04584DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6413497PMC
June 2018

Origin of pK Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water.

J Phys Chem B 2017 04 18;121(15):3318-3330. Epub 2016 Oct 18.

Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States.

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http://pubs.acs.org/doi/10.1021/acs.jpcb.6b08249
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http://dx.doi.org/10.1021/acs.jpcb.6b08249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6415756PMC
April 2017

The ubiquitin ligase Ubr4 controls stability of podocin/MEC-2 supercomplexes.

Hum Mol Genet 2016 Apr 19;25(7):1328-44. Epub 2016 Jan 19.

Department II of Internal Medicine, Center for Molecular Medicine Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany,

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http://dx.doi.org/10.1093/hmg/ddw016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787903PMC
April 2016

Self-guided Langevin dynamics via generalized Langevin equation.

J Comput Chem 2016 Mar 16;37(6):595-601. Epub 2015 Jul 16.

Courant Institute of Mathematical Sciences, New York University, New York, New York, 10012.

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http://dx.doi.org/10.1002/jcc.24015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4715807PMC
March 2016

A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water.

PLoS Comput Biol 2015 Oct 27;11(10):e1004480. Epub 2015 Oct 27.

Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland, United States of America.

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https://dx.plos.org/10.1371/journal.pcbi.1004480
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http://dx.doi.org/10.1371/journal.pcbi.1004480DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4624693PMC
October 2015

2.2 Å resolution cryo-EM structure of β-galactosidase in complex with a cell-permeant inhibitor.

Science 2015 Jun 7;348(6239):1147-51. Epub 2015 May 7.

Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.aab1576
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http://dx.doi.org/10.1126/science.aab1576DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6512338PMC
June 2015

Comparative phosphoproteomic analysis of mammalian glomeruli reveals conserved podocin C-terminal phosphorylation as a determinant of slit diaphragm complex architecture.

Proteomics 2015 Apr 19;15(7):1326-31. Epub 2015 Jan 19.

Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany.

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http://dx.doi.org/10.1002/pmic.201400235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6512310PMC
April 2015

Maturation of the HIV-1 core by a non-diffusional phase transition.

Nat Commun 2015 Jan 8;6:5854. Epub 2015 Jan 8.

Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

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http://search.proquest.com/openview/97a5f785ecef05150fd6326d
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http://www.nature.com/doifinder/10.1038/ncomms6854
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http://dx.doi.org/10.1038/ncomms6854DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288007PMC
January 2015

Phosphoproteomic analysis reveals regulatory mechanisms at the kidney filtration barrier.

J Am Soc Nephrol 2014 Jul 7;25(7):1509-22. Epub 2014 Feb 7.

Department of Internal Medicine II, Center for Molecular Medicine, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Systems Biology of Ageing Cologne,

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http://dx.doi.org/10.1681/ASN.2013070760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073431PMC
July 2014

Targeted conformational search with map-restrained self-guided Langevin dynamics: application to flexible fitting into electron microscopic density maps.

J Struct Biol 2013 Sep 20;183(3):429-440. Epub 2013 Jul 20.

Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1016/j.jsb.2013.07.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785014PMC
September 2013

Protein-Protein Docking Using EMAP in CHARMM and Support Vector Machine: Application to Ab/Ag Complexes.

J Chem Theory Comput 2013 Sep 16;9(9):4186-94. Epub 2013 Aug 16.

Institute of Biomedical Sciences, Academia Sinica , Taipei 115, Taiwan.

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http://dx.doi.org/10.1021/ct400508sDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6415758PMC
September 2013

Accurate high-throughput structure mapping and prediction with transition metal ion FRET.

Structure 2013 Jan 27;21(1):9-19. Epub 2012 Dec 27.

Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address:

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http://dx.doi.org/10.1016/j.str.2012.11.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3700372PMC
January 2013

Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett's Acceptance Ratio and Enveloping Distribution Sampling Methods.

J Chem Theory Comput 2012 Oct 3;8(10):3650-62. Epub 2012 Jul 3.

Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States.

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http://dx.doi.org/10.1021/ct300116rDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6413517PMC
October 2012

Maintain rigid structures in Verlet based cartesian molecular dynamics simulations.

J Chem Phys 2012 Oct;137(13):134110

Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1063/1.4756796DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3477181PMC
October 2012

Weak intra-ring allosteric communications of the archaeal chaperonin thermosome revealed by normal mode analysis.

Biophys J 2012 Sep;103(6):1285-95

Department of Chemistry, Northern Kentucky University, Highland Heights, Kentucky, USA.

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http://dx.doi.org/10.1016/j.bpj.2012.07.049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446675PMC
September 2012

Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling.

J Chem Phys 2012 Jul;137(4):044106

Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1063/1.4737094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416874PMC
July 2012

A common molecular basis for exogenous and endogenous cannabinoid potentiation of glycine receptors.

J Neurosci 2012 Apr;32(15):5200-8

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.

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http://www.jneurosci.org/content/32/15/5200.full.pdf
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http://www.jneurosci.org/cgi/doi/10.1523/JNEUROSCI.6347-11.2
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http://dx.doi.org/10.1523/JNEUROSCI.6347-11.2012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334839PMC
April 2012

Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics.

Adv Chem Phys 2012 Jan;150:255-326

Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health(NIH), 5635 Fishers Lane, Room T900, Bethesda, MD 20892-9314.

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http://dx.doi.org/10.1002/9781118197714.ch6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3731171PMC
January 2012

Automatic Spot Identification for High Throughput Microarray Analysis.

J Bioeng Biomed Sci 2011 Nov;Suppl 5

Thomas Jefferson High School for Science and Technology, Alexandria, VA.

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http://dx.doi.org/10.4172/2155-9538.S5-005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3843961PMC
November 2011

Force-momentum-based self-guided Langevin dynamics: a rapid sampling method that approaches the canonical ensemble.

J Chem Phys 2011 Nov;135(20):204101

Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA.

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http://aip.scitation.org/doi/10.1063/1.3662489
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http://dx.doi.org/10.1063/1.3662489DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3248022PMC
November 2011

Lateral density of receptor arrays in the membrane plane influences sensitivity of the E. coli chemotaxis response.

EMBO J 2011 May 25;30(9):1719-29. Epub 2011 Mar 25.

Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1038/emboj.2011.77DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3101988PMC
May 2011

Toward canonical ensemble distribution from self-guided Langevin dynamics simulation.

J Chem Phys 2011 Apr;134(13):134108

Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA.

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http://aip.scitation.org/doi/10.1063/1.3574397
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http://dx.doi.org/10.1063/1.3574397DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087419PMC
April 2011

Isotropic periodic sum of electrostatic interactions for polar systems.

J Chem Phys 2009 Jul;131(2):024107

Laboratory of Computational Biology, NHLBI, NIH, Bethesda, Maryland 20892, USA.

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http://aip.scitation.org/doi/10.1063/1.3160730
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http://dx.doi.org/10.1063/1.3160730DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723922PMC
July 2009

Chemoreceptors in Caulobacter crescentus: trimers of receptor dimers in a partially ordered hexagonally packed array.

J Bacteriol 2008 Oct 8;190(20):6805-10. Epub 2008 Aug 8.

Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1128/JB.00640-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2566187PMC
October 2008

Role of HAMP domains in chemotaxis signaling by bacterial chemoreceptors.

Proc Natl Acad Sci U S A 2008 Oct 21;105(43):16555-60. Epub 2008 Oct 21.

Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1073/pnas.0806401105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570609PMC
October 2008

Using the isotropic periodic sum method to calculate long-range interactions of heterogeneous systems.

J Chem Phys 2008 Oct;129(15):154115

Laboratory of Computational Biology, NHLBI, NIH, Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1063/1.2992601DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2736616PMC
October 2008

Molecular dynamics simulations of perylene and tetracene librations: comparison with femtosecond upconversion data.

J Phys Chem A 2008 Jun 29;112(25):5593-7. Epub 2008 May 29.

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.

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http://pubs.acs.org/doi/abs/10.1021/jp7117289
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http://dx.doi.org/10.1021/jp7117289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439201PMC
June 2008

Extended polypeptide linkers establish the spatial architecture of a pyruvate dehydrogenase multienzyme complex.

Structure 2008 Jan;16(1):93-103

Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1016/j.str.2007.10.017DOI Listing
January 2008

Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum method.

J Phys Chem B 2007 May 11;111(17):4393-400. Epub 2007 Apr 11.

Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1021/jp068767mDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6413507PMC
May 2007

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 hydrolysis.

Biochemistry 2006 Dec 5;45(51):15301-9. Epub 2006 Dec 5.

Laboratory of Cell Signaling, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-0301, USA.

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http://dx.doi.org/10.1021/bi061824hDOI Listing
December 2006

Isotropic periodic sum: a method for the calculation of long-range interactions.

J Chem Phys 2005 Jan;122(4):44107

Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1063/1.1836733DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6488042PMC
January 2005

Beta-hairpin folding mechanism of a nine-residue peptide revealed from molecular dynamics simulations in explicit water.

Biophys J 2004 Apr;86(4):1946-58

Laboratory of Biophysical Chemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304050PMC
http://dx.doi.org/10.1016/S0006-3495(04)74258-7DOI Listing
April 2004

A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy.

J Struct Biol 2003 Jan;141(1):63-76

Laboratory of Biophysical Chemistry, NHLBI, National Institutes of Health, Building 50, Room 3308, 50 South Drive, Bethesda, MD 20892, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6413516PMC
January 2003

Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation.

J Am Chem Soc 2002 May;124(19):5282-3

Laboratory of Biophysical Chemistry, NHLBI, NIH, Building 50, Room 3308, Bethesda, Maryland 20892, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6413514PMC
http://dx.doi.org/10.1021/ja0257321DOI Listing
May 2002