Nikolay V Dokholyan

Nikolay V Dokholyan

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Nikolay V Dokholyan

Publications by authors named "Nikolay V Dokholyan"

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Stabilization of μ-opioid receptor facilitates its cellular translocation and signaling.

Proteins 2019 Oct 12;87(10):878-884. Epub 2019 Jun 12.

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.

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https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.25751
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http://dx.doi.org/10.1002/prot.25751DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6718349PMC
October 2019

Distinct Binding Modes of Vinculin Isoforms Underlie Their Functional Differences.

Structure 2019 Oct 15;27(10):1527-1536.e3. Epub 2019 Aug 15.

Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Departments of Pharmacology and Departments of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA. Electronic address:

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http://dx.doi.org/10.1016/j.str.2019.07.013DOI Listing
October 2019

A central core disease mutation in the Ca-binding site of skeletal muscle ryanodine receptor impairs single-channel regulation.

Am J Physiol Cell Physiol 2019 Aug 5;317(2):C358-C365. Epub 2019 Jun 5.

Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina.

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http://dx.doi.org/10.1152/ajpcell.00052.2019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6732417PMC
August 2019

Inter-Active Site Communication Mediated by the Dimer Interface β-Sheet in the Half-the-Sites Enzyme, Thymidylate Synthase.

Biochemistry 2019 Jul 18;58(30):3302-3313. Epub 2019 Jul 18.

Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , The University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599-7355 , United States.

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http://dx.doi.org/10.1021/acs.biochem.9b00486DOI Listing
July 2019

β-Methylamino-L-alanine substitution of serine in SOD1 suggests a direct role in ALS etiology.

PLoS Comput Biol 2019 Jul 19;15(7):e1007225. Epub 2019 Jul 19.

Departments of Pharmacology, Biochemistry & Molecular Biology, Chemistry, and Biomedical Engineering, The Pennsylvania State University, Hershey, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1007225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6668853PMC
July 2019

MedusaDock 2.0: Efficient and Accurate Protein-Ligand Docking With Constraints.

J Chem Inf Model 2019 Jun 17;59(6):2509-2515. Epub 2019 Apr 17.

Department of Pharmacology , Penn State University College of Medicine , Hershey , Pennsylvania 17033 , United States.

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http://dx.doi.org/10.1021/acs.jcim.8b00905DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6597311PMC
June 2019

Engineering proteins for allosteric control by light or ligands.

Nat Protoc 2019 06 10;14(6):1863-1883. Epub 2019 May 10.

Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

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http://dx.doi.org/10.1038/s41596-019-0165-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6648709PMC
June 2019

Limits in accuracy and a strategy of RNA structure prediction using experimental information.

Nucleic Acids Res 2019 Jun;47(11):5563-5572

Department of Pharmacology, Penn State University College of Medicine, Hershey, PA 17033, USA.

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http://dx.doi.org/10.1093/nar/gkz427DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582333PMC
June 2019

Uncovered Dynamic Coupling Resolves the Ambiguous Mechanism of Phenylalanine Hydroxylase Oxygen Binding.

J Phys Chem B 2019 May 17;123(21):4534-4539. Epub 2019 May 17.

Department of Chemistry and Biochemistry , University of California, Los Angeles , Los Angeles , California 90095-1569 , United States.

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http://pubs.acs.org/doi/10.1021/acs.jpcb.9b02893
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http://dx.doi.org/10.1021/acs.jpcb.9b02893DOI Listing
May 2019

Molecular mechanisms of heterogeneous oligomerization of huntingtin proteins.

Sci Rep 2019 May 20;9(1):7615. Epub 2019 May 20.

Center for Complexity and Biosystems, Department of Environmental Science and Policy, University of Milano, via Celoria 26, 20133, Milano, Italy.

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http://dx.doi.org/10.1038/s41598-019-44151-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6527588PMC
May 2019

Cardiomyopathy Mutations in Metavinculin Disrupt Regulation of Vinculin-Induced F-Actin Assemblies.

J Mol Biol 2019 Apr 5;431(8):1604-1618. Epub 2019 Mar 5.

Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00222836193010
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http://dx.doi.org/10.1016/j.jmb.2019.02.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6693633PMC
April 2019

Viral DNA Binding to NLRC3, an Inhibitory Nucleic Acid Sensor, Unleashes STING, a Cyclic Dinucleotide Receptor that Activates Type I Interferon.

Immunity 2019 03;50(3):591-599.e6

Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10747613193007
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http://dx.doi.org/10.1016/j.immuni.2019.02.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469509PMC
March 2019

Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations.

PLoS Comput Biol 2019 03 27;15(3):e1006859. Epub 2019 Mar 27.

University of Victoria -Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada.

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http://dx.doi.org/10.1371/journal.pcbi.1006859DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6453469PMC
March 2019

Ca-mediated activation of the skeletal-muscle ryanodine receptor ion channel.

J Biol Chem 2018 12 19;293(50):19501-19509. Epub 2018 Oct 19.

From the Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599-7260,

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http://www.jbc.org/lookup/doi/10.1074/jbc.RA118.004453
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http://dx.doi.org/10.1074/jbc.RA118.004453DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302159PMC
December 2018

Computational design of chemogenetic and optogenetic split proteins.

Nat Commun 2018 10 2;9(1):4042. Epub 2018 Oct 2.

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.

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http://www.nature.com/articles/s41467-018-06531-4
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http://dx.doi.org/10.1038/s41467-018-06531-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168510PMC
October 2018

miRNA-711 Binds and Activates TRPA1 Extracellularly to Evoke Acute and Chronic Pruritus.

Neuron 2018 08 19;99(3):449-463.e6. Epub 2018 Jul 19.

Center for Translational Pain Medicine, Department of Anesthesiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2018.06.039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6091677PMC
August 2018

Large SOD1 aggregates, unlike trimeric SOD1, do not impact cell viability in a model of amyotrophic lateral sclerosis.

Proc Natl Acad Sci U S A 2018 05 16;115(18):4661-4665. Epub 2018 Apr 16.

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1800187115
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http://dx.doi.org/10.1073/pnas.1800187115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5939103PMC
May 2018

High-speed atomic force microscopy reveals structural dynamics of α-synuclein monomers and dimers.

J Chem Phys 2018 Mar;148(12):123322

Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 69198, USA.

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http://dx.doi.org/10.1063/1.5008874DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5764752PMC
March 2018

G4941K substitution in the pore-lining S6 helix of the skeletal muscle ryanodine receptor increases RyR1 sensitivity to cytosolic and luminal Ca.

J Biol Chem 2018 02 18;293(6):2015-2028. Epub 2017 Dec 18.

From the Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599

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http://dx.doi.org/10.1074/jbc.M117.803247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5808763PMC
February 2018

Computational Protein Design Through Grafting and Stabilization.

Methods Mol Biol 2017 ;1529:227-241

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.

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http://dx.doi.org/10.1007/978-1-4939-6637-0_11DOI Listing
January 2018

Structural complexity and functional diversity of plant NADPH oxidases.

Amino Acids 2018 01 25;50(1):79-94. Epub 2017 Oct 25.

Department of Biotechnology, Guru Nanak Dev University, Amritsar, India.

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http://dx.doi.org/10.1007/s00726-017-2491-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6492275PMC
January 2018

Structure modeling of RNA using sparse NMR constraints.

Nucleic Acids Res 2017 Dec;45(22):12638-12647

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.1093/nar/gkx1058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5728392PMC
December 2017

Molecular Mechanisms of the R61T Mutation in Apolipoprotein E4: A Dynamic Rescue.

Biophys J 2017 Nov 12;113(10):2192-2198. Epub 2017 Sep 12.

Biochemistry and Biophysics Department, University of North Carolina, Chapel Hill, North Carolina. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2017.08.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5700245PMC
November 2017

Redundant Functions for Nap1 and Chz1 in H2A.Z Deposition.

Sci Rep 2017 09 7;7(1):10791. Epub 2017 Sep 7.

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.

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http://dx.doi.org/10.1038/s41598-017-11003-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5589762PMC
September 2017

Ion-pulling simulations provide insights into the mechanisms of channel opening of the skeletal muscle ryanodine receptor.

J Biol Chem 2017 08 5;292(31):12947-12958. Epub 2017 Jun 5.

From the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7260

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http://dx.doi.org/10.1074/jbc.M116.760199DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5546034PMC
August 2017

Engineering Pak1 Allosteric Switches.

ACS Synth Biol 2017 07 6;6(7):1257-1262. Epub 2017 Apr 6.

Center for Disease Biology and Integrative Medicine, The University of Tokyo , Bunko-ku, Tokyo 113-0033, Japan.

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http://dx.doi.org/10.1021/acssynbio.6b00359DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5562282PMC
July 2017

Protein folding: Over half a century lasting quest: Comment on "There and back again: Two views on the protein folding puzzle" by Alexei V. Finkelstein et al.

Phys Life Rev 2017 07 14;21:72-74. Epub 2017 Jun 14.

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Electronic address:

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http://dx.doi.org/10.1016/j.plrev.2017.06.002DOI Listing
July 2017

Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo.

Biophys J 2017 Jul 15;113(2):290-301. Epub 2017 Jun 15.

Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2017.05.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529173PMC
July 2017

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations.

Sci Adv 2017 07 7;3(7):e1700479. Epub 2017 Jul 7.

University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham Street, Victoria, British Columbia V8Z7X8, Canada.

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http://dx.doi.org/10.1126/sciadv.1700479DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501500PMC
July 2017

Predicting the functional consequences of non-synonymous single nucleotide polymorphisms in IL8 gene.

Sci Rep 2017 07 26;7(1):6525. Epub 2017 Jul 26.

Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA.

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http://dx.doi.org/10.1038/s41598-017-06575-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529537PMC
July 2017

Physicochemical code for quinary protein interactions in .

Proc Natl Acad Sci U S A 2017 06 23;114(23):E4556-E4563. Epub 2017 May 23.

Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden;

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http://dx.doi.org/10.1073/pnas.1621227114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5468600PMC
June 2017

Transmembrane helical interactions in the CFTR channel pore.

PLoS Comput Biol 2017 Jun 22;13(6):e1005594. Epub 2017 Jun 22.

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005594DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501672PMC
June 2017

A Structural Model for Vinculin Insertion into PIP-Containing Membranes and the Effect of Insertion on Vinculin Activation and Localization.

Structure 2017 02 12;25(2):264-275. Epub 2017 Jan 12.

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Electronic address:

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http://dx.doi.org/10.1016/j.str.2016.12.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5299030PMC
February 2017

Direct identification of base-paired RNA nucleotides by correlated chemical probing.

RNA 2017 01 1;23(1):6-13. Epub 2016 Nov 1.

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.

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http://dx.doi.org/10.1261/rna.058586.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5159650PMC
January 2017

Computational Modeling of Small Molecule Ligand Binding Interactions and Affinities.

Methods Mol Biol 2016 ;1414:23-32

Department of Biochemistry and Biophysics, University of North Carolina, 120 Mason Farm Road, 27599, Chapel Hill, NC, USA.

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http://dx.doi.org/10.1007/978-1-4939-3569-7_2DOI Listing
December 2016

Engineering extrinsic disorder to control protein activity in living cells.

Science 2016 12;354(6318):1441-1444

Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.1126/science.aah3404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5362825PMC
December 2016

A Phosphomimetic Mutation Stabilizes SOD1 and Rescues Cell Viability in the Context of an ALS-Associated Mutation.

Structure 2016 11 22;24(11):1898-1906. Epub 2016 Sep 22.

Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Program in Molecular and Cellular Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA. Electronic address:

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http://dx.doi.org/10.1016/j.str.2016.08.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5093072PMC
November 2016

Harnessing Nature's Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins.

Sci Rep 2016 11 15;6:37175. Epub 2016 Nov 15.

Department of Biochemistry and Biophysics, University of North Carolina Chapel Hill, 120 Mason Farm Rd, Campus Box 7260, 3rd Floor, Genetic Medicine Building, Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.1038/srep37175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5109037PMC
November 2016

Restoration of R117H CFTR folding and function in human airway cells through combination treatment with VX-809 and VX-770.

Am J Physiol Lung Cell Mol Physiol 2016 09 8;311(3):L550-9. Epub 2016 Jul 8.

Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina, Chapel Hill, North Carolina; Department of Cell Biology and Physiology. University of North Carolina, Chapel Hill, North Carolina; and.

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http://dx.doi.org/10.1152/ajplung.00186.2016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5142211PMC
September 2016

Controlling Allosteric Networks in Proteins.

Chem Rev 2016 06 19;116(11):6463-87. Epub 2016 Feb 19.

Department of Biochemistry and Biophysics, University of North Carolina , Chapel Hill, North Carolina 27599, United States.

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http://dx.doi.org/10.1021/acs.chemrev.5b00544DOI Listing
June 2016

Docking and Scoring with Target-Specific Pose Classifier Succeeds in Native-Like Pose Identification But Not Binding Affinity Prediction in the CSAR 2014 Benchmark Exercise.

J Chem Inf Model 2016 06 20;56(6):1032-41. Epub 2016 Apr 20.

Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States.

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http://dx.doi.org/10.1021/acs.jcim.5b00751DOI Listing
June 2016

Pharmacological Chaperones: Design and Development of New Therapeutic Strategies for the Treatment of Conformational Diseases.

ACS Chem Biol 2016 06 28;11(6):1471-89. Epub 2016 Apr 28.

Department of Biochemistry and Biophysics, University of North Carolina , 120 Mason Farm Road, Chapel Hill, North Carolina 27599, United States.

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http://dx.doi.org/10.1021/acschembio.6b00195DOI Listing
June 2016

A hidden aggregation-prone structure in the heart of hypoxia inducible factor prolyl hydroxylase.

Proteins 2016 May 6;84(5):611-23. Epub 2016 Mar 6.

Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.

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http://dx.doi.org/10.1002/prot.25011DOI Listing
May 2016

Applications of Discrete Molecular Dynamics in biology and medicine.

Curr Opin Struct Biol 2016 Apr 28;37:9-13. Epub 2015 Nov 28.

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, United States. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2015.11.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4834256PMC
April 2016

Gain-of-Function Mutation W493R in the Epithelial Sodium Channel Allosterically Reconfigures Intersubunit Coupling.

J Biol Chem 2016 Feb 14;291(8):3682-92. Epub 2015 Dec 14.

From the Program in Molecular and Cellular Biophysics, Curriculum in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, and Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599

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http://dx.doi.org/10.1074/jbc.M115.678052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4759151PMC
February 2016

Dynamic Docking of Conformationally Constrained Macrocycles: Methods and Applications.

ACS Chem Biol 2016 Jan 4;11(1):10-24. Epub 2015 Dec 4.

Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States.

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http://dx.doi.org/10.1021/acschembio.5b00663DOI Listing
January 2016

Protein Destabilization as a Common Factor in Diverse Inherited Disorders.

J Mol Evol 2016 Jan 19;82(1):11-6. Epub 2015 Nov 19.

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.

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http://dx.doi.org/10.1007/s00239-015-9717-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4712097PMC
January 2016

Nonnative SOD1 trimer is toxic to motor neurons in a model of amyotrophic lateral sclerosis.

Proc Natl Acad Sci U S A 2016 Jan 30;113(3):614-9. Epub 2015 Dec 30.

Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; Program in Molecular and Cellular Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599;

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http://www.pnas.org/content/113/3/614.full.pdf
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http://www.pnas.org/lookup/doi/10.1073/pnas.1516725113
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http://dx.doi.org/10.1073/pnas.1516725113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4725519PMC
January 2016

A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms.

Struct Dyn 2016 Jan 24;3(1):012101. Epub 2016 Feb 24.

Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7260, USA.

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http://dx.doi.org/10.1063/1.4941599DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4769271PMC
January 2016

Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models.

Methods Enzymol 2015 3;553:65-89. Epub 2015 Feb 3.

Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA. Electronic address:

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http://dx.doi.org/10.1016/bs.mie.2014.10.052DOI Listing
December 2015

μ-Opioid receptor 6-transmembrane isoform: A potential therapeutic target for new effective opioids.

Prog Neuropsychopharmacol Biol Psychiatry 2015 Oct 6;62:61-7. Epub 2014 Dec 6.

The Alan Edwards Centre for Research on Pain, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec H3A 0G1, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.pnpbp.2014.11.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4646084PMC
October 2015

COMT gene locus: new functional variants.

Pain 2015 Oct;156(10):2072-83

aThe Alan Edwards Centre for Research on Pain, McGill University, Montreal, QC, Canada bCenter for Pain Research and Innovation, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA cNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA dDepartment of Prosthesis and Periodontology, Piracicaba Dental School, State University of Campinas, Piracicaba, SP, Brazil eDepartment of Medicine, Division of Gastroenterology, College of Medicine, University of Florida, Gainesville, FL, USA fDepartment of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC, USA gDepartment of Community Dentistry and Behavioral Science, University of Florida, College of Dentistry, and Pain, Research and Intervention Center of Excellence, Clinical and Translational Research Building (CTRB), Gainesville, FL, USA hDepartment of Neural and Pain Sciences, and Brotman Facial Pain Clinic, University of Maryland School of Dentistry, Baltimore, MD, USA iDepartment of Oral Diagnostic Sciences, University at Buffalo, Buffalo, NY, USA jBattelle Memorial Institute, Battelle Centers for Public Health Research and Evaluation (CPHRE), Durham, NC, USA kNational Institute of Environmental Health Sciences, Durham, NC, USA lDivision of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.

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October 2015

ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations.

PLoS Comput Biol 2015 Oct 27;11(10):e1004359. Epub 2015 Oct 27.

Biochemistry and Biophysics Department, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America.

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October 2015

iFoldRNA v2: folding RNA with constraints.

Bioinformatics 2015 Sep 24;31(17):2891-3. Epub 2015 Apr 24.

Department of Biochemistry & Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA.

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September 2015

Channel Gating Dependence on Pore Lining Helix Glycine Residues in Skeletal Muscle Ryanodine Receptor.

J Biol Chem 2015 Jul 21;290(28):17535-45. Epub 2015 May 21.

From the Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599

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July 2015

Non-canonical Bromodomain within DNA-PKcs Promotes DNA Damage Response and Radioresistance through Recognizing an IR-Induced Acetyl-Lysine on H2AX.

Chem Biol 2015 Jul 25;22(7):849-61. Epub 2015 Jun 25.

Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 20032, China; Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Program in Molecular & Cellular Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Electronic address:

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July 2015

Light-cleavable rapamycin dimer as an optical trigger for protein dimerization.

Chem Commun (Camb) 2015 Apr;51(26):5702-5

Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.

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April 2015

Rational Coupled Dynamics Network Manipulation Rescues Disease-Relevant Mutant Cystic Fibrosis Transmembrane Conductance Regulator.

Chem Sci 2015 Feb;6(2):1237-1246

Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA ; Program in Molecular and Cellular Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA ; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA ; Cystic Fibrosis Treatment and Research Center, University of North Carolina, Chapel Hill, NC 27599, USA.

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February 2015

Discrete molecular dynamics can predict helical prestructured motifs in disordered proteins.

PLoS One 2014 24;9(4):e95795. Epub 2014 Apr 24.

MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Budapest, Hungary; Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary; Institute of Molecular Pharmacology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.

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January 2015

Cu,Zn-superoxide dismutase without Zn is folded but catalytically inactive.

J Mol Biol 2014 Dec 30;426(24):4112-4124. Epub 2014 Jul 30.

Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; California NanoSystems Institute, 570 Westwood Plaza, Building 114, Los Angeles, CA 90095, USA. Electronic address:

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December 2014

RNA tertiary structure analysis by 2'-hydroxyl molecular interference.

Biochemistry 2014 Nov 23;53(43):6825-33. Epub 2014 Oct 23.

Departments of Chemistry and ‡Biochemistry and Biophysics, University of North Carolina , Chapel Hill, North Carolina 27599-3290, United States.

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November 2014

Traffic within the cytochrome b6f lipoprotein complex: gating of the quinone portal.

Biophys J 2014 Oct;107(7):1620-8

Department of Biological Sciences, Hockmeyer Hall of Structural Biology, Purdue University, West Lafayette, Indiana. Electronic address:

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October 2014

The N-terminal domain allosterically regulates cleavage and activation of the epithelial sodium channel.

J Biol Chem 2014 Aug 28;289(33):23029-42. Epub 2014 Jun 28.

From the Departments of Biochemistry and Biophysics, Molecular and Cellular Biophysics, and the Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center, University of North Carolina, Chapel Hill, North Carolina 27599,

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August 2014

Potentiator ivacaftor abrogates pharmacological correction of ΔF508 CFTR in cystic fibrosis.

Sci Transl Med 2014 Jul;6(246):246ra96

Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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July 2014

Pore dynamics and conductance of RyR1 transmembrane domain.

Biophys J 2014 Jun;106(11):2375-84

Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina. Electronic address:

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June 2014

Intrinsic disorder mediates cooperative signal transduction in STIM1.

J Mol Biol 2014 May 17;426(10):2082-97. Epub 2014 Mar 17.

Laboratory of Systems Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan. Electronic address:

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May 2014

Identification of an actin binding surface on vinculin that mediates mechanical cell and focal adhesion properties.

Structure 2014 May 27;22(5):697-706. Epub 2014 Mar 27.

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Electronic address:

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May 2014

The maturation of HIV-1 protease precursor studied by discrete molecular dynamics.

Proteins 2014 Apr 22;82(4):633-9. Epub 2013 Nov 22.

Department of Physics and INFN, Università degli Studi di Milano, Milano, 20133, Italy.

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April 2014

Non-native soluble oligomers of Cu/Zn superoxide dismutase (SOD1) contain a conformational epitope linked to cytotoxicity in amyotrophic lateral sclerosis (ALS).

Biochemistry 2014 Apr 2;53(14):2423-32. Epub 2014 Apr 2.

Department of Biochemistry and Biophysics, 120 Mason Farm Road, CB# 7260, University of North Carolina , Chapel Hill, North Carolina, United States 27599.

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April 2014

Identification of novel integrin binding partners for calcium and integrin binding protein 1 (CIB1): structural and thermodynamic basis of CIB1 promiscuity.

Biochemistry 2013 Oct 25;52(40):7082-90. Epub 2013 Sep 25.

Department of Biochemistry and Biophysics, ‡Lineberger Comprehensive Cancer Center, and §McAllister Heart Institute, School of Medicine, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States.

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October 2013

Incorporating backbone flexibility in MedusaDock improves ligand-binding pose prediction in the CSAR2011 docking benchmark.

J Chem Inf Model 2013 Aug 24;53(8):1871-9. Epub 2012 Dec 24.

Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA.

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August 2013

Predicting binding affinity of CSAR ligands using both structure-based and ligand-based approaches.

J Chem Inf Model 2013 Aug 17;53(8):1915-22. Epub 2013 Jul 17.

Laboratory for Molecular Modeling, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA.

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August 2013

Protein HP1028 from the human pathogen Helicobacter pylori belongs to the lipocalin family.

Acta Crystallogr D Biol Crystallogr 2013 Aug 13;69(Pt 8):1387-94. Epub 2013 Jul 13.

Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy.

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August 2013

Highly covarying residues have a functional role in antibody constant domains.

Proteins 2013 May 27;81(5):884-95. Epub 2013 Feb 27.

Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina 27599-7260, USA.

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May 2013

Rational design of a ligand-controlled protein conformational switch.

Proc Natl Acad Sci U S A 2013 Apr 8;110(17):6800-4. Epub 2013 Apr 8.

Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA.

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April 2013

Structural determinants of skeletal muscle ryanodine receptor gating.

J Biol Chem 2013 Mar 14;288(9):6154-65. Epub 2013 Jan 14.

Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7260, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3585052PMC
March 2013

Dynamics intrinsic to cystic fibrosis transmembrane conductance regulator function and stability.

Cold Spring Harb Perspect Med 2013 Mar 1;3(3):a009522. Epub 2013 Mar 1.

Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3579207PMC
March 2013

Metric to distinguish closely related domain families using sequence information.

J Mol Biol 2013 Feb 3;425(3):475-8. Epub 2012 Dec 3.

Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA.

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February 2013

Statistical analysis of SHAPE-directed RNA secondary structure modeling.

Biochemistry 2013 Jan 14;52(4):596-9. Epub 2013 Jan 14.

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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January 2013

Principles for understanding the accuracy of SHAPE-directed RNA structure modeling.

Biochemistry 2013 Jan 14;52(4):588-95. Epub 2013 Jan 14.

Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA.

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January 2013