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Items: 1 to 50 of 83

1.

Detecting Functional Dynamics in Proteins with Comparative Perturbed-Ensembles Analysis.

Yao XQ, Hamelberg D.

Acc Chem Res. 2019 Dec 17;52(12):3455-3464. doi: 10.1021/acs.accounts.9b00485. Epub 2019 Dec 3.

PMID:
31793290
2.

Synergistic mutations in soluble guanylyl cyclase (sGC) reveal a key role for interfacial regions in the sGC activation mechanism.

Childers KC, Yao XQ, Giannakoulias S, Amason J, Hamelberg D, Garcin ED.

J Biol Chem. 2019 Nov 29;294(48):18451-18464. doi: 10.1074/jbc.RA119.011010. Epub 2019 Oct 23.

3.

Second Generation G-Quadruplex Stabilizing Trimethine Cyanines.

Owens EA, Huynh HT, Stroeva EM, Barman A, Ziabrev K, Paul A, Nguyen SV, Laramie M, Hamelberg D, Germann MW, Wilson WD, Henary M.

Bioconjug Chem. 2019 Oct 16;30(10):2647-2663. doi: 10.1021/acs.bioconjchem.9b00571. Epub 2019 Sep 26.

PMID:
31518105
4.

Establishing a Framework of Using Residue-Residue Interactions in Protein Difference Network Analysis.

Yao XQ, Momin M, Hamelberg D.

J Chem Inf Model. 2019 Jul 22;59(7):3222-3228. doi: 10.1021/acs.jcim.9b00320. Epub 2019 Jul 3.

PMID:
31268315
5.

Combinatorial Coarse-Graining of Molecular Dynamics Simulations for Detecting Relationships between Local Configurations and Overall Conformations.

Ho KC, Hamelberg D.

J Chem Theory Comput. 2018 Nov 13;14(11):6026-6034. doi: 10.1021/acs.jctc.8b00333. Epub 2018 Oct 29.

PMID:
30351007
6.

Elucidating Allosteric Communications in Proteins with Difference Contact Network Analysis.

Yao XQ, Momin M, Hamelberg D.

J Chem Inf Model. 2018 Jul 23;58(7):1325-1330. doi: 10.1021/acs.jcim.8b00250. Epub 2018 Jul 11.

PMID:
29956925
7.

Decoding Allosteric Communication Pathways in Cyclophilin A with a Comparative Analysis of Perturbed Conformational Ensembles.

Rodriguez-Bussey I, Yao XQ, Shouaib AD, Lopez J, Hamelberg D.

J Phys Chem B. 2018 Jun 28;122(25):6528-6535. doi: 10.1021/acs.jpcb.8b03824. Epub 2018 Jun 13.

PMID:
29852734
8.

Substrate Sequence Determines Catalytic Activities, Domain-Binding Preferences, and Allosteric Mechanisms in Pin1.

Momin M, Yao XQ, Thor W, Hamelberg D.

J Phys Chem B. 2018 Jun 28;122(25):6521-6527. doi: 10.1021/acs.jpcb.8b03819. Epub 2018 Jun 13.

PMID:
29851476
9.

Redox-Specific Allosteric Modulation of the Conformational Dynamics of κB DNA by Pirin in the NF-κB Supramolecular Complex.

Adeniran C, Hamelberg D.

Biochemistry. 2017 Sep 19;56(37):5002-5010. doi: 10.1021/acs.biochem.7b00528. Epub 2017 Sep 6.

PMID:
28825294
10.

Enzyme-Mediated Conversion of Flavin Adenine Dinucleotide (FAD) to 8-Formyl FAD in Formate Oxidase Results in a Modified Cofactor with Enhanced Catalytic Properties.

Robbins JM, Souffrant MG, Hamelberg D, Gadda G, Bommarius AS.

Biochemistry. 2017 Jul 25;56(29):3800-3807. doi: 10.1021/acs.biochem.7b00335. Epub 2017 Jul 11.

PMID:
28640638
11.

Allosteric Fine-Tuning of the Binding Pocket Dynamics in the ITK SH2 Domain by a Distal Molecular Switch: An Atomistic Perspective.

Momin M, Xin Y, Hamelberg D.

J Phys Chem B. 2017 Jun 29;121(25):6131-6138. doi: 10.1021/acs.jpcb.7b03470. Epub 2017 Jun 15.

PMID:
28570811
12.

Importance of Loop L1 Dynamics for Substrate Capture and Catalysis in Pseudomonas aeruginosa d-Arginine Dehydrogenase.

Ouedraogo D, Souffrant M, Vasquez S, Hamelberg D, Gadda G.

Biochemistry. 2017 May 16;56(19):2477-2487. doi: 10.1021/acs.biochem.7b00098. Epub 2017 May 2.

PMID:
28445031
13.

Fe(II)/Fe(III) Redox Process Can Significantly Modulate the Conformational Dynamics and Electrostatics of Pirin in NF-κB Regulation.

Barman A, Hamelberg D.

ACS Omega. 2016 Nov 7;1(5):837-842. doi: 10.1021/acsomega.6b00231. eCollection 2016 Nov 30.

14.

Coupled Dynamics and Entropic Contribution to the Allosteric Mechanism of Pin1.

Barman A, Hamelberg D.

J Phys Chem B. 2016 Aug 25;120(33):8405-15. doi: 10.1021/acs.jpcb.6b02123. Epub 2016 Apr 28.

PMID:
27077947
15.

Dynamical network of residue-residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation.

Doshi U, Holliday MJ, Eisenmesser EZ, Hamelberg D.

Proc Natl Acad Sci U S A. 2016 Apr 26;113(17):4735-40. doi: 10.1073/pnas.1523573113. Epub 2016 Apr 11.

16.

Role of F357 as an Oxygen Gate in the Oxidative Half-Reaction of Choline Oxidase.

Salvi F, Rodriguez I, Hamelberg D, Gadda G.

Biochemistry. 2016 Mar 15;55(10):1473-84. doi: 10.1021/acs.biochem.5b01356. Epub 2016 Mar 3.

PMID:
26907558
17.

Conserved Hydration Sites in Pin1 Reveal a Distinctive Water Recognition Motif in Proteins.

Barman A, Smitherman C, Souffrant M, Gadda G, Hamelberg D.

J Chem Inf Model. 2016 Jan 25;56(1):139-47. doi: 10.1021/acs.jcim.5b00560. Epub 2015 Dec 23.

PMID:
26651388
18.

Oscillatory Diffusion and Second-Order Cyclostationarity in Alanine Tripeptide from Molecular Dynamics Simulation.

Ho KC, Hamelberg D.

J Chem Theory Comput. 2016 Jan 12;12(1):372-82. doi: 10.1021/acs.jctc.5b00876. Epub 2015 Dec 16.

PMID:
26636883
19.

Pushing the Limits of a Molecular Mechanics Force Field To Probe Weak CH···π Interactions in Proteins.

Barman A, Batiste B, Hamelberg D.

J Chem Theory Comput. 2015 Apr 14;11(4):1854-63. doi: 10.1021/ct501036r.

PMID:
26574391
20.

Enhanced molecular dynamics sampling of drug target conformations.

Rodriguez-Bussey IG, Doshi U, Hamelberg D.

Biopolymers. 2016 Jan;105(1):35-42. doi: 10.1002/bip.22740. Review.

PMID:
26352326
21.

An Iron Reservoir to the Catalytic Metal: THE RUBREDOXIN IRON IN AN EXTRADIOL DIOXYGENASE.

Liu F, Geng J, Gumpper RH, Barman A, Davis I, Ozarowski A, Hamelberg D, Liu A.

J Biol Chem. 2015 Jun 19;290(25):15621-34. doi: 10.1074/jbc.M115.650259. Epub 2015 Apr 27.

22.

Design, synthesis and biological evaluation of di-substituted noscapine analogs as potent and microtubule-targeted anticancer agents.

Mishra RC, Gundala SR, Karna P, Lopus M, Gupta KK, Nagaraju M, Hamelberg D, Tandon V, Panda D, Reid MD, Aneja R.

Bioorg Med Chem Lett. 2015;25(10):2133-40. doi: 10.1016/j.bmcl.2015.03.076. Epub 2015 Mar 31.

23.

Dynamical role of phosphorylation on serine/threonine-proline Pin1 substrates from constant force molecular dynamics simulations.

Velazquez HA, Hamelberg D.

J Chem Phys. 2015 Feb 21;142(7):075102. doi: 10.1063/1.4907884.

PMID:
25702031
24.

Computational perspective and evaluation of plausible catalytic mechanisms of peptidyl-prolyl cis-trans isomerases.

Ladani ST, Souffrant MG, Barman A, Hamelberg D.

Biochim Biophys Acta. 2015 Oct;1850(10):1994-2004. doi: 10.1016/j.bbagen.2014.12.023. Epub 2015 Jan 10. Review.

PMID:
25585011
25.

Loss of intramolecular electrostatic interactions and limited conformational ensemble may promote self-association of cis-tau peptide.

Barman A, Hamelberg D.

Proteins. 2015 Mar;83(3):436-44. doi: 10.1002/prot.24740. Epub 2015 Jan 21.

PMID:
25524218
26.

Role of Ca2+ and L-Phe in regulating functional cooperativity of disease-associated "toggle" calcium-sensing receptor mutations.

Zhang C, Mulpuri N, Hannan FM, Nesbit MA, Thakker RV, Hamelberg D, Brown EM, Yang JJ.

PLoS One. 2014 Nov 24;9(11):e113622. doi: 10.1371/journal.pone.0113622. eCollection 2014.

27.

Cyclodextrin complexes of reduced bromonoscapine in guar gum microspheres enhance colonic drug delivery.

Madan J, Gundala SR, Baruah B, Nagaraju M, Yates C, Turner T, Rangari V, Hamelberg D, Reid MD, Aneja R.

Mol Pharm. 2014 Dec 1;11(12):4339-49. doi: 10.1021/mp500408n. Epub 2014 Nov 18.

28.

Towards fast, rigorous and efficient conformational sampling of biomolecules: Advances in accelerated molecular dynamics.

Doshi U, Hamelberg D.

Biochim Biophys Acta. 2015 May;1850(5):878-888. doi: 10.1016/j.bbagen.2014.08.003. Epub 2014 Aug 19. Review.

PMID:
25153688
29.

Novel third-generation water-soluble noscapine analogs as superior microtubule-interfering agents with enhanced antiproliferative activity.

Henary M, Narayana L, Ahad S, Gundala SR, Mukkavilli R, Sharma V, Owens EA, Yadav Y, Nagaraju M, Hamelberg D, Tandon V, Panda D, Aneja R.

Biochem Pharmacol. 2014 Nov 15;92(2):192-205. doi: 10.1016/j.bcp.2014.07.020. Epub 2014 Aug 11.

30.

Cysteine-mediated dynamic hydrogen-bonding network in the active site of Pin1.

Barman A, Hamelberg D.

Biochemistry. 2014 Jun 17;53(23):3839-50. doi: 10.1021/bi5000977. Epub 2014 Jun 3.

PMID:
24840168
31.

Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent.

Doshi U, Hamelberg D.

J Phys Chem Lett. 2014 Apr 3;5(7):1217-24. doi: 10.1021/jz500179a. Epub 2014 Mar 24.

PMID:
26274474
32.

The dilemma of conformational dynamics in enzyme catalysis: perspectives from theory and experiment.

Doshi U, Hamelberg D.

Adv Exp Med Biol. 2014;805:221-43. doi: 10.1007/978-3-319-02970-2_10. Review.

PMID:
24446364
33.

Identification of an L-phenylalanine binding site enhancing the cooperative responses of the calcium-sensing receptor to calcium.

Zhang C, Huang Y, Jiang Y, Mulpuri N, Wei L, Hamelberg D, Brown EM, Yang JJ.

J Biol Chem. 2014 Feb 21;289(8):5296-309. doi: 10.1074/jbc.M113.537357. Epub 2014 Jan 6.

34.

Extracellular calcium modulates actions of orthosteric and allosteric ligands on metabotropic glutamate receptor 1α.

Jiang JY, Nagaraju M, Meyer RC, Zhang L, Hamelberg D, Hall RA, Brown EM, Conn PJ, Yang JJ.

J Biol Chem. 2014 Jan 17;289(3):1649-61. doi: 10.1074/jbc.M113.507665. Epub 2013 Nov 26.

35.

Conformation-directed catalysis and coupled enzyme-substrate dynamics in Pin1 phosphorylation-dependent cis-trans isomerase.

Velazquez HA, Hamelberg D.

J Phys Chem B. 2013 Oct 3;117(39):11509-17. doi: 10.1021/jp405271s. Epub 2013 Sep 17.

PMID:
23980573
36.

Conformational plasticity of an enzyme during catalysis: intricate coupling between cyclophilin A dynamics and substrate turnover.

McGowan LC, Hamelberg D.

Biophys J. 2013 Jan 8;104(1):216-26. doi: 10.1016/j.bpj.2012.11.3815. Epub 2013 Jan 8.

37.

Cyclophilin A inhibition: targeting transition-state-bound enzyme conformations for structure-based drug design.

Nagaraju M, McGowan LC, Hamelberg D.

J Chem Inf Model. 2013 Feb 25;53(2):403-10. doi: 10.1021/ci300432w. Epub 2013 Jan 28.

PMID:
23312027
38.

Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions.

Doshi U, Hamelberg D.

J Chem Theory Comput. 2012 Nov 13;8(11):4004-12. doi: 10.1021/ct3004194. Epub 2012 Sep 11.

PMID:
26605567
39.

Entropic and surprisingly small intramolecular polarization effects in the mechanism of cyclophilin A.

Ladani ST, Hamelberg D.

J Phys Chem B. 2012 Sep 6;116(35):10771-8. doi: 10.1021/jp305917c. Epub 2012 Aug 27.

PMID:
22891696
40.

Molecular cycloencapsulation augments solubility and improves therapeutic index of brominated noscapine in prostate cancer cells.

Madan J, Baruah B, Nagaraju M, Abdalla MO, Yates C, Turner T, Rangari V, Hamelberg D, Aneja R.

Mol Pharm. 2012 May 7;9(5):1470-80. doi: 10.1021/mp300063v. Epub 2012 Apr 27.

41.

High-pressure effect on the dynamics of solvated peptides.

Nellas RB, Glover MM, Hamelberg D, Shen T.

J Chem Phys. 2012 Apr 14;136(14):145103. doi: 10.1063/1.3700183.

PMID:
22502549
42.

Resolving the complex role of enzyme conformational dynamics in catalytic function.

Doshi U, McGowan LC, Ladani ST, Hamelberg D.

Proc Natl Acad Sci U S A. 2012 Apr 10;109(15):5699-704. doi: 10.1073/pnas.1117060109. Epub 2012 Mar 26.

43.

Atomic-level insights into metabolite recognition and specificity of the SAM-II riboswitch.

Doshi U, Kelley JM, Hamelberg D.

RNA. 2012 Feb;18(2):300-7. doi: 10.1261/rna.028779.111. Epub 2011 Dec 22.

44.

Clicking 1,2,4,5-tetrazine and cyclooctynes with tunable reaction rates.

Chen W, Wang D, Dai C, Hamelberg D, Wang B.

Chem Commun (Camb). 2012 Feb 7;48(12):1736-8. doi: 10.1039/c2cc16716f. Epub 2011 Dec 12.

PMID:
22159330
45.

Protein conformational dynamics in the mechanism of HIV-1 protease catalysis.

Torbeev VY, Raghuraman H, Hamelberg D, Tonelli M, Westler WM, Perozo E, Kent SB.

Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):20982-7. doi: 10.1073/pnas.1111202108. Epub 2011 Dec 8.

46.

Insights on the mechanism of amine oxidation catalyzed by D-arginine dehydrogenase through pH and kinetic isotope effects.

Yuan H, Xin Y, Hamelberg D, Gadda G.

J Am Chem Soc. 2011 Nov 23;133(46):18957-65. doi: 10.1021/ja2082729. Epub 2011 Oct 31.

PMID:
21999550
47.

Conformational selection in the recognition of phosphorylated substrates by the catalytic domain of human Pin1.

Velazquez HA, Hamelberg D.

Biochemistry. 2011 Nov 8;50(44):9605-15. doi: 10.1021/bi2009954. Epub 2011 Oct 11.

PMID:
21967280
48.

Extracting Realistic Kinetics of Rare Activated Processes from Accelerated Molecular Dynamics Using Kramers' Theory.

Doshi U, Hamelberg D.

J Chem Theory Comput. 2011 Mar 8;7(3):575-81. doi: 10.1021/ct1005399. Epub 2011 Jan 27.

PMID:
26596291
49.

Deciphering the role of glucosamine-6-phosphate in the riboswitch action of glmS ribozyme.

Xin Y, Hamelberg D.

RNA. 2010 Dec;16(12):2455-63. doi: 10.1261/rna.2334110. Epub 2010 Oct 22.

50.

Water's Contribution to the Energetic Roughness from Peptide Dynamics.

Johnson Q, Doshi U, Shen T, Hamelberg D.

J Chem Theory Comput. 2010 Sep 14;6(9):2591-7. doi: 10.1021/ct100183s.

PMID:
26616063

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