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Tandem domain swapping: determinants of multidomain protein misfolding.

Lafita A, Tian P, Best RB, Bateman A.

Curr Opin Struct Biol. 2019 Jun 28;58:97-104. doi: 10.1016/ [Epub ahead of print] Review.


Disordered RNA chaperones can enhance nucleic acid folding via local charge screening.

Holmstrom ED, Liu Z, Nettels D, Best RB, Schuler B.

Nat Commun. 2019 Jun 5;10(1):2453. doi: 10.1038/s41467-019-10356-0.


Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties.

Zerze GH, Zheng W, Best RB, Mittal J.

J Phys Chem Lett. 2019 May 2;10(9):2227-2234. doi: 10.1021/acs.jpclett.9b00850. Epub 2019 Apr 22.


Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions.

Kührová P, Mlýnský V, Zgarbová M, Krepl M, Bussi G, Best RB, Otyepka M, Šponer J, Banáš P.

J Chem Theory Comput. 2019 May 14;15(5):3288-3305. doi: 10.1021/acs.jctc.8b00955. Epub 2019 Apr 2.


TADOSS: computational estimation of tandem domain swap stability.

Lafita A, Tian P, Best RB, Bateman A.

Bioinformatics. 2018 Nov 30. doi: 10.1093/bioinformatics/bty974. [Epub ahead of print]


The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding.

Kudva R, Tian P, Pardo-Avila F, Carroni M, Best RB, Bernstein HD, von Heijne G.

Elife. 2018 Nov 26;7. pii: e36326. doi: 10.7554/eLife.36326.


Accurate Transfer Efficiencies, Distance Distributions, and Ensembles of Unfolded and Intrinsically Disordered Proteins From Single-Molecule FRET.

Holmstrom ED, Holla A, Zheng W, Nettels D, Best RB, Schuler B.

Methods Enzymol. 2018;611:287-325. doi: 10.1016/bs.mie.2018.09.030. Epub 2018 Nov 16.


Folding pathway of an Ig domain is conserved on and off the ribosome.

Tian P, Steward A, Kudva R, Su T, Shilling PJ, Nickson AA, Hollins JJ, Beckmann R, von Heijne G, Clarke J, Best RB.

Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):E11284-E11293. doi: 10.1073/pnas.1810523115. Epub 2018 Nov 9.


A small single-domain protein folds through the same pathway on and off the ribosome.

Guinn EJ, Tian P, Shin M, Best RB, Marqusee S.

Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):12206-12211. doi: 10.1073/pnas.1810517115. Epub 2018 Nov 8.


Molecular Determinants of Aβ42 Adsorption to Amyloid Fibril Surfaces.

Bellaiche MMJ, Best RB.

J Phys Chem Lett. 2018 Nov 15;9(22):6437-6443. doi: 10.1021/acs.jpclett.8b02375. Epub 2018 Oct 29.


Origin of Internal Friction in Disordered Proteins Depends on Solvent Quality.

Zheng W, Hofmann H, Schuler B, Best RB.

J Phys Chem B. 2018 Dec 13;122(49):11478-11487. doi: 10.1021/acs.jpcb.8b07425. Epub 2018 Oct 2.


Relation between single-molecule properties and phase behavior of intrinsically disordered proteins.

Dignon GL, Zheng W, Best RB, Kim YC, Mittal J.

Proc Natl Acad Sci U S A. 2018 Oct 2;115(40):9929-9934. doi: 10.1073/pnas.1804177115. Epub 2018 Sep 14.


Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water".

Best RB, Zheng W, Borgia A, Buholzer K, Borgia MB, Hofmann H, Soranno A, Nettels D, Gast K, Grishaev A, Schuler B.

Science. 2018 Aug 31;361(6405). pii: eaar7101. doi: 10.1126/science.aar7101.


Instrumental Effects in the Dynamics of an Ultrafast Folding Protein under Mechanical Force.

De Sancho D, Schönfelder J, Best RB, Perez-Jimenez R, Muñoz V.

J Phys Chem B. 2018 Dec 13;122(49):11147-11154. doi: 10.1021/acs.jpcb.8b05975. Epub 2018 Aug 21.


Correction to Identification of Mutational Hot Spots for Substrate Diffusion: Application to Myoglobin.

De Sancho D, Kubas A, Wang PH, Blumberger J, Best RB.

J Chem Theory Comput. 2018 May 8;14(5):2822. doi: 10.1021/acs.jctc.8b00325. Epub 2018 Apr 30. No abstract available.


Editorial overview: Theory and simulation: Interpreting experimental data at the molecular level.

Best RB, Lindorff-Larsen K.

Curr Opin Struct Biol. 2018 Apr;49:iv-v. doi: 10.1016/ No abstract available.


Inferring properties of disordered chains from FRET transfer efficiencies.

Zheng W, Zerze GH, Borgia A, Mittal J, Schuler B, Best RB.

J Chem Phys. 2018 Mar 28;148(12):123329. doi: 10.1063/1.5006954.


An Extended Guinier Analysis for Intrinsically Disordered Proteins.

Zheng W, Best RB.

J Mol Biol. 2018 Aug 3;430(16):2540-2553. doi: 10.1016/j.jmb.2018.03.007. Epub 2018 Mar 21.


Co-Evolutionary Fitness Landscapes for Sequence Design.

Tian P, Louis JM, Baber JL, Aniana A, Best RB.

Angew Chem Int Ed Engl. 2018 May 14;57(20):5674-5678. doi: 10.1002/anie.201713220. Epub 2018 Mar 25.


Highly Disordered Amyloid-β Monomer Probed by Single-Molecule FRET and MD Simulation.

Meng F, Bellaiche MMJ, Kim JY, Zerze GH, Best RB, Chung HS.

Biophys J. 2018 Feb 27;114(4):870-884. doi: 10.1016/j.bpj.2017.12.025.


Race to the native state.

Best RB.

Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):2267-2269. doi: 10.1073/pnas.1722622115. Epub 2018 Feb 22. No abstract available.


Extreme disorder in an ultrahigh-affinity protein complex.

Borgia A, Borgia MB, Bugge K, Kissling VM, Heidarsson PO, Fernandes CB, Sottini A, Soranno A, Buholzer KJ, Nettels D, Kragelund BB, Best RB, Schuler B.

Nature. 2018 Mar 1;555(7694):61-66. doi: 10.1038/nature25762. Epub 2018 Feb 21.


Balancing Force Field Protein-Lipid Interactions To Capture Transmembrane Helix-Helix Association.

Domański J, Sansom MSP, Stansfeld PJ, Best RB.

J Chem Theory Comput. 2018 Mar 13;14(3):1706-1715. doi: 10.1021/acs.jctc.7b00983. Epub 2018 Feb 9.


Sequence determinants of protein phase behavior from a coarse-grained model.

Dignon GL, Zheng W, Kim YC, Best RB, Mittal J.

PLoS Comput Biol. 2018 Jan 24;14(1):e1005941. doi: 10.1371/journal.pcbi.1005941. eCollection 2018 Jan.


How Many Protein Sequences Fold to a Given Structure? A Coevolutionary Analysis.

Tian P, Best RB.

Biophys J. 2017 Oct 17;113(8):1719-1730. doi: 10.1016/j.bpj.2017.08.039.


Phosphorylation of the FUS low-complexity domain disrupts phase separation, aggregation, and toxicity.

Monahan Z, Ryan VH, Janke AM, Burke KA, Rhoads SN, Zerze GH, O'Meally R, Dignon GL, Conicella AE, Zheng W, Best RB, Cole RN, Mittal J, Shewmaker F, Fawzi NL.

EMBO J. 2017 Oct 16;36(20):2951-2967. doi: 10.15252/embj.201696394. Epub 2017 Aug 8.


Computational and theoretical advances in studies of intrinsically disordered proteins.

Best RB.

Curr Opin Struct Biol. 2017 Feb;42:147-154. doi: 10.1016/ Epub 2017 Mar 1. Review.


Mechanism of O2 diffusion and reduction in FeFe hydrogenases.

Kubas A, Orain C, De Sancho D, Saujet L, Sensi M, Gauquelin C, Meynial-Salles I, Soucaille P, Bottin H, Baffert C, Fourmond V, Best RB, Blumberger J, Léger C.

Nat Chem. 2017 Jan;9(1):88-95. doi: 10.1038/nchem.2592. Epub 2016 Aug 22.


Correction to Variational Optimization of an All-Atom Implicit Solvent Force Field To Match Explicit Solvent Simulation Data.

Bottaro S, Lindorff-Larsen K, Best RB.

J Chem Theory Comput. 2017 Jan 10;13(1):392. doi: 10.1021/acs.jctc.6b01188. Epub 2016 Dec 19. No abstract available.


Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association.

Domański J, Hedger G, Best RB, Stansfeld PJ, Sansom MSP.

J Phys Chem B. 2017 Apr 20;121(15):3364-3375. doi: 10.1021/acs.jpcb.6b08445. Epub 2016 Nov 17.


Reconciling Intermediates in Mechanical Unfolding Experiments with Two-State Protein Folding in Bulk.

de Sancho D, Best RB.

J Phys Chem Lett. 2016 Oct 6;7(19):3798-3803. Epub 2016 Sep 14.


Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment.

Zheng W, Borgia A, Buholzer K, Grishaev A, Schuler B, Best RB.

J Am Chem Soc. 2016 Sep 14;138(36):11702-13. doi: 10.1021/jacs.6b05443. Epub 2016 Sep 1.


Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods.

Borgia A, Zheng W, Buholzer K, Borgia MB, Schüler A, Hofmann H, Soranno A, Nettels D, Gast K, Grishaev A, Best RB, Schuler B.

J Am Chem Soc. 2016 Sep 14;138(36):11714-26. doi: 10.1021/jacs.6b05917. Epub 2016 Sep 1.


Computation of Rate Constants for Diffusion of Small Ligands to and from Buried Protein Active Sites.

Wang PH, De Sancho D, Best RB, Blumberger J.

Methods Enzymol. 2016;578:299-326. doi: 10.1016/bs.mie.2016.05.039. Epub 2016 Jun 27. Review.


Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies.

Kührová P, Best RB, Bottaro S, Bussi G, Šponer J, Otyepka M, Banáš P.

J Chem Theory Comput. 2016 Sep 13;12(9):4534-48. doi: 10.1021/acs.jctc.6b00300. Epub 2016 Aug 4.


Structural Determinants of Misfolding in Multidomain Proteins.

Tian P, Best RB.

PLoS Comput Biol. 2016 May 10;12(5):e1004933. doi: 10.1371/journal.pcbi.1004933. eCollection 2016 May.


Microscopic interpretation of folding ϕ-values using the transition path ensemble.

Best RB, Hummer G.

Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):3263-8. doi: 10.1073/pnas.1520864113. Epub 2016 Mar 8.


Modulation of Folding Internal Friction by Local and Global Barrier Heights.

Zheng W, de Sancho D, Best RB.

J Phys Chem Lett. 2016 Mar 17;7(6):1028-34. doi: 10.1021/acs.jpclett.6b00329. Epub 2016 Mar 7.


Diffusive Dynamics of Contact Formation in Disordered Polypeptides.

Zerze GH, Mittal J, Best RB.

Phys Rev Lett. 2016 Feb 12;116(6):068102. doi: 10.1103/PhysRevLett.116.068102. Epub 2016 Feb 11.


Markov state models of protein misfolding.

Sirur A, De Sancho D, Best RB.

J Chem Phys. 2016 Feb 21;144(7):075101. doi: 10.1063/1.4941579.


Reduction of All-Atom Protein Folding Dynamics to One-Dimensional Diffusion.

Zheng W, Best RB.

J Phys Chem B. 2015 Dec 10;119(49):15247-55. doi: 10.1021/acs.jpcb.5b09741. Epub 2015 Nov 25.


Correction to Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association.

Best RB, Zheng W, Mittal J.

J Chem Theory Comput. 2015 Apr 14;11(4):1978. doi: 10.1021/acs.jctc.5b00219. No abstract available.


Identification of Mutational Hot Spots for Substrate Diffusion: Application to Myoglobin.

De Sancho D, Kubas A, Wang PH, Blumberger J, Best RB.

J Chem Theory Comput. 2015 Apr 14;11(4):1919-27. doi: 10.1021/ct5011455. Erratum in: J Chem Theory Comput. 2018 May 8;14 (5):2822.


Empirical Optimization of Interactions between Proteins and Chemical Denaturants in Molecular Simulations.

Zheng W, Borgia A, Borgia MB, Schuler B, Best RB.

J Chem Theory Comput. 2015 Nov 10;11(11):5543-53. doi: 10.1021/acs.jctc.5b00778. Epub 2015 Oct 13.


Transient misfolding dominates multidomain protein folding.

Borgia A, Kemplen KR, Borgia MB, Soranno A, Shammas S, Wunderlich B, Nettels D, Best RB, Clarke J, Schuler B.

Nat Commun. 2015 Nov 17;6:8861. doi: 10.1038/ncomms9861.


Sequence- and Temperature-Dependent Properties of Unfolded and Disordered Proteins from Atomistic Simulations.

Zerze GH, Best RB, Mittal J.

J Phys Chem B. 2015 Nov 19;119(46):14622-30. doi: 10.1021/acs.jpcb.5b08619. Epub 2015 Nov 10.


Pressure-induced structural transition of mature HIV-1 protease from a combined NMR/MD simulation approach.

Roche J, Louis JM, Bax A, Best RB.

Proteins. 2015 Dec;83(12):2117-23. doi: 10.1002/prot.24931. Epub 2015 Oct 16.


Quantitative interpretation of FRET experiments via molecular simulation: force field and validation.

Best RB, Hofmann H, Nettels D, Schuler B.

Biophys J. 2015 Jun 2;108(11):2721-31. doi: 10.1016/j.bpj.2015.04.038.


Dependence of internal friction on folding mechanism.

Zheng W, De Sancho D, Hoppe T, Best RB.

J Am Chem Soc. 2015 Mar 11;137(9):3283-90. doi: 10.1021/ja511609u. Epub 2015 Feb 27.


Role of solvation in pressure-induced helix stabilization.

Best RB, Miller C, Mittal J.

J Chem Phys. 2014 Dec 14;141(22):22D522. doi: 10.1063/1.4901112.

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