Literature DB >> 22802678

Crystal and NMR structures of a Trp-cage mini-protein benchmark for computational fold prediction.

Michele Scian1, Jasper C Lin, Isolde Le Trong, George I Makhatadze, Ronald E Stenkamp, Niels H Andersen.   

Abstract

To provide high-resolution X-ray crystallographic structures of a peptide with the Trp-cage fold, we prepared a cyclized version of this motif. Cyclized Trp-cage is remarkably stable and afforded two crystal forms suitable for X-ray diffraction. The resulting higher resolution crystal structures validate the prior NMR models and provide explanations for experimental observations that could not be rationalized by NMR structural data, including the structural basis for the increase in fold stability associated with motif cyclization and the manner in which a polar serine side chain is accommodated in the hydrophobic interior. A hexameric oligomer of the cyclic peptide is found in both crystal forms and indicates that under appropriate conditions, this minimized system may also serve as a model for protein-protein interactions.

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Year:  2012        PMID: 22802678      PMCID: PMC3411959          DOI: 10.1073/pnas.1121421109

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  37 in total

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Authors:  Jonathan W Neidigh; R Matthew Fesinmeyer; Niels H Andersen
Journal:  Nat Struct Biol       Date:  2002-06

3.  The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations.

Authors:  Christopher D Snow; Bojan Zagrovic; Vijay S Pande
Journal:  J Am Chem Soc       Date:  2002-12-11       Impact factor: 15.419

4.  Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution.

Authors:  Shibasish Chowdhury; Mathew C Lee; Guoming Xiong; Yong Duan
Journal:  J Mol Biol       Date:  2003-03-28       Impact factor: 5.469

5.  All-atom structure prediction and folding simulations of a stable protein.

Authors:  Carlos Simmerling; Bentley Strockbine; Adrian E Roitberg
Journal:  J Am Chem Soc       Date:  2002-09-25       Impact factor: 15.419

6.  Trp-cage: folding free energy landscape in explicit water.

Authors:  Ruhong Zhou
Journal:  Proc Natl Acad Sci U S A       Date:  2003-10-27       Impact factor: 11.205

7.  Design and characterization of helical peptides that inhibit the E6 protein of papillomavirus.

Authors:  Yuqi Liu; Zhiguo Liu; Elliot Androphy; Jason Chen; James D Baleja
Journal:  Biochemistry       Date:  2004-06-15       Impact factor: 3.162

8.  Enhanced hairpin stability through loop design: the case of the protein G B1 domain hairpin.

Authors:  R Matthew Fesinmeyer; F Michael Hudson; Niels H Andersen
Journal:  J Am Chem Soc       Date:  2004-06-16       Impact factor: 15.419

9.  The CCP4 suite: programs for protein crystallography.

Authors: 
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1994-09-01

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Authors:  Huan-Xiang Zhou
Journal:  J Mol Biol       Date:  2003-09-05       Impact factor: 5.469

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  12 in total

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Authors:  Kavestri Yegambaram; Esther M M Bulloch; Richard L Kingston
Journal:  Protein Sci       Date:  2013-09-20       Impact factor: 6.725

2.  Correlation analysis for heat denaturation of Trp-cage miniprotein with explicit solvent.

Authors:  Fumitaka Kamo; Ryosuke Ishizuka; Nobuyuki Matubayasi
Journal:  Protein Sci       Date:  2015-08-06       Impact factor: 6.725

3.  Unperturbed Detection of the Dynamic Structure in the Hydrophobic Core of Trp-Cage via Two-Dimensional Infrared Spectroscopy.

Authors:  Farzaneh Chalyavi; Andrew J Schmitz; Matthew J Tucker
Journal:  J Phys Chem Lett       Date:  2020-01-21       Impact factor: 6.475

4.  Aryl-aryl interactions in designed peptide folds: Spectroscopic characteristics and optimal placement for structure stabilization.

Authors:  Jordan M Anderson; Brandon L Kier; Brice Jurban; Aimee Byrne; Irene Shu; Lisa A Eidenschink; Alexander A Shcherbakov; Mike Hudson; R M Fesinmeyer; Niels H Andersen
Journal:  Biopolymers       Date:  2016-06       Impact factor: 2.505

5.  Cation-π binding ability of BN indole.

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Journal:  Chem Commun (Camb)       Date:  2020-03-31       Impact factor: 6.222

6.  Structure of the extracellular domain of matrix protein 2 of influenza A virus in complex with a protective monoclonal antibody.

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Journal:  J Virol       Date:  2015-01-21       Impact factor: 5.103

7.  Generating reservoir conformations for replica exchange through the use of the conformational space annealing method.

Authors:  Asim Okur; Benjamin T Miller; Keehyoung Joo; Jooyoung Lee; Bernard R Brooks
Journal:  J Chem Theory Comput       Date:  2013-02-01       Impact factor: 6.006

8.  Circular Permutation of the Trp-cage: Fold Rescue upon Addition of a Hydrophobic Staple.

Authors:  Aimee Byrne; Brandon L Kier; D V Williams; Michele Scian; Niels H Andersen
Journal:  RSC Adv       Date:  2013-11-21       Impact factor: 3.361

9.  Role of tryptophan side chain dynamics on the Trp-cage mini-protein folding studied by molecular dynamics simulations.

Authors:  Srinivasaraghavan Kannan; Martin Zacharias
Journal:  PLoS One       Date:  2014-02-07       Impact factor: 3.240

10.  Folding dynamics and pathways of the trp-cage miniproteins.

Authors:  Aimee Byrne; D Victoria Williams; Bipasha Barua; Stephen J Hagen; Brandon L Kier; Niels H Andersen
Journal:  Biochemistry       Date:  2014-09-16       Impact factor: 3.162

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