Literature DB >> 18950166

Crystal structure of a ten-amino acid protein.

Shinya Honda1, Toshihiko Akiba, Yusuke S Kato, Yoshito Sawada, Masakazu Sekijima, Miyuki Ishimura, Ayako Ooishi, Hideki Watanabe, Takayuki Odahara, Kazuaki Harata.   

Abstract

What is the smallest protein? This is actually not such a simple question to answer, because there is no established consensus among scientists as to the definition of a protein. We describe here a designed molecule consisting of only 10 amino acids. Despite its small size, its essential characteristics, revealed by its crystal structure, solution structure, thermal stability, free energy surface, and folding pathway network, are consistent with the properties of natural proteins. The existence of this kind of molecule deepens our understanding of proteins and impels us to define an "ideal protein" without inquiring whether the molecule actually occurs in nature.

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Year:  2008        PMID: 18950166     DOI: 10.1021/ja8030533

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  41 in total

1.  Stabilizing capping motif for beta-hairpins and sheets.

Authors:  Brandon L Kier; Irene Shu; Lisa A Eidenschink; Niels H Andersen
Journal:  Proc Natl Acad Sci U S A       Date:  2010-05-19       Impact factor: 11.205

2.  Characterizing protein energy landscape by self-learning multiscale simulations: application to a designed β-hairpin.

Authors:  Wenfei Li; Shoji Takada
Journal:  Biophys J       Date:  2010-11-03       Impact factor: 4.033

3.  Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations.

Authors:  Saugat Kandel; Romelia Salomon-Ferrer; Adrien B Larsen; Abhinandan Jain; Nagarajan Vaidehi
Journal:  J Chem Phys       Date:  2016-01-28       Impact factor: 3.488

4.  Tracing primordial protein evolution through structurally guided stepwise segment elongation.

Authors:  Hideki Watanabe; Kazuhiko Yamasaki; Shinya Honda
Journal:  J Biol Chem       Date:  2013-12-19       Impact factor: 5.157

5.  Extensive tests and evaluation of the CHARMM36IDPSFF force field for intrinsically disordered proteins and folded proteins.

Authors:  Hao Liu; Dong Song; Yangpeng Zhang; Sheng Yang; Ray Luo; Hai-Feng Chen
Journal:  Phys Chem Chem Phys       Date:  2019-10-09       Impact factor: 3.676

6.  Dynamics of an ultrafast folding subdomain in the context of a larger protein fold.

Authors:  Caitlin M Davis; R Brian Dyer
Journal:  J Am Chem Soc       Date:  2013-12-13       Impact factor: 15.419

7.  Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field.

Authors:  Fang-Yu Lin; Jing Huang; Poonam Pandey; Chetan Rupakheti; Jing Li; Benoı T Roux; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2020-04-27       Impact factor: 6.006

8.  Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations.

Authors:  Ramu Anandakrishnan; Aleksander Drozdetski; Ross C Walker; Alexey V Onufriev
Journal:  Biophys J       Date:  2015-03-10       Impact factor: 4.033

9.  ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.

Authors:  James A Maier; Carmenza Martinez; Koushik Kasavajhala; Lauren Wickstrom; Kevin E Hauser; Carlos Simmerling
Journal:  J Chem Theory Comput       Date:  2015-07-23       Impact factor: 6.006

10.  Mutational effects on the folding dynamics of a minimized hairpin.

Authors:  Michele Scian; Irene Shu; Katherine A Olsen; Khalil Hassam; Niels H Andersen
Journal:  Biochemistry       Date:  2013-04-05       Impact factor: 3.162

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