Literature DB >> 15184682

Prediction of protein folding rates from the amino acid sequence-predicted secondary structure.

Dmitry N Ivankov1, Alexei V Finkelstein.   

Abstract

We present a method for predicting folding rates of proteins from their amino acid sequences only, or rather, from their chain lengths and their helicity predicted from their sequences. The method achieves 82% correlation with experiment over all 64 "two-state" and "multistate" proteins (including two artificial peptides) studied up to now.

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Year:  2004        PMID： 15184682      PMCID： PMC428451          DOI： 10.1073/pnas.0402659101

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


  24 in total

1.  Protein secondary structure prediction based on position-specific scoring matrices.

Authors:  D T Jones
Journal:  J Mol Biol       Date:  1999-09-17       Impact factor: 5.469

Review 2.  Keeping it in the family: folding studies of related proteins.

Authors:  K Gunasekaran; S J Eyles; A T Hagler; L M Gierasch
Journal:  Curr Opin Struct Biol       Date:  2001-02       Impact factor: 6.809

3.  Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation.

Authors:  U Mayor; C M Johnson; V Daggett; A R Fersht
Journal:  Proc Natl Acad Sci U S A       Date:  2000-12-05       Impact factor: 11.205

4.  Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model.

Authors:  N Koga; S Takada
Journal:  J Mol Biol       Date:  2001-10-12       Impact factor: 5.469

Review 5.  Protein folding theory: from lattice to all-atom models.

Authors:  L Mirny; E Shakhnovich
Journal:  Annu Rev Biophys Biomol Struct       Date:  2001

6.  Preorganized secondary structure as an important determinant of fast protein folding.

Authors:  J K Myers; T G Oas
Journal:  Nat Struct Biol       Date:  2001-06

7.  Local secondary structure content predicts folding rates for simple, two-state proteins.

Authors:  Haipeng Gong; Daniel G Isom; Rajgopal Srinivasan; George D Rose
Journal:  J Mol Biol       Date:  2003-04-11       Impact factor: 5.469

8.  Contact order, transition state placement and the refolding rates of single domain proteins.

Authors:  K W Plaxco; K T Simons; D Baker
Journal:  J Mol Biol       Date:  1998-04-10       Impact factor: 5.469

9.  Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

Authors:  W Kabsch; C Sander
Journal:  Biopolymers       Date:  1983-12       Impact factor: 2.505

10.  Comparison of the folding processes of distantly related proteins. Importance of hydrophobic content in folding.

Authors:  Giulia Calloni; Niccolò Taddei; Kevin W Plaxco; Giampietro Ramponi; Massimo Stefani; Fabrizio Chiti
Journal:  J Mol Biol       Date:  2003-07-11       Impact factor: 5.469
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  36 in total

1.  Real value prediction of protein folding rate change upon point mutation.

Authors:  Liang-Tsung Huang; M Michael Gromiha
Journal:  J Comput Aided Mol Des       Date:  2012-03-18       Impact factor: 3.686

2.  Reversible thermal denaturation of a 60-kDa genetically engineered beta-sheet polypeptide.

Authors:  Igor K Lednev; Vladimir V Ermolenkov; Seiichiro Higashiya; Ludmila A Popova; Natalya I Topilina; John T Welch
Journal:  Biophys J       Date:  2006-08-04       Impact factor: 4.033

Review 3.  Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet.

Authors:  Eugene Shakhnovich
Journal:  Chem Rev       Date:  2006-05       Impact factor: 60.622

4.  Protein folding: then and now.

Authors:  Yiwen Chen; Feng Ding; Huifen Nie; Adrian W Serohijos; Shantanu Sharma; Kyle C Wilcox; Shuangye Yin; Nikolay V Dokholyan
Journal:  Arch Biochem Biophys       Date:  2007-06-08       Impact factor: 4.013

5.  On the role of structural class of a protein with two-state folding kinetics in determining correlations between its size, topology, and folding rate.

Authors:  Andrei Y Istomin; Donald J Jacobs; Dennis R Livesay
Journal:  Protein Sci       Date:  2007-11       Impact factor: 6.725

6.  Capillarity-like growth of protein folding nuclei.

Authors:  Xianghong Qi; John J Portman
Journal:  Proc Natl Acad Sci U S A       Date:  2008-08-04       Impact factor: 11.205

7.  Submillisecond elastic recoil reveals molecular origins of fibrin fiber mechanics.

Authors:  Nathan E Hudson; Feng Ding; Igal Bucay; E Timothy O'Brien; Oleg V Gorkun; Richard Superfine; Susan T Lord; Nikolay V Dokholyan; Michael R Falvo
Journal:  Biophys J       Date:  2013-06-18       Impact factor: 4.033

8.  Conformational dynamics is more important than helical propensity for the folding of the all α-helical protein Im7.

Authors:  Angelo Miguel Figueiredo; Sara B-M Whittaker; Stuart E Knowling; Sheena E Radford; Geoffrey R Moore
Journal:  Protein Sci       Date:  2013-10-19       Impact factor: 6.725

9.  Predicting protein folding rates from geometric contact and amino acid sequence.

Authors:  Zheng Ouyang; Jie Liang
Journal:  Protein Sci       Date:  2008-04-23       Impact factor: 6.725

Review 10.  The protein folding problem.

Authors:  Ken A Dill; S Banu Ozkan; M Scott Shell; Thomas R Weikl
Journal:  Annu Rev Biophys       Date:  2008       Impact factor: 12.981
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