Literature DB >> 12586361

Protein folding: could hydrophobic collapse be coupled with hydrogen-bond formation?

Ariel Fernández1, József Kardos, Yuji Goto.   

Abstract

A judicious examination of an exhaustive PDB sample of soluble globular proteins of moderate size (N<102) reveals a commensurable relationship between hydrophobic surface burial and number of backbone hydrogen bonds. An analysis of 50,000 conformations along the longest all-atom MD trajectory allows us to infer that not only the hydrophobic collapse is concurrent with the formation of backbone amide-carbonyl hydrogen bonds, they are also dynamically coupled processes. In statistical terms, hydrophobic clustering of the side chains is inevitably conducive to backbone burial and the latter process becomes thermodynamically too costly and kinetically unfeasible without amide-carbonyl hydrogen-bond formation. Furthermore, the desolvation of most hydrogen bonds is exhaustive along the pathway, implying that such bonds guide the collapse process.

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Year:  2003        PMID: 12586361     DOI: 10.1016/s0014-5793(03)00056-5

Source DB:  PubMed          Journal:  FEBS Lett        ISSN: 0014-5793            Impact factor:   4.124


  13 in total

1.  H-bonding mediates polarization of peptide groups in folded proteins.

Authors:  Nenad Juranić; Slobodan Macura; Franklyn G Prendergast
Journal:  Protein Sci       Date:  2003-11       Impact factor: 6.725

2.  Collapse and search dynamics of apomyoglobin folding revealed by submillisecond observations of alpha-helical content and compactness.

Authors:  Takanori Uzawa; Shuji Akiyama; Tetsunari Kimura; Satoshi Takahashi; Koichiro Ishimori; Isao Morishima; Tetsuro Fujisawa
Journal:  Proc Natl Acad Sci U S A       Date:  2004-01-07       Impact factor: 11.205

3.  Conserved quantitative stability/flexibility relationships (QSFR) in an orthologous RNase H pair.

Authors:  Dennis R Livesay; Donald J Jacobs
Journal:  Proteins       Date:  2006-01-01

4.  Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a distance constraint model.

Authors:  Donald J Jacobs; Dennis R Livesay; Jeremy Hules; Maria Luisa Tasayco
Journal:  J Mol Biol       Date:  2006-02-24       Impact factor: 5.469

5.  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

6.  Fast in silico protein folding by introduction of alternating hydrogen bond potentials.

Authors:  M G Wolf; S W de Leeuw
Journal:  Biophys J       Date:  2008-05-15       Impact factor: 4.033

Review 7.  Intrinsically disordered proteins in the neurodegenerative processes: formation of tau protein paired helical filaments and their analysis.

Authors:  Rostislav Skrabana; Jozef Sevcik; Michal Novak
Journal:  Cell Mol Neurobiol       Date:  2006-06-16       Impact factor: 5.046

8.  Predicting the melting point of human C-type lysozyme mutants.

Authors:  Deeptak Verma; Donald J Jacobs; Dennis R Livesay
Journal:  Curr Protein Pept Sci       Date:  2010-11       Impact factor: 3.272

9.  Conformational Entropy of an Ideal Cross-Linking Polymer Chain.

Authors:  Oleg K Vorov; Dennis R Livesay; Donald J Jacobs
Journal:  Entropy (Basel)       Date:  2008-09-20       Impact factor: 2.524

10.  Inhibitor design by wrapping packing defects in HIV-1 proteins.

Authors:  Ariel Fernández; Kristina Rogale; Ridgway Scott; Harold A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  2004-08-02       Impact factor: 11.205

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