Literature DB >> 32497828

Funneled angle landscapes for helical proteins.

John J Kozak1, Harry B Gray2, Roberto A Garza-López3.   

Abstract

We use crystallographic data for four helical iron proteins (cytochrome c-b562, cytochrome c', sperm whale myoglobin, human cytoglobin) to calculate radial and angular signatures as each unfolds from the native state stepwise though four unfolded states. From these data we construct an angle phase diagram to display the evolution of each protein from its native state; and, in turn, the phase diagram is used to construct a funneled angle landscape for comparison with the topography of its folding energy landscape. We quantify the departure of individual helical and turning regions from the areal, angular profile of corresponding regions of the native state. This procedure allows us to identify the similarities and differences among individual helical and turning regions in the early stages of unfolding of the four helical heme proteins.
Copyright © 2020 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Cytochromes; Myoglobin; Protein folding

Mesh:

Substances:

Year:  2020        PMID: 32497828      PMCID: PMC7453651          DOI: 10.1016/j.jinorgbio.2020.111091

Source DB:  PubMed          Journal:  J Inorg Biochem        ISSN: 0162-0134            Impact factor:   4.155


  35 in total

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Review 2.  Development of novel statistical potentials for protein fold recognition.

Authors:  N-V Buchete; J E Straub; D Thirumalai
Journal:  Curr Opin Struct Biol       Date:  2004-04       Impact factor: 6.809

3.  How do metal ions direct ribozyme folding?

Authors:  Natalia A Denesyuk; D Thirumalai
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4.  A protein folding pathway with multiple folding intermediates at atomic resolution.

Authors:  Hanqiao Feng; Zheng Zhou; Yawen Bai
Journal:  Proc Natl Acad Sci U S A       Date:  2005-03-25       Impact factor: 11.205

5.  Fast folding kinetics and stabilization of apo-cytochrome c.

Authors:  Alessandro Borgia; Stefano Gianni; Maurizio Brunori; Carlo Travaglini-Allocatelli
Journal:  FEBS Lett       Date:  2008-02-26       Impact factor: 4.124

6.  Electrostatic effects on funneled landscapes and structural diversity in denatured protein ensembles.

Authors:  Patrick Weinkam; Ekaterina V Pletneva; Harry B Gray; Jay R Winkler; Peter G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  2009-01-30       Impact factor: 11.205

7.  Folding energy landscape of cytochrome cb562.

Authors:  Tetsunari Kimura; Jennifer C Lee; Harry B Gray; Jay R Winkler
Journal:  Proc Natl Acad Sci U S A       Date:  2009-04-28       Impact factor: 11.205

Review 8.  Theory of protein folding: the energy landscape perspective.

Authors:  J N Onuchic; Z Luthey-Schulten; P G Wolynes
Journal:  Annu Rev Phys Chem       Date:  1997       Impact factor: 12.703

9.  Characterisation of the conformational properties of urea-unfolded Im7: implications for the early stages of protein folding.

Authors:  Cécile S Le Duff; Sara B-M Whittaker; Sheena E Radford; Geoffrey R Moore
Journal:  J Mol Biol       Date:  2006-09-16       Impact factor: 5.469

Review 10.  Protein Misfolding, Amyloid Formation, and Human Disease: A Summary of Progress Over the Last Decade.

Authors:  Fabrizio Chiti; Christopher M Dobson
Journal:  Annu Rev Biochem       Date:  2017-05-12       Impact factor: 23.643

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  2 in total

1.  Dramatic Shape Changes Occur as Cytochrome c Folds.

Authors:  Serdal Kirmizialtin; Felicia Pitici; Alfredo E Cardenas; Ron Elber; D Thirumalai
Journal:  J Phys Chem B       Date:  2020-09-09       Impact factor: 2.991

2.  Structural stability of the SARS-CoV-2 main protease: Can metal ions affect function?

Authors:  John J Kozak; Harry B Gray; Roberto A Garza-López
Journal:  J Inorg Biochem       Date:  2020-07-16       Impact factor: 4.155

  2 in total

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