Literature DB >> 34079958

Outline of an experimental design aimed to detect a protein A mirror image in solution.

Osvaldo A Martin1, Yury Vorobjev2, Harold A Scheraga3, Jorge A Vila1,3.   

Abstract

There is abundant theoretical evidence indicating that a mirror image of Protein A may occur during the protein folding process. However, as to whether such mirror image exists in solution is an unsolved issue. Here we provide outline of an experimental design aimed to detect the mirror image of Protein A in solution. The proposal is based on computational simulations indicating that the use of a mutant of protein A, namely Q10H, could be used to detect the mirror image conformation in solution. Our results indicate that the native conformation of the protein A should have a pKa, for the Q10H mutant, at ≈6.2, while the mirror-image conformation should have a pKa close to ≈7.3. Naturally, if all the population is in the native state for the Q10H mutant, the pKa should be ≈6.2, while, if all are in the mirror-image state, it would be ≈7.3, and, if it is a mixture, the pKa should be largerthan 6.2, presumably in proportion to the mirror population. In addition, evidence is provided indicating the tautomeric distribution of H10 must also change between the native and mirror conformations. Although this may not be completely relevant for the purpose of determining whether the protein A mirror image exists in solution, it could provide valuable information to validate the pKa findings. We hope this proposal will foster experimental work on this problem either by direct application of our proposed experimental design or serving as inspiration and motivation for other experiments.

Entities:  

Year:  2019        PMID: 34079958      PMCID: PMC8168520          DOI: 10.7717/peerj-pchem.2

Source DB:  PubMed          Journal:  PeerJ Phys Chem        ISSN: 2689-7733


  32 in total

1.  Testing protein-folding simulations by experiment: B domain of protein A.

Authors:  Satoshi Sato; Tomasz L Religa; Valerie Daggett; Alan R Fersht
Journal:  Proc Natl Acad Sci U S A       Date:  2004-04-06       Impact factor: 11.205

2.  Crystal structure of diisopropylfluorophosphatase from Loligo vulgaris.

Authors:  E I Scharff; J Koepke; G Fritzsch; C Lücke; H Rüterjans
Journal:  Structure       Date:  2001-06       Impact factor: 5.006

3.  PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta.

Authors:  Sidhartha Chaudhury; Sergey Lyskov; Jeffrey J Gray
Journal:  Bioinformatics       Date:  2010-01-07       Impact factor: 6.937

4.  Tautomerism in neutral histidine.

Authors:  Celina Bermúdez; Santiago Mata; Carlos Cabezas; José L Alonso
Journal:  Angew Chem Int Ed Engl       Date:  2014-08-21       Impact factor: 15.336

5.  Limiting Values of the one-bond C-H Spin-Spin Coupling Constants of the Imidazole Ring of Histidine at High-pH.

Authors:  Jorge A Vila; Harold A Scheraga
Journal:  J Mol Struct       Date:  2017-01-08       Impact factor: 3.196

6.  Coupled molecular dynamics and continuum electrostatic method to compute the ionization pKa's of proteins as a function of pH. Test on a large set of proteins.

Authors:  Yury N Vorobjev; Harold A Scheraga; Jorge A Vila
Journal:  J Biomol Struct Dyn       Date:  2017-02-24

7.  Structure and mechanism of the M2 proton channel of influenza A virus.

Authors:  Jason R Schnell; James J Chou
Journal:  Nature       Date:  2008-01-31       Impact factor: 49.962

8.  Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures.

Authors:  H Gouda; H Torigoe; A Saito; M Sato; Y Arata; I Shimada
Journal:  Biochemistry       Date:  1992-10-13       Impact factor: 3.162

9.  Characterization of conformational exchange of a histidine side chain: protonation, rotamerization, and tautomerization of His61 in plastocyanin from Anabaena variabilis.

Authors:  Mathias A S Hass; D Flemming Hansen; Hans E M Christensen; Jens J Led; Lewis E Kay
Journal:  J Am Chem Soc       Date:  2008-06-07       Impact factor: 15.419

10.  BioMagResBank.

Authors:  Eldon L Ulrich; Hideo Akutsu; Jurgen F Doreleijers; Yoko Harano; Yannis E Ioannidis; Jundong Lin; Miron Livny; Steve Mading; Dimitri Maziuk; Zachary Miller; Eiichi Nakatani; Christopher F Schulte; David E Tolmie; R Kent Wenger; Hongyang Yao; John L Markley
Journal:  Nucleic Acids Res       Date:  2007-11-04       Impact factor: 16.971

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