Dynamic and Conformational Switching in Proteins

Overview

Journal Biopolymers

Publisher Wiley

Date 2020 Dec 3

PMID 33270217

Citations 2

Authors

H A Scheraga

S Rackovsky

Affiliations

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Abstract

Using bioinformatic methods for treating protein dynamics, developed in earlier work, we study the relationship between sequence mobility and dynamics in proteins. It is shown that sequence mobility drives a transition between two dynamic regimes in proteins, and that the specific details of this transition differ qualitatively between α-helical proteins and those in other structural classes. We examine the possibility that conformational switching is related to dynamic switching, by considering a specific system of sequences which exhibit the switching phenomenon. It is shown that a relationship between dynamic and conformational switching is entirely plausible.

Citing Articles

Application of artificial intelligence and machine learning techniques to the analysis of dynamic protein sequences.

Kombo D, LaMarche M, Konkankit C, Rackovsky S Proteins. 2024; 92(10):1234-1241.

PMID: 38808365 PMC: 11511649. DOI: 10.1002/prot.26704.

The dynamic basis of structural order in proteins.

Konkankit C, Rackovsky S Proteins. 2022; 90(5):1115-1118.

PMID: 34981860 PMC: 9007817. DOI: 10.1002/prot.26296.

References

Anderson T, Cordes M, Sauer R . Sequence determinants of a conformational switch in a protein structure. Proc Natl Acad Sci U S A. 2005; 102(51):18344-9. PMC: 1317976. DOI: 10.1073/pnas.0509349102. View

Rackovsky S . Sequence determinants of protein architecture. Proteins. 2013; 81(10):1681-5. DOI: 10.1002/prot.24328. View

Rackovsky S . "Hidden" sequence periodicities and protein architecture. Proc Natl Acad Sci U S A. 1998; 95(15):8580-4. PMC: 21118. DOI: 10.1073/pnas.95.15.8580. View

Rackovsky S . Quantitative organization of the known protein x-ray structures. I. Methods and short-length-scale results. Proteins. 1990; 7(4):378-402. DOI: 10.1002/prot.340070409. View

Richardson J . The anatomy and taxonomy of protein structure. Adv Protein Chem. 1981; 34:167-339. DOI: 10.1016/s0065-3233(08)60520-3. View

Doruker P, Jernigan R . Functional motions can be extracted from on-lattice construction of protein structures. Proteins. 2003; 53(2):174-81. DOI: 10.1002/prot.10486. View

Alexander P, He Y, Chen Y, Orban J, Bryan P . A minimal sequence code for switching protein structure and function. Proc Natl Acad Sci U S A. 2009; 106(50):21149-54. PMC: 2779201. DOI: 10.1073/pnas.0906408106. View

Scheraga H, Rackovsky S . Global informatics and physical property selection in protein sequences. Proc Natl Acad Sci U S A. 2016; 113(7):1808-10. PMC: 4763726. DOI: 10.1073/pnas.1525745113. View

Scheraga H, Rackovsky S . Sequence-specific dynamic information in proteins. Proteins. 2019; 87(10):799-804. PMC: 6718326. DOI: 10.1002/prot.25747. View

10.

Rackovsky S . Spectral analysis of a protein conformational switch. Phys Rev Lett. 2011; 106(24):248101. DOI: 10.1103/PhysRevLett.106.248101. View

11.

Orengo C, Michie A, Jones S, Jones D, Swindells M, Thornton J . CATH--a hierarchic classification of protein domain structures. Structure. 1997; 5(8):1093-108. DOI: 10.1016/s0969-2126(97)00260-8. View

12.

Roessler C, Hall B, Anderson W, Ingram W, Roberts S, Montfort W . Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds. Proc Natl Acad Sci U S A. 2008; 105(7):2343-8. PMC: 2268138. DOI: 10.1073/pnas.0711589105. View

13.

Scheraga H, Rackovsky S . Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences. Proc Natl Acad Sci U S A. 2014; 111(14):5225-9. PMC: 3986189. DOI: 10.1073/pnas.1403599111. View

14.

Ambroggio X, Kuhlman B . Design of protein conformational switches. Curr Opin Struct Biol. 2006; 16(4):525-30. DOI: 10.1016/j.sbi.2006.05.014. View

15.

Ming D, Kong Y, Lambert M, Huang Z, Ma J . How to describe protein motion without amino acid sequence and atomic coordinates. Proc Natl Acad Sci U S A. 2002; 99(13):8620-5. PMC: 124334. DOI: 10.1073/pnas.082148899. View

16.

Rackovsky S . Characterization of architecture signals in proteins. J Phys Chem B. 2006; 110(38):18771-8. DOI: 10.1021/jp0575097. View