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Exploring Protein Conformational Diversity

  • Alexander Miguel Monzon
  • Maria Silvina Fornasari
  • Diego Javier Zea
  • Gustavo Parisi
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1851)

Abstract

The native state of proteins is composed of conformers in dynamical equilibrium. In this chapter, different issues related to conformational diversity are explored using a curated and experimentally based database called CoDNaS (Conformational Diversity in the Native State). This database is a collection of redundant structures for the same sequence. CoDNaS estimates the degree of conformational diversity using different global and local structural similarity measures. It allows the user to explore how structural differences among conformers change as a function of several structural features providing further biological information. This chapter explores the measurement of conformational diversity and its relationship with sequence divergence. Also, it discusses how proteins with high conformational diversity could affect homology modeling techniques.

Key words

Conformational diversity CoDNaS database Conformers Native state Protein dynamics Protein evolution 

Notes

Acknowledgments

Authors would like to thank Paula Benencio for helping us with manuscript proofreading.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Alexander Miguel Monzon
    • 1
  • Maria Silvina Fornasari
    • 1
  • Diego Javier Zea
    • 2
  • Gustavo Parisi
    • 1
  1. 1.Departamento de Ciencia y TecnologíaUniversidad Nacional de Quilmes, CONICETBernalArgentina
  2. 2.Structural Bioinformatics Unit, Fundación Instituto Leloir, CONICETBuenos AiresArgentina

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