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Artículo

Homology modeling in a dynamical world

Monzón, AlexanderIcon ; Zea, Diego JavierIcon ; Marino, Cristina EsterIcon ; Parisi, Gustavo DanielIcon
Fecha de publicación: 11/2017
Editorial: John Wiley & Sons Inc
Revista: Protein Science
ISSN: 0961-8368
Idioma: Inglés
Tipo de recurso: Artículo publicado
Clasificación temática:
Otras Ciencias Biológicas

Resumen

A key concept in template‐based modeling (TBM) is the high correlation between sequence and structural divergence, with the practical consequence that homologous proteins that are similar at the sequence level will also be similar at the structural level. However, conformational diversity of the native state will reduce the correlation between structural and sequence divergence, because structural variation can appear without sequence diversity. In this work, we explore the impact that conformational diversity has on the relationship between structural and sequence divergence. We find that the extent of conformational diversity can be as high as the maximum structural divergence among families. Also, as expected, conformational diversity impairs the well‐established correlation between sequence and structural divergence, which is nosier than previously suggested. However, we found that this noise can be resolved using a priori information coming from the structure‐function relationship. We show that protein families with low conformational diversity show a well‐correlated relationship between sequence and structural divergence, which is severely reduced in proteins with larger conformational diversity. This lack of correlation could impair TBM results in highly dynamical proteins. Finally, we also find that the presence of order/disorder can provide useful beforehand information for better TBM performance.
Palabras clave: Protein Structure , Homology Modeling , Protein Dynamics , Conformational Diversity
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info:eu-repo/semantics/openAccess Excepto donde se diga explícitamente, este item se publica bajo la siguiente descripción: Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Unported (CC BY-NC-SA 2.5)
Identificadores
URI: http://hdl.handle.net/11336/41402
URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.3274
DOI: http://dx.doi.org/10.1002/pro.3274
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Citación
Monzón, Alexander; Zea, Diego Javier; Marino, Cristina Ester; Parisi, Gustavo Daniel; Homology modeling in a dynamical world; John Wiley & Sons Inc; Protein Science; 26; 11; 11-2017; 2195-2206
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