Unveiling crucial amino acids in the carbohydrate recognition domain of a viral protein through a structural bioinformatic approach

Author:

Gamarra Marcelo D12ORCID,Dieterle Maria Eugenia123ORCID,Ortigosa Juan12ORCID,Lannot Jorge O12ORCID,Blanco Capurro Juan I12ORCID,Di Paola Matias12ORCID,Radusky Leandro12ORCID,Duette Gabriel45ORCID,Piuri Mariana12ORCID,Modenutti Carlos P12ORCID

Affiliation:

1. Departamento de Química Biológica , Facultad de Ciencias Exactas y Naturales, , Pabellón 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina

2. Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET , Facultad de Ciencias Exactas y Naturales, , Pabellón 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina

3. Department of Microbiology and Immunology , Albert Einstein College of Medicine, New York, NY 10461, United States

4. The Westmead Institute for Medical Research, Centre for Virus Research , Westmead, NSW 2145, Australia

5. Faculty of Medicine and Health, University of Sydney , Sydney, NSW 2050, Australia

Abstract

Abstract Carbohydrate binding modules (CBMs) are protein domains that typically reside near catalytic domains, increasing substrate-protein proximity by constraining the conformational space of carbohydrates. Due to the flexibility and variability of glycans, the molecular details of how these protein regions recognize their target molecules are not always fully understood. Computational methods, including molecular docking and molecular dynamics simulations, have been employed to investigate lectin-carbohydrate interactions. In this study, we introduce a novel approach that integrates multiple computational techniques to identify the critical amino acids involved in the interaction between a CBM located at the tip of bacteriophage J-1’s tail and its carbohydrate counterparts. Our results highlight three amino acids that play a significant role in binding, a finding we confirmed through in vitro experiments. By presenting this approach, we offer an intriguing alternative for pinpointing amino acids that contribute to protein-sugar interactions, leading to a more thorough comprehension of the molecular determinants of protein-carbohydrate interactions.

Funder

PICT

Publisher

Oxford University Press (OUP)

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