Molecular dynamics simulations of enzymes of biotechnological interest

• Grant number: 22/04703-5
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: July 01, 2022
• End date: May 31, 2026
• Field of knowledge: Physical Sciences and Mathematics - Chemistry - Physical-Chemistry
• Principal Investigator: Munir Salomao Skaf
• Grantee: Clauber Henrique Souza da Costa
• Host Institution: Instituto de Química (IQ). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Associated research grant: 13/08293-7 - CCES - Center for Computational Engineering and Sciences, AP.CEPID
• Associated scholarship(s): 23/13707-7 - Computational Studies of the Enzymatic Biodegradation of Polyethylene Terephthalate (PET): Exploring the Stability and Efficiency of PETases, BE.EP.PD

Abstract

We propose applying extensive classical MD and QM/MM simulation techniques to design mutations that may increase the thermal stability and catalytic efficiency of enzymes for industrial applications. The primary focus of the project will be on xylanases and other Glicoside Hydrolases (GHs) for sacharification of linear polysaccharides from lignocellulosic biomass, but other enzymes of industrial interest, including esterases, phytases, and possibly others, may also be considered as the project evolves. Analysis of the conformational landscape, ligand binding affinity, and catalytic itinerary will be performed on putative mutants and compared between them and with the wild type. Strategies for prospecting candidate mutations for in silico molecular evaluation will rely on the Rosetta scans for sequence alignment and disulfidize scans, in addition to our own automated search. (AU)

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

DOS SANTOS, ALBERTO M.; DA COSTA, CLAUBER H. S.; SILVA, PEDRO H. A.; SKAF, MUNIR S.; LAMEIRA, JERONIMO. Exploring the Reaction Mechanism of Polyethylene Terephthalate Biodegradation through QM/MM Approach. Journal of Physical Chemistry B, v. 128, n. 31, p. 14-pg., 2024-07-29. (13/08293-7, 22/04703-5, 22/04695-2)

EHRLICH, HERMANN; MIKSIK, IVAN; TSURKAN, MIKHAIL V.; SIMON, PAUL; PORZUCEK, FILIP; RYBKA, JAKUB DALIBOR; MANKOWSKA, MONIKA; GALLI, ROBERTA; VIEHWEGER, CHRISTINE; BRENDLER, ERICA; et al. Discovery of mammalian collagens I and III within ancient poriferan biopolymer spongin. NATURE COMMUNICATIONS, v. 16, n. 1, p. 13-pg., 2025-03-13. (13/08293-7, 18/18503-2, 22/04695-2, 22/04703-5, 22/03410-4)

DOS SANTOS, ALBERTO M.; DA COSTA, CLAUBER H. S.; MARTINS, MANOELA; GOLDBECK, ROSANA; SKAF, MUNIR S.. Exploring the Structural and Dynamic Properties of a Chimeric Glycoside Hydrolase Protein in the Presence of Calcium Ions. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, v. 25, n. 22, p. 16-pg., 2024-11-01. (22/04695-2, 20/02871-2, 22/04703-5, 13/08293-7, 19/17874-0)