Molecular dynamics of cellulose enzymatic hydrolysis and QM / MM simulations of chemical reactions in biomolecular systems

• Grant number: 16/04963-6
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: May 01, 2016
• End date: August 09, 2018
• Field of knowledge: Physical Sciences and Mathematics - Chemistry - Physical-Chemistry
• Principal Investigator: Munir Salomao Skaf
• Grantee: Gabriel Heerdt
• 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

Abstract

The post-doctoral fellow will extensively apply modern techniques of MD simulations to study proteins of interest to cellulosic biomass conversion into simple soluble sugars. Our interest is to explore protein-cellulose substrate binding at the atomistic level and to understand the mechanisms of catalytic hydrolysis of the polysaccharides by the enzymes. For that, we propose applying QM/MM methods to polysaccharides docked into the corresponding enzyme active sites. Similar approaches may be used to study phosphorylation and acetylation reactions in other proteins, especially in nuclear receptors, which is an important class of proteins that our group has been studying for nearly a decade. Generalized correlation maps in protein complexes are also of interest of our Cepid Center, particularly on NRs and other transcription factor regulators. Recently, we obtained outstanding results regarding allosteric mechanism in NRs using generalized correlations and community network analysis of the full PPARg/RXR/DNA complex. Here we propose to address a natural extension of this work by investigating community network analysis in the groundbreaking CRISPR/cas protein complexes. (AU)

Scientific publications

(6)

(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)

ZANOTTO, LEANDRO; HEERDT, GABRIEL; SOUZA, PAULO C. T.; ARAUJO, GUIDO; SKAF, MUNIR S.. High performance collision cross section calculationHPCCS. Journal of Computational Chemistry, v. 39, n. 21, p. 1675-1681, AUG 5 2018. (13/08293-7, 16/04963-6, 12/24750-6)

DE OLIVEIRA, JULIANA MANSO; ANGNES, RICARDO ALMIR; KHAN, ISMAT ULLAH; POLO, ELLEN CHRISTINE; HEERDT, GABRIEL; SERVILHA, BRUNO M.; MENEZES DA SILVA, VITOR H.; BRAGA, ATAUALPA A. C.; DUARTE CORREIA, CARLOS ROQUE. Enantioselective, Noncovalent, Substrate-Directable Heck-Matsuda and Oxidative Heck Arylations of Unactivated Five-Membered Carbocyclic Olefins. CHEMISTRY-A EUROPEAN JOURNAL, v. 24, n. 45, p. 11738-11747, AUG 9 2018. (17/18207-1, 13/00544-0, 14/25770-6, 13/07600-3, 15/01491-3, 16/04963-6, 13/25849-9)

SOUSA, IRAN DA L.; HEERDT, GABRIEL; XIMENES, VALDECIR F.; DE SOUZA, AGUINALDO R.; MORGON, NELSON H.. TD-DFT Analysis of the Dissymmetry Factor in Camphor. Journal of the Brazilian Chemical Society, v. 31, n. 3, p. 613-618, MAR 2020. (14/50926-0, 16/20549-5, 15/22338-9, 16/04963-6, 19/12294-5)

CAJAHUARINGA, SAMUEL; ZANOTTO, LEANDRO N.; CAETANO, DANIEL L. Z.; RIGO, SANDRO; YVIQUEL, HERVE; SKAF, MUNIR S.; ARAUJO, GUIDO; IEEE COMP SOC. Ion-Molecule Collision Cross-Section Simulation using Linked-cell and Trajectory Parallelization. 2022 IEEE 34TH INTERNATIONAL SYMPOSIUM ON COMPUTER ARCHITECTURE AND HIGH PERFORMANCE COMPUTING (SBAC-PAD 2022), v. N/A, p. 10-pg., 2022-01-01. (12/24750-6, 16/04963-6, 13/08293-7, 21/03224-3, 19/19662-0)

DE SOUSA, IRAN DA LUZ; XIMENES, VALDECIR FARIAS; DE SOUZA, AGUINALDO ROBINSON; MORGON, NELSON HENRIQUE. Solvent-induced Stokes' shift in DCJTB: Experimental and theoretical results. Journal of Molecular Structure, v. 1192, p. 186-191, SEP 15 2019. (15/22338-9, 16/20549-5, 14/50926-0, 16/04963-6)

HEERDT, GABRIEL; TRANCA, IONUT; MARKVOORT, ALBERT J.; SZYJA, BARTLOMIEJ M.; MORGON, NELSON H.; HENSEN, EMIEL J. M.. Photoisomerization induced scission of rod-like micelles unravelled with multiscale modeling. Journal of Colloid and Interface Science, v. 510, p. 357-367, JAN 15 2018. (16/04963-6)