A5060155336- Protein Structure and Dynamics
- Hemoglobin structure and function
- Spectroscopy and Quantum Chemical Studies
- Computational Drug Discovery Methods
- Photosynthetic Processes and Mechanisms
- Bacteriophages and microbial interactions
- Enzyme Catalysis and Immobilization
- SARS-CoV-2 and COVID-19 Research
- Bioinformatics and Genomic Networks
- Metal-Catalyzed Oxygenation Mechanisms
- RNA and protein synthesis mechanisms
- Viral gastroenteritis research and epidemiology
- Lipid Membrane Structure and Behavior
- vaccines and immunoinformatics approaches
- Nitric Oxide and Endothelin Effects
- Monoclonal and Polyclonal Antibodies Research
- Electron Spin Resonance Studies
- Mass Spectrometry Techniques and Applications
- RNA Research and Splicing
- Photochemistry and Electron Transfer Studies
- CAR-T cell therapy research
- Machine Learning in Bioinformatics
- Luminescence and Fluorescent Materials
- Endoplasmic Reticulum Stress and Disease
- Genetics and Neurodevelopmental Disorders
Brazilian Center for Research in Energy and Materials
2021-2025
Instituto de Química y Fisicoquímica Biológicas
2014-2025
Consejo Nacional de Investigaciones Científicas y Técnicas
2013-2025
University of Buenos Aires
2014-2025
Brazilian Biosciences National Laboratory
2021-2025
Fundación Ciencias Exactas y Naturales
2014-2023
Universidade Estadual de Campinas (UNICAMP)
2016-2019
Pontifícia Universidade Católica de Campinas
2017
Universidad Nacional de Córdoba
2011-2014
The nucleocapsid (N) protein of the SARS-CoV-2 virus, causal agent COVID-19, is a multifunction phosphoprotein that plays critical roles in virus life cycle, including transcription and packaging viral RNA. To play such diverse roles, N has two globular RNA-binding modules, N- (NTD) C-terminal (CTD) domains, which are connected by an intrinsically disordered region. Despite wealth structural data available for isolated NTD CTD, how these domains arranged full-length oligomerization...
Transition-state theory has provided the theoretical framework to explain enormous rate accelerations of chemical reactions by enzymes. Given that proteins display large ensembles conformations, unique transition states would pose a huge entropic bottleneck for enzyme catalysis. To shed light on this question, we studied nature enzymatic state phosphoryl-transfer step in adenylate kinase quantum-mechanics/molecular-mechanics calculations. We find structurally wide set energetically...
Transition-state (TS) theory has provided the theoretical framework to explain enormous rate accelerations of chemical reactions by enzymes. Given that proteins display large ensembles conformations, unique TSs would pose a huge entropic bottleneck for enzyme catalysis. To shed light on this question, we studied nature enzymatic TS phosphoryl-transfer step in adenylate kinase quantum-mechanics/molecular-mechanics calculations. We find structurally wide set energetically equivalent...
Coronavirus disease 2019 is a multi-systemic syndrome that caused pandemic. Proteomic studies have shown changes in protein expression and interaction involved signaling pathways related to SARS-CoV-2 infections. Protein phosphatases play crucial role regulating cell signaling. In this study, we assessed the potential involvement of their associated during infection by conducting meta-analysis proteome databases from COVID-19 patients. We identified both direct indirect interactions between...
Human Mn-containing superoxide dismutase (hMnSOD) is a mitochondrial enzyme that metabolizes radical (O2(•-)). O2(•-) reacts at diffusional rates with nitric oxide to yield potent nitrating species, peroxynitrite anion (ONOO(-)). MnSOD nitrated and inactivated in vivo, active site Tyr34 as the key oxidatively modified residue. We previously reported k of ∼1.0 × 10(5) M(-1) s(-1) for reaction hMnSOD ONOO(-) by direct stopped-flow spectroscopy critical role Mn nitration process. In this study,...
Biomolecular interactions that modulate biological processes occur mainly in cavities throughout the surface of biomolecular structures. In data science era, structural biology has benefited from increasing availability biostructural due to advances determination and computational methods. this scenario, data-intensive cavity analysis demands efficient scripting routines built on easily manipulated To fulfill need, we developed pyKVFinder, a Python package detect characterize structures for...
The fundamental object for studying a (bio)chemical reaction obtained from simulations is the free energy profile, which can be directly related to experimentally determined properties. Although quite accurate hybrid quantum (DFT based)-classical methods are available, achieving statistically and well converged results at moderate computational cost still an open challenge. Here, we present thoroughly test differential relaxation algorithm (HyDRA), allows faster equilibration of classical...
Structure and thermodynamics of lipase activation at aqueous–organic interfaces.
Edema Factor (EF) is one of three major toxins anthrax. EF an adenylyl cyclase that disrupts cell signaling by accelerating the conversion ATP into cyclic-AMP. has a much higher catalytic rate than mammalian cyclases (mACs). Crystal structures were obtained for mACs and EF, but molecular basis different activities remained poorly understood. In particular, arrangement active site in unclear what concerns number ions present conformation substrate. Here, we use quantum mechanics-molecular...
Deep learning methods, trained on the increasing set of available protein 3D structures and sequences, have substantially impacted modeling design field. These advancements facilitated creation novel proteins, or optimization existing ones designed for specific functions, such as binding a target protein. Despite demonstrated potential approaches in designing general binders, their application immunotherapeutics remains relatively underexplored. A relevant is T cell receptors (TCRs). Given...
This work aims at describing the water structure characteristics that influence electron transfer superexchange mechanism by explicitly calculating solvent mediated conductance between donor and acceptor in a generic pair. The method employed here is based on non-equilibrium Green function formalism for over trajectories previously determined molecular dynamics methods. A non-exponential dependence of observed with respect to distance acceptor. Local fluctuations are responsible...
Abstract Transition-state theory has provided the theoretical framework to explain enormous rate accelerations of chemical reactions by enzymes. Given that proteins display large ensembles conformations, unique transition states would pose a huge entropic bottleneck for enzyme catalysis. To shed light on this question, we studied nature enzymatic state phosphoryl-transfer step in adenylate kinase quantum-mechanics/molecular-mechanics calculations. We find structurally wide set energetically...
Deep learning methods, trained on the increasing set of available protein 3D structures and sequences, have substantially impacted modeling design field. These advancements facilitated creation novel proteins, or optimization existing ones designed for specific functions, such as binding a target protein. Despite demonstrated potential approaches in designing general binders, their application immunotherapeutics remains relatively unexplored. A relevant is T cell receptors (TCRs). Given...
Transition-state theory has provided the theoretical framework to explain enormous rate accelerations of chemical reactions by enzymes. Given that proteins display large ensembles conformations, unique transition states would pose a huge entropic bottleneck for enzyme catalysis. To shed light on this question, we studied nature enzymatic state phosphoryl-transfer step in adenylate kinase quantum-mechanics/molecular-mechanics calculations. We find structurally wide set energetically...
Transition-state theory has provided the theoretical framework to explain enormous rate accelerations of chemical reactions by enzymes. Given that proteins display large ensembles conformations, unique transition states would pose a huge entropic bottleneck for enzyme catalysis. To shed light on this question, we studied nature enzymatic state phosphoryl-transfer step in adenylate kinase quantum-mechanics/molecular-mechanics calculations. We find structurally wide set energetically...