A5056416170- Protein Structure and Dynamics
- Advanced Chemical Physics Studies
- Spectroscopy and Quantum Chemical Studies
- Enzyme Structure and Function
- Evolution and Genetic Dynamics
- Microbial Metabolic Engineering and Bioproduction
- RNA and protein synthesis mechanisms
- Spectroscopy and Laser Applications
- Genomics and Phylogenetic Studies
- Quantum, superfluid, helium dynamics
- Hemoglobin structure and function
- Photoreceptor and optogenetics research
- Cold Atom Physics and Bose-Einstein Condensates
- Photosynthetic Processes and Mechanisms
- Bioinformatics and Genomic Networks
- Atmospheric Ozone and Climate
- Photochemistry and Electron Transfer Studies
- Quantum chaos and dynamical systems
- Quantum optics and atomic interactions
- Nonlinear Dynamics and Pattern Formation
- Enzyme function and inhibition
- Molecular spectroscopy and chirality
- Quantum Mechanics and Non-Hermitian Physics
- Gene expression and cancer classification
- Light effects on plants
Universidad Nacional de San Martín
2024
National University of General San Martín
2012-2022
Consejo Nacional de Investigaciones Científicas y Técnicas
2004-2022
Centro Científico Tecnológico - San Juan
2017
Uni Research (Norway)
2012
University of Bergen
2012
Universidad Nacional de La Plata
2006-2010
Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas
1987-2010
École Polytechnique Fédérale de Lausanne
2010
National University of Quilmes
1996-2006
Abstract Motivation: The function of a protein depends not only on its structure but also dynamics. This is at the basis large body experimental and theoretical work Further insight into dynamics–function relationship can be gained by studying evolutionary divergence motions. To investigate this, we need appropriate comparative dynamics methods. most used dynamical similarity score correlation between root mean square fluctuations (RMSF) aligned residues. Despite usefulness, RMSF in general...
Functional residues in proteins tend to be highly conserved over evolutionary time. However, what extent functional sites impose constraints on nearby or even more distant is not known. Here, we report pervasive conservation gradients toward catalytic a dataset of 524 distinct enzymes: decreases approximately linearly with increasing distance the nearest residue protein structure. This trend encompasses, average, 80% any enzyme, and it independent known structural evolution such as packing...
Protein sequences evolve under selection pressures imposed by functional and biophysical requirements, resulting in site-dependent rates of amino acid substitution. Relative solvent accessibility (RSA) local packing density (LPD) have emerged as the best candidates to quantify structural constraint. Recent research assumes that RSA is main determinant sequence divergence. However, it not yet clear which predictor substitution rates. To address this issue, we compared LPD with site-specific...
Protein sites evolve at different rates due to functional and biophysical constraints. It is usually considered that the main structural determinant of a site's rate evolution its Relative Solvent Accessibility (RSA). However, recent comparative study has shown Local Packing Density (LPD). LPD related with dynamical flexibility, which also been correlate sequence variability. Our purpose investigate mechanism connects evolution. We consider two models: an empirical Flexibility Model...
An exact quantum mechanical theory is developed to treat four-atom reactions of the type AB+CD↔(BCD+A, ACD+B), where atoms are constrained move in a plane. The makes use an unbiased set hyperspherical coordinates. A method proposed for implementing that exploits potential optimized discrete variable representation. Application made calculation rovibrational state-to-state reaction probabilities H2+OH↔H2O+H, which length OH spectator bond held fixed. results show rotating approximation, H2...
Evolutionary-rate variation among sites within proteins depends on functional and biophysical properties that constrain protein evolution.It is generally accepted must be able to fold stably in order function.However, the relationship between stability constraints among-sites rate not well understood.Here, we present a model links thermodynamic changes due mutations at (ΔΔG) which accumulate those over evolutionary time.We find such "stability model" performs well, displaying correlations...
In protein evolution, due to functional and biophysical constraints, the rates of amino acid substitution differ from site site. Among best predictors site-specific are solvent accessibility packing density. The density measure that correlates with is weighted contact number (WCN), sum inverse square distances between a site's C α other sites. According mechanistic stress model proposed recently, determined by because mutating packed sites stresses destabilizes protein's active conformation....
An arrangement channel hyperspherical coordinate method for performing quantum scattering calculations on four-atom reactions is formulated. This treats the vibrational and rotational states in different channels by a close-coupling expansion nonorthogonal functions. The applied to calculation of state-to-state probabilities OH+H2→H2O+H reaction. Good agreement found with cumulative state-selected reaction previously calculated other methods. major advantage this general approach that whole...
Six-dimensional (6D) quantum scattering calculations of reaction probabilities are reported for the
The aim of this work was to study the relationship between structure conservation and sequence divergence in protein evolution. To end, we developed a model structurally constrained evolution (SCPE) which trial sequences, generated by random mutations at gene level, are selected against departure from reference three-dimensional structure. Since mutational level SCPE is completely unbiased, any emergent pattern will be due exclusively structural constraints. In first report, it shown that...
Functional and biophysical constraints result in site-dependent patterns of protein sequence variability. It is commonly assumed that the key structural determinant site-specific rates evolution Relative Solvent Accessibility (RSA). However, a recent study found amino acid substitution correlate better with two Local Packing Density (LPD) measures, Weighted Contact Number (WCN) (CN), than RSA. This work aims at more thorough assessment. To this end, addition to rates, we considered four...
It was recently found that the lowest-energy collective normal modes dominate evolutionary divergence of protein structures. This attributed to a presumed functional importance such motions, i.e., natural selection. In contrast this selectionist explanation, we proposed observed behavior could be just expected physical response proteins random mutations. proposal based on success linearly forced elastic network model (LFENM) mutational effects structure account for pattern structural...
The rate of evolution varies among sites within proteins. In enzymes, two gradients are observed: decreases with increasing local packing and it increases distance from catalytic residues. rate-packing gradient would be mainly due to stability constraints is well reproduced by biophysical models selection for protein stability. However, unlikely account the rate-distance gradient. Here, explore mechanistic underpinnings observed in I propose a stability-activity model enzyme evolution, MSA....