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Luciano Andres Abriata

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Related publications (71)

Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes

Matteo Dal Peraro, Luciano Andres Abriata, Alexander Mayorov

A recent analysis of evolutionary rates in >500 globular soluble enzymes revealed pervasive conservation gradients toward catalytic residues. By looking at amino acid preference profiles rather than evolutionary rates in the same data set, we quantified th ...

OXFORD UNIV PRESS2019

A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments

Matteo Dal Peraro, Luciano Andres Abriata, Giorgio Elikem Tamo

We present our assessment of tertiary structure predictions for hard targets in Critical Assessment of Structure Prediction round 13 (CASP13). The analysis includes (a) assignment and discussion of best models through scores-aided visual inspection of mode ...

WILEY2019

Computational Tools for Structural Analysis of Proteins

Luciano Andres Abriata

This article deals with computational tools for the analysis of protein structures, and how they bring information about dynamic and functional aspects of proteins. A focus on online tools is intentional given their ease of use, but important tools availab ...

Elsevier2019

An experiment-informed signal transduction model for the role of the Staphylococcus aureus MecR1 protein in beta-lactam resistance

Matteo Dal Peraro, Luciano Andres Abriata

The treatment of hospital- and community-associated infections by methicillin-resistant Staphylococcus aureus (MRSA) is a perpetual challenge. This Gram-positive bacterium is resistant specifically to beta-lactam antibiotics, and generally to many other an ...

Springer Nature2019

Transmembrane Prolines Mediate Signal Sensing and Decoding in Bacillus subtilis DesK Histidine Kinase

Matteo Dal Peraro, Luciano Andres Abriata

Environmental awareness is an essential attribute of all organisms. The homeoviscous adaptation system of Bacillus subtilis provides a powerful experimental model for the investigation of stimulus detection and signaling mechanisms at the molecular level. ...

2019

Assessment of data-assisted prediction by inclusion of crosslinking/mass-spectrometry and small angle X-ray scattering data in the 12(th) Critical Assessment of protein Structure Prediction experiment

Matteo Dal Peraro, Luciano Andres Abriata, Giorgio Elikem Tamo, Giulia Fonti

2018

Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods

Matteo Dal Peraro, Luciano Andres Abriata, Giorgio Elikem Tamo

2018

Augmenting Research, Education, and Outreach with Client-Side Web Programming

Luciano Andres Abriata, Marcel Salathé

2018

Definition and classification of evaluation units for tertiary structure prediction in CASP12 facilitated through semi-automated metrics

Matteo Dal Peraro, Luciano Andres Abriata, Giorgio Elikem Tamo

2018

Electron transfer in an acidophilic bacterium: interaction between a diheme cytochrome and a cupredoxin

Luciano Andres Abriata, Xi Wang

2018

Mitochondrial cytochrome c oxidase biogenesis: Recent developments

Luciano Andres Abriata

2018

Nucleo-cytosolic Shuttling of ARGONAUTE1 Prompts a Revised Model of the Plant MicroRNA Pathway

Matteo Dal Peraro, Luciano Andres Abriata

2018

Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics

Matteo Dal Peraro, Enrico Spiga, Luciano Andres Abriata

Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known e ...

Cell Press2016

Immobilization of the N-terminal helix stabilizes prefusion paramyxovirus fusion proteins

Matteo Dal Peraro, Luciano Andres Abriata, Albert Sanghoon Song

Parainfluenza virus 5 (PIV5) is an enveloped, single-stranded, negative-sense RNA virus of the Paramyxoviridae family. PIV5 fusion and entry are mediated by the coordinated action of the receptor-binding protein, hemagglutinin-neuraminidase (HN), and the f ...

National Academy of Sciences2016

Optimization of Conformational Dynamics in an Epistatic Evolutionary Trajectory

Luciano Andres Abriata

The understanding of protein evolution depends on the ability to relate the impact of mutations on molecular traits to organismal fitness. Biological activity and robustness have been regarded as important features in shaping protein evolutionary landscape ...

Oxford Univ Press2016

XacFhaB adhesin, an important Xanthomonas citri ssp citri virulence factor, is recognized as a pathogen-associated molecular pattern

Luciano Andres Abriata

Adhesion to host tissue is one of the key steps of the bacterial pathogenic process. Xanthomonas citri ssp. citri possesses a non-fimbrial adhesin protein, XacFhaB, required for bacterial attachment, which we have previously demonstrated to be an important ...

Wiley-Blackwell2016

Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server

Matteo Dal Peraro, Christophe Bovigny, Luciano Andres Abriata

Background: Protein variability can now be studied by measuring high-resolution tolerance-to-substitution maps and fitness landscapes in saturated mutational libraries. But these rich and expensive datasets are typically interpreted coarsely, restricting d ...

2016

Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server(vol 1, 242, 2016)

Matteo Dal Peraro, Christophe Bovigny, Luciano Andres Abriata

2016

How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme

Matteo Dal Peraro, Luciano Andres Abriata

The need for interfacing structural biology and biophysics to molecular evolution is being increasingly recognized. One part of the big problem is to understand how physics and chemistry shape the sequence space available to functional proteins, while sati ...

Public Library Science2015

GtrA Protein Rv3789 Is Required for Arabinosylation of Arabinogalactan in Mycobacterium tuberculosis

Gaëlle Séraphine Kolly, Stewart Cole, Claudia Sala, Matteo Dal Peraro, Mahé Cécile Raccaud, Raju Mukherjee, Luciano Andres Abriata

Mycobacterium tuberculosis possesses a thick and highly hydrophobic cell wall principally composed of a mycolyl-arabinogalactan-peptidoglycan complex, which is critical for survival and virulence. DprE1 is a well-characterized component of decaprenyl-phosp ...

American Society for Microbiology2015

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