24 citations · 63 across the 19 of their papers we have counts for
20 papers · 1 filter
Dark energy: the cost of function in protein evolution
Ezequiel A. Galpern, Federico Caamaño, Ignacio E. Sánchez +1
The evolutionary fate of proteins is driven by both folding stability and biological function, dual constraints that often conflict, creating frustration and imposing functional co…
Probing the Dark Energy in the Functional Protein Universe
Ezequiel A. Galpern, Carlos Bueno, Ignacio E. Sánchez +2
We show how to localize and quantify the functional evolutionary constraints on natural proteins. The method compares the perturbations caused by local sequence variants to the ene…
Predicting protein folding dynamics using sequence information
Ezequiel A. Galpern, Federico Caamaño, Diego U. Ferreiro
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which protei…
Frustration, dynamics and catalysis
R. Gonzalo Parra, Diego U. Ferreiro
The controlled dissipation of chemical potentials is the fundamental way cells make a living. Enzyme-mediated catalysis allows the various transformations to proceed at biologicall…
Frustration In Physiology And Molecular Medicine
R. Gonzalo Parra, Elizabeth A. Komives, Peter G. Wolynes +1
Molecules provide the ultimate language in terms of which physiology and pathology must be understood. Myriads of proteins participate in elaborate networks of interactions and per…
Inferring protein folding mechanisms from natural sequence diversity
Ezequiel A. Galpern, Ernesto A. Roman, Diego U. Ferreiro
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to…
Reassessing the Exon-Foldon correspondence using Frustration Analysis
Ezequiel A. Galpern, Hana Jaafari, Carlos Bueno +2
Protein folding and evolution are intimately linked phenomena. Here, we revisit the concept of exons as potential protein folding modules across 38 abundant and conserved protein f…
Solvent constraints for biopolymer folding and evolution in extraterrestrial environments
Ignacio E. Sánchez, Ezequiel A. Galpern, Diego U. Ferreiro
We propose that spontaneous folding and molecular evolution of biopolymers are two universal aspects that must concur for life to happen. These aspects are fundamentally related to…
Molecular information theory meets protein folding
Ignacio E. Sánchez, Ezequiel A. Galpern, Martín M. Garibaldi +1
We propose an application of molecular information theory to analyze the folding of single domain proteins. We analyze results from various areas of protein science, such as sequen…
From evolution to folding of repeat proteins
Ezequiel A. Galpern, Jacopo Marchi, Thierry Mora +2
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model…
A structural model for the Coronavirus Nucleocapsid
Federico Coscio, Alejandro D. Nadra, Diego U. Ferreiro
We propose a mesoscale model structure for the coronavirus nucleocapsid, assembled from the high resolution structures of the basic building blocks of the N-protein, CryoEM imaging…
Size and structure of the sequence space of repeat proteins
Jacopo Marchi, Ezequiel A. Galpern, Rocio Espada +3
The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family--…
Localization of Energetic Frustration in Proteins
A. Brenda Guzovsky, Nicholas P. Schafer, Peter G. Wolynes +1
We present a detailed heuristic method to quantify the degree of local energetic frustration manifested by protein molecules. Current applications are realized in computational exp…
On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences
Pablo Turjanski, Diego U. Ferreiro
All known terrestrial proteins are coded as continuous strings of ~20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the na…
Frustration, function and folding
Diego U. Ferreiro, Elizabeth A. Komives, Peter G. Wolynes
Natural protein molecules are exceptional polymers. Encoded in apparently random strings of amino-acids, these objects perform clear physical tasks that are rare to find by simple…
Inferring repeat protein energetics from evolutionary information
Rocío Espada, R. Gonzalo Parra, Thierry Mora +2
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown poss…
Protein Repeats from First Principles
Pablo Turjanski, R. Gonzalo Parra, Rocío Espada +2
Some natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repetitions within a single repeat protein can be extreme…
Capturing coevolutionary signals in repeat proteins
Rocío Espada, R. Gonzalo Parra, Thierry Mora +2
The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the cha…
Frustration in Biomolecules
Diego U. Ferreiro, Elizabeth A. Komives, Peter G. Wolynes
Biomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their structures and dynamics using as input…
Detecting Repetitions and Periodicities in Proteins by Tiling the Structural Space
R. Gonzalo Parra, Rocío Espada, Ignacio E. Sánchez +2
The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy Landscape Theory indicates that it is much easi…