15 results for "Ivan Coluzza"

A coarse-grained approach to protein design: learning from design to understand folding.

Ivan Coluzza

PLoS ONE, Vol. 6 No. 7 · 2011 · English · DOAJ Scopus

Computational studies have given a great contribution in building our current understanding of the complex behavior of protein molecules; nevertheless, a complete characterization of their free energy landscape still represents a major challenge. Here, we introduce a new coarse-grained approach…

Also available at: PLOS

Transferable coarse-grained potential for de novo protein folding and design.

Ivan Coluzza

PLoS ONE, Vol. 9 No. 12 · 2014 · English · DOAJ Scopus

Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here we provide evidence of how a novel parametrization of the Caterpillar model may be used for both quantitative protein design and folding. With computer…

Also available at: PLOS

Virtual-move Parallel Tempering

Frenkel, Ivan Coluzza Daan

arXiv · 2005 · English · arXiv

We report a novel Monte Carlo scheme that greatly enhances the power of parallel-tempering simulations. In this method, we boost the accumulation of statistical averages by including information about all potential parallel tempering trial moves, rather than just those trial moves that are…

Role of Water in the Selection of Stable Proteins at Ambient and Extreme Thermodynamic Conditions

Valentino Bianco; Giancarlo Franzese; Christoph Dellago et al.

Physical Review X, Vol. 7 No. 2 · 2017 · English · DOAJ Scopus

Proteins that are functional at ambient conditions do not necessarily work at extreme conditions of temperature T and pressure P. Furthermore, there are limits of T and P above which no protein has a stable functional state. Here, we show that these limits and the selection mechanisms for working…

Multi-scale simulations provide supporting evidence for the hypothesis of intramolecular protein translocation in GroEL/GroES complexes.

Ivan Coluzza; Alfonso De Simone; Franca Fraternali et al.

PLoS Computational Biology, Vol. 4 No. 2 · 2008 · English · DOAJ Scopus

The biological function of chaperone complexes is to assist the folding of non-native proteins. The widely studied GroEL chaperonin is a double-barreled complex that can trap non-native proteins in one of its two barrels. The ATP-driven binding of a GroES cap then results in a major structural…

Also available at: PLOS

Hierarchical self-assembly of telechelic star polymers: from soft patchy particles to gels and diamond crystals

Barbara Capone; Ivan Coluzza; Ronald Blaak et al.

New Journal of Physics, Vol. 15 No. 9 · 2013 · English · DOAJ Scopus

The design of self-assembling materials in the nanometer scale focuses on the fabrication of a class of organic and inorganic subcomponents that can be reliably produced on a large scale and tailored according to their vast applications for, e.g. electronics, therapeutic vectors and diagnostic…

Analytic Markovian Rates for Generalized Protein Structure Evolution

Ivan Coluzza; James T. MacDonald; Michael I. Sadowski et al.

PLoS ONE, Vol. 7 No. 5 · 2012 · English · PLOS Scopus

A general understanding of the complex phenomenon of protein evolution requires the accurate description of the constraints that define the sub-space of proteins with mutations that do not appreciably reduce the fitness of the organism. Such constraints can have multiple origins, in this work we…

Also available at: DOAJ

The role of directional interactions in the designability of generalized heteropolymers

Chiara Cardelli; Valentino Bianco; Lorenzo Rovigatti et al.

Scientific Reports, Vol. 7 No. 1 · 2017 · English · DOAJ Scopus

Abstract Heteropolymers are important examples of self-assembling systems. However, in the design of artificial heteropolymers the control over the single chain self-assembling properties does not reach that of the natural bio-polymers, and in particular proteins. Here, we introduce a sufficiency…

Targeting the Spike: Repurposing Mithramycin and Dihydroergotamine to Block SARS-CoV‑2 Infection

Soledad Stagnoli; Gabriele Macari; Pietro Corsi et al.

ACS Omega, Vol. 8 No. 46 · 2023 · English · DOAJ Scopus

Correction to “Targeting the Spike: Repurposing Mithramycin and Dihydroergotamine to Block SARS-CoV‑2 Infection”

Soledad Stagnoli; Gabriele Macari; Pietro Corsi et al.

ACS Omega, Vol. 9 No. 4 · 2024 · English · DOAJ Scopus

Perspectives on the Future of Ice Nucleation Research: Research Needs and Unanswered Questions Identified from Two International Workshops

Ivan Coluzza; Jessie Creamean; Michel J. Rossi et al.

Atmosphere, Vol. 8 No. 8 · 2017 · English · DOAJ Scopus

There has been increasing interest in ice nucleation research in the last decade. To identify important gaps in our knowledge of ice nucleation processes and their impacts, two international workshops on ice nucleation were held in Vienna, Austria in 2015 and 2016. Experts from these workshops…