14 hasil untuk "Coluzza, Ivan"
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Artikel Jurnal Teks lengkap
A Coarse-Grained Approach to Protein Design: Learning from Design to Understand Folding
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…
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Artikel Jurnal Teks lengkap
Transferable Coarse-Grained Potential for De Novo Protein Folding and Design
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…
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Artikel Jurnal Teks lengkap
Monte Carlo Study of Substrate-Induced Folding and Refolding of Lattice Proteins
Many proteins can switch from one conformation to another under the influence of an external driving force, such as the binding to a specific substrate. Using a simple lattice model we show that it is feasible to design protein-like lattice proteins that can have two different conformations…
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Artikel Jurnal Teks lengkap
Assessment of the MARTINI 3 Performance for Short Peptide Self-Assembly
[Image: see text] The coarse-grained MARTINI force field, initially developed for membranes, has proven to be an exceptional tool for investigating supramolecular peptide assemblies. Over the years, the force field underwent refinements to enhance accuracy, enabling, for example, the reproduction…
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Artikel Jurnal Teks lengkap
Translocation Boost Protein-Folding Efficiency of Double-Barreled Chaperonins
Incorrect folding of proteins in living cells may lead to malfunctioning of the cell machinery. To prevent such cellular disasters from happening, all cells contain molecular chaperones that assist nonnative proteins in folding into the correct native structure. One of the most studied chaperone…
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Artikel Jurnal Teks lengkap
Multi-Scale Simulations Provide Supporting Evidence for the Hypothesis of Intramolecular Protein Translocation in GroEL/GroES Complexes
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…
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Artikel Jurnal Teks lengkap
Protein design under competing conditions for the availability of amino acids
Isolating the properties of proteins that allow them to convert sequence into the structure is a long-lasting biophysical problem. In particular, studies focused extensively on the effect of a reduced alphabet size on the folding properties. However, the natural alphabet is a compromise between…
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Artikel Jurnal Teks lengkap
Designing proteins: Mimicking natural protein sequence heterogeneity
This study presents an enhanced protein design algorithm that aims to emulate natural heterogeneity of protein sequences. Initial analysis revealed that natural proteins exhibit a permutation composition lower than the theoretical maximum, suggesting a selective utilization of the 20-letter amino…
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Artikel Jurnal Teks lengkap
Machine learning in biological physics: From biomolecular prediction to design
Machine learning has been proposed as an alternative to theoretical modeling when dealing with complex problems in biological physics. However, in this perspective, we argue that a more successful approach is a proper combination of these two methodologies. We discuss how ideas coming from physical…
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Artikel Jurnal Teks lengkap
Analytic Markovian Rates for Generalized Protein Structure Evolution
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…
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Artikel Jurnal Teks lengkap
Author Correction: The role of directional interactions in the designability of generalized heteropolymers
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Artikel Jurnal Teks lengkap
The role of directional interactions in the designability of generalized heteropolymers
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 criterion…
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Artikel Jurnal Teks lengkap
Correction to “Targeting the Spike: Repurposing Mithramycin and Dihydroergotamine to Block SARS-CoV-2 Infection”
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Artikel Jurnal Teks lengkap
Targeting the Spike: Repurposing Mithramycin and Dihydroergotamine to Block SARS-CoV-2 Infection
[Image: see text] The urgency to find complementary therapies to current SARS-CoV-2 vaccines, whose effectiveness is preserved over time and not compromised by the emergence of new and emerging variants, has become a critical health challenge. We investigate the possibility of jamming the opening…