Search Results - "Gosavi, Shachi"
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Understanding the folding-function tradeoff in proteins
Published in PloS one (12-04-2013)“…When an amino-acid sequence cannot be optimized for both folding and function, folding can get compromised in favor of function. To understand this tradeoff…”
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A five-residue motif for the design of domain swapping in proteins
Published in Nature communications (28-01-2019)“…Domain swapping is the process by which identical monomeric proteins exchange structural elements to generate dimers/oligomers. Although engineered domain…”
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The diversity of protein-protein interaction interfaces within T=3 icosahedral viral capsids
Published in Frontiers in molecular biosciences (20-10-2022)“…Some non-enveloped virus capsids assemble from multiple copies of a single type of coat-protein (CP). The comparative energetics of the diverse CP-CP…”
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4
Amino‐acid composition after loop deletion drives domain swapping
Published in Protein science (01-10-2017)“…Rational engineering of a protein to enable domain swapping requires an understanding of the sequence, structural and energetic factors that favor the…”
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Designed protein reveals structural determinants of extreme kinetic stability
Published in Proceedings of the National Academy of Sciences - PNAS (24-11-2015)“…The design of stable, functional proteins is difficult. Improved design requires a deeper knowledge of the molecular basis for design outcomes and properties…”
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A Method for Assessing the Robustness of Protein Structures by Randomizing Packing Interactions
Published in Frontiers in molecular biosciences (27-06-2022)“…Many single-domain proteins are not only stable and water-soluble, but they also populate few to no intermediates during folding. This reduces interactions…”
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In the multi-domain protein adenylate kinase, domain insertion facilitates cooperative folding while accommodating function at domain interfaces
Published in PLoS computational biology (01-11-2014)“…Having multiple domains in proteins can lead to partial folding and increased aggregation. Folding cooperativity, the all or nothing folding of a protein, can…”
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Extracting function from a β-trefoil folding motif
Published in Proceedings of the National Academy of Sciences - PNAS (29-07-2008)“…Despite having remarkably similar three-dimensional structures and stabilities, IL-1β promotes signaling, whereas IL-1Ra inhibits it. Their energy landscapes…”
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Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity
Published in Frontiers in molecular biosciences (08-02-2023)“…Kinetic stability, defined as the rate of protein unfolding, is central to determining the functional lifetime of proteins, both in nature and in wide-ranging…”
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Structure dictates the mechanism of ligand recognition in the histidine and maltose binding proteins
Published in Current research in structural biology (01-01-2020)“…Two mechanisms, induced fit (IF) and conformational selection (CS), have been proposed to explain ligand recognition coupled conformational changes. The…”
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Nonadiabatic Electron Transfer at Metal Surfaces
Published in The journal of physical chemistry. B (09-03-2000)“…The present article treats the role of the density of electronic states ρF at the Fermi level of a metal in affecting the rate of nonadiabatic electron…”
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β-Bulge triggers route-switching on the functional landscape of interleukin-1β
Published in Proceedings of the National Academy of Sciences - PNAS (31-01-2012)“…Proteins fold into three-dimensional structures in a funneled energy landscape. This landscape is also used for functional activity. Frustration in this…”
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Folding circular permutants of IL-1β: route selection driven by functional frustration
Published in PloS one (05-06-2012)“…Interleukin-1β (IL-1β) is the cytokine crucial to inflammatory and immune response. Two dominant routes are populated in the folding to native structure. These…”
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Multiple Routes Lead to the Native State in the Energy Landscape of the β-Trefoil Family
Published in Proceedings of the National Academy of Sciences - PNAS (05-07-2006)“…In general, the energy landscapes of real proteins are sufficiently well designed that the depths of local energetic minima are small compared with the global…”
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15
dual-basin landscape in GFP folding
Published in Proceedings of the National Academy of Sciences - PNAS (26-08-2008)“…Recent experimental studies suggest that the mature GFP has an unconventional landscape composed of an early folding event with a typical funneled landscape,…”
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Protein Folding and Conformational Frustration
Published in Biophysical journal (07-02-2020)Get full text
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Potential Self-Peptide Inhibitors of the SARS-CoV‑2 Main Protease
Published in The journal of physical chemistry. B (02-02-2023)“…The SARS-CoV-2 main protease (Mpro) plays an essential role in viral replication, cleaving viral polyproteins into functional proteins. This makes Mpro an…”
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Editorial overview: Molecular interactions that drive folding and binding: new challenges and opportunities
Published in Current opinion in structural biology (01-02-2020)Get full text
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Conformational Transitions in Adenylate Kinase
Published in The Journal of biological chemistry (25-01-2008)“…Large conformational changes in the LID and NMP domains of adenylate kinase (AKE) are known to be key to ligand binding and catalysis, yet the order of binding…”
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Functionally Relevant Specific Packing Can Determine Protein Folding Routes
Published in Journal of molecular biology (29-01-2016)“…Functional residues can modulate the folding mechanisms of proteins. In some proteins, mutations to such residues can radically change the primary folding…”
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