107 Result(s)
within
Michele Vendruscolo
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Article
Three key residues form a critical contact network in a protein folding transition state
Determining how a protein folds is a central problem in structural biology. The rate of folding of many proteins is determined by the transition state, so that a knowledge of its structure is essential for und...
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Statistical Properties of Neutral Evolution
Neutral evolution is the simplest model of molecular evolution and thus it is most amenable to a comprehensive theoretical investigation. In this paper, we characterize the statistical properties of neutral ev...
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Transition states for protein folding have native topologies despite high structural variability
We present a structural analysis of the folding transition states of three SH3 domains. Our results reveal that the secondary structure is not yet fully formed at this stage of folding and that the solvent is ...
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Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR
Many biochemical processes proceed through the formation of functionally significant intermediates1,2. Although the identification and characterization of such species can provide vital clues about the mechanisms...
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Simultaneous determination of protein structure and dynamics
We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengt...
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Interpreting Dynamically-Averaged Scalar Couplings in Proteins
The experimental determination of scalar three-bond coupling constants represents a powerful method to probe both the structure and dynamics of proteins. The detailed structural interpretation of such coupling...
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Open AccessA protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank
Since thermodynamic stability is a global property of proteins that has to be conserved during evolution, the selective pressure at a given site of a protein sequence depends on the amino acids present at othe...
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The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins
While reliable procedures for determining the conformations of proteins are available, methods for generating ensembles of structures that also reflect their flexibility are much less well established. Here we...
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More charges against aggregation
Protein aggregation causes problems for biotechnology and leads to many fatal human diseases. But a grasp of the physical principles involved enables 'superproteins' to be designed that have exceptional solubi...
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Protein dynamics under light control
A stochastic view of allostery is providing quantitative estimates of the energy made available through protein photoswitches.
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Open AccessCompetition between protein aggregation and protein complex formation
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Open AccessStochastic reconstruction of protein structures from effective connectivity profiles
We discuss a stochastic approach for reconstructing the native structures of proteins from the knowledge of the "effective connectivity", which is a one-dimensional structural profile constructed as a linear c...
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The mechanism of folding of Im7 reveals competition between functional and kinetic evolutionary constraints
Im7 is a small Escherichia coli colicin binding protein that uses a remarkably complex folding pathway. Analysis of the Im7 folding landscape reveals details of the earliest transition state in its folding pathwa...
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Structural characterization of a misfolded intermediate populated during the folding process of a PDZ domain
A high-resolution structure of an off-pathway misfolded intermediate state of a PDZ domain is now obtained, through a combination of phi-value analysis and computational modeling. The structure reveals that a ...
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The statistical theory of allostery
The combination of NMR spectroscopy and statistical mechanics represents a powerful approach to characterize the behavior of macromolecules. Two recent studies demonstrate that the application of this strategy...
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Structure-based prediction of methyl chemical shifts in proteins
Protein methyl groups have recently been the subject of much attention in NMR spectroscopy because of the opportunities that they provide to obtain information about the structure and dynamics of proteins and ...
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Article
1H, 13C and 15N resonance assignments of human muscle acylphosphatase
Human muscle acylphosphatase (mAcP) is an enzyme with a ferrodoxin-like topology whose primary role is to hydrolyze the carboxyl-phosphate bonds of acylphosphates. The protein has been widely used as a model s...
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Prediction of variable translation rate effects on cotranslational protein folding
The concomitant folding of a protein with its synthesis on the ribosome is influenced by a number of different timescales including the translation rate. Here we present a kinetic formalism to describe cotrans...
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Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings
Residual dipolar couplings (RDCs) have the potential of providing detailed information about the conformational fluctuations of proteins. It is very challenging, however, to extract such information because of...
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Erratum: Prediction of variable translation rate effects on cotranslational protein folding
Nature Communications 3: Article number: 868 (2012); Published: 29 May 2012; Updated: 26 February 2013. This article contains typographical errors in equations (3) and (4) that were introduced during the produ...
