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Results 11 - 20
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357
Distance Geometry Generates Native-Like Folds for Small Helical Proteins Using the Consensus Distances of Predicted Protein Structures
, 1998
"... For successful ab initio protein structure prediction, a method is needed to identify native-like structures from a set containing both native and non-native protein-like conformations. In this regard, the use of distance geometry has shown promise when accurate inter-residue distances are available ..."
Abstract
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Cited by 14 (8 self)
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For successful ab initio protein structure prediction, a method is needed to identify native-like structures from a set containing both native and non-native protein-like conformations. In this regard, the use of distance geometry has shown promise when accurate inter-residue distances
Comparison of Solution Structures and Stabilities of Native, Partially Unfolded and Partially Refolded Pepsin†
, 2006
"... ABSTRACT: A zymogen-derived protein, pepsin, appears to be incapable of folding to the native state without the presence of the prosegment. To better understand the nature of the irreversible denaturation of pepsin, the present study reports on the characterization of the stability and low-resolutio ..."
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Cited by 1 (1 self)
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-refolded pepsin (>10 mg/mL) (CRp) were native-like, in contrast to the intermediate nature of Rp, refolded under dilute concentration (<10 mg/mL). Despite a native-like conformation, CRp was more stable and had substantially reduced activity compared to that of the native state, suggesting that the protein
Scoring Functions for De Novo Protein Structure Prediction Revisited
"... De novo protein structure prediction methods attempt to predict tertiary structures from sequences based on general principles that govern protein folding energetics and/or statistical tendencies of conformational features that native structures acquire, without the use of explicit templates. A gene ..."
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general paradigm for de novo prediction involves sampling the conformational space, guided by scoring functions and other sequence-dependent biases, such that a large set of candidate (“decoy”) structures are generated, and then selecting native-like conformations from those decoys using scoring functions
Poster Presentation: Protein Folding Simulation in CCP
"... Background. A protein is a list of linked units called aminoacids. There are 20 different kinds of aminoacids and the typical length of a protein is 100–500 units. The Protein Structure Prediction Problem (PSP) is the problem of predicting the 3D native conformation of a protein, when its aminoacid ..."
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. We can identify two main problems: the first is to choose a representation of the protein and an energy function, which must be at minimum for native-like conformations. The second is, given the representation and the energy function, to find the 3D conformation that minimizes the function. Due
Iterative Molecular DynamicsRosetta Protein Structure Refinement Protocol to Improve Model Quality
"... ABSTRACT: Rosetta is one of the prime tools for high resolution protein structure refinement. While its scoring func-tion can distinguish native-like from non-native-like conforma-tions in many cases, the method is limited by conformational sampling for larger proteins, that is, leaving a local ener ..."
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Cited by 1 (0 self)
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ABSTRACT: Rosetta is one of the prime tools for high resolution protein structure refinement. While its scoring func-tion can distinguish native-like from non-native-like conforma-tions in many cases, the method is limited by conformational sampling for larger proteins, that is, leaving a local
Optimization of Potential-Energy Parameters for Folding of Several Proteins
, 2003
"... We introduce a novel approach to the study of the folding of proteins whose native structures are already known. We use an off-lattice atomistic potential energy. The parameters of the potential energy are simultaneously optimized for several proteins. The low-lying local-energy minima for these pro ..."
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for these proteins are found by conformational space annealing. The parameters are modified in such a way that the native-like conformations are energetically more favored than the others. After the parameter optimization, one set of the parameters is obtained for the proteins. We then investigate Monte Carlo
Protein structure prediction based on fragment assembly and parameter optimization
, 2005
"... We propose a novel method for ab-initio prediction of protein tertiary structures based on the fragment assembly and global optimization. Fifteen residue long fragment libraries are constructed using the secondary structure prediction method PREDICT, and fragments in these libraries are assembled to ..."
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the performance of the prediction method, we optimize the linear parameters of the energy function, so that the native-like conformations become energetically more favorable than the non-native ones for proteins with known structures. We test the feasibility of the parameter optimization procedure by applying
Folding simulations of small proteins
, 2005
"... Understanding how a protein folds is a long-standing challenge in modern science. We have used an optimized atomistic model (unitedresidue force field) to simulate folding of small proteins of various structures: HP-36 (a protein), protein A (h), 1fsd (a+h), and betanova (h). Extensive Monte Carlo f ..."
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folding simulations (ten independent runs with 10 9 Monte Carlo steps at a temperature) starting from non-native conformations are carried out for each protein. In all cases, proteins fold into their native-like conformations at appropriate temperatures, and glassy transitions occur at low temperatures
Progress and challenges in high-resolution refinement of protein structure models
- Proteins
, 2005
"... ABSTRACT Achieving atomic level accuracy in de novo structure prediction presents a formidable challenge even in the context of protein models with correct topologies. High-resolution refinement is a fundamental test of force field accuracy and sampling methodology, and its limited success in both c ..."
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Cited by 40 (10 self)
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on their energies, and in several cases many of the buried side chains adopted native-like conformations. We also showed that the differences in backbone and side-chain conformations between the refined de novo models and the native structures are largely localized to loop regions and regions where the native
Liposome-Mediated Cellular Delivery of Active gp91 phox
"... Background. Gp91 phox is a transmembrane protein and the catalytic core of the NADPH oxidase complex of neutrophils. Lack of this protein causes chronic granulomatous disease (CGD), a rare genetic disorder characterized by severe and recurrent infections due to the incapacity of phagocytes to kill m ..."
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Cited by 2 (0 self)
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with a ‘‘native-like’ ’ conformation. All the proteins exhibit diaphorase activity in the presence of cytosolic factors (p67 phox, p47 phox, p40 phox and Rac) and arachidonic acid. We also produce proteoliposomes containing gp91 phox protein and demonstrate that these proteins exhibit activities similar
Results 11 - 20
of
357
