The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Yingjiu Zhang - One of the best experts on this subject based on the ideXlab platform.
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Crystal Structure of a rhomboid family intramembrane protease
Nature, 2006Co-Authors: Yongcheng Wang, Yingjiu Zhang, Ya HaAbstract:Escherichia coli GlpG is an integral membrane protein that belongs to the widespread rhomboid protease family. Rhomboid proteases, like site-2 protease (S2P) and γ-secretase, are unique in that they cleave the transmembrane domain of other membrane proteins. Here we describe the 2.1 A resolution Crystal Structure of the GlpG core domain. This Structure contains six transmembrane segments. Residues previously shown to be involved in catalysis, including a Ser–His dyad, and several water molecules are found at the protein interior at a depth below the membrane surface. This putative active site is accessible by substrate through a large ‘V-shaped’ opening that faces laterally towards the lipid, but is blocked by a half-submerged loop Structure. These observations indicate that, in intramembrane proteolysis, the scission of peptide bonds takes place within the hydrophobic environment of the membrane bilayer. The Crystal Structure also suggests a gating mechanism for GlpG that controls substrate access to its hydrophilic active site. Rhomboid, γ-secretase and related membrane proteins function specifically within the membrane: many signalling proteins undergo intramembrane proteolysis to become activated, and others are converted to poorly soluble and amyloidal peptide fragments. The Crystal Structure of rhomboid has now been determined, revealing how it utilizes water molecules from outside of the membrane to cleave membrane-embedded protein substrates. This mechanism is likely to be shared by other proteins that catalyse similar reactions. Mutations in one of them, presenilin, are linked to familial Alzheimer's disease. The first description of the Crystal Structure of an intramembrane protease suggests a model where the substrate enters through a gated opening, unfolds, and becomes cleaved inside the membrane-embedded protease.
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Crystal Structure of a rhomboid family intramembrane protease
Nature, 2006Co-Authors: Yongcheng Wang, Yingjiu ZhangAbstract:Escherichia coli GlpG is an integral membrane protein that belongs to the widespread rhomboid protease family. Rhomboid proteases, like site-2 protease (S2P) and gamma-secretase, are unique in that they cleave the transmembrane domain of other membrane proteins. Here we describe the 2.1 A resolution Crystal Structure of the GlpG core domain. This Structure contains six transmembrane segments. Residues previously shown to be involved in catalysis, including a Ser-His dyad, and several water molecules are found at the protein interior at a depth below the membrane surface. This putative active site is accessible by substrate through a large 'V-shaped' opening that faces laterally towards the lipid, but is blocked by a half-submerged loop Structure. These observations indicate that, in intramembrane proteolysis, the scission of peptide bonds takes place within the hydrophobic environment of the membrane bilayer. The Crystal Structure also suggests a gating mechanism for GlpG that controls substrate access to its hydrophilic active site.
Artem R. Oganov - One of the best experts on this subject based on the ideXlab platform.
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How evolutionary Crystal Structure prediction works-and why
Accounts of Chemical Research, 2011Co-Authors: Artem R. Oganov, Andriy O. Lyakhov, Mario ValleAbstract:Once the Crystal Structure of a chemical substance is known, many properties can be predicted reliably and routinely. Therefore if researchers could predict the Crystal Structure of a material before it is synthesized, they could significantly accelerate the discovery of new materials. In addition, the ability to predict Crystal Structures at arbitrary conditions of pressure and temperature is invaluable for the study of matter at extreme conditions, where experiments are difficult.Crystal Structure prediction (CSP), the problem of finding the most stable arrangement of atoms given only the chemical composition, has long remained a major unsolved scientific problem. Two problems are entangled here: search, the efficient exploration of the multidimensional energy landscape, and ranking, the correct calculation of relative energies. For organic Crystals, which contain a few molecules in the unit cell, search can be quite simple as long as a researcher does not need to include many possible isomers or confor...
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modern methods of Crystal Structure prediction
2011Co-Authors: Artem R. OganovAbstract:1. Introduction: The Problem and some basic Concepts 2. Periodic-graph Approaches in Crystal Structure Prediction 3. Energy Landscapes 4. Random and Quasirandom Sampling Methods 5. Simulated Annealing for Crystal Structure Prediction 6. Metadynamics 7. Minima Hopping Methods 8. Evolutionary Algorithms for Crystal Structure Prediction 9. Pathways of Structural Transformations in Reconstructive Phase Transitions: Insights from Transition Path Sampling Molecular Dynamics Appendix "Blind Test" for Inorganic Structure Prediction
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uspex evolutionary Crystal Structure prediction
Computer Physics Communications, 2006Co-Authors: Colin W Glass, Artem R. Oganov, Nikolaus HansenAbstract:We approach the problem of computational Crystal Structure prediction, implementing an evolutionary algorithm—USPEX (Universal Structure Predictor: Evolutionary Xtallography). Starting from chemical composition we have tested USPEX on numerous systems (with up to 80 atoms in the unit cell) for which the stable Structure is known and have observed a success rate of nearly 100%, simultaneously finding large sets of
Yongcheng Wang - One of the best experts on this subject based on the ideXlab platform.
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Crystal Structure of a rhomboid family intramembrane protease
Nature, 2006Co-Authors: Yongcheng Wang, Yingjiu Zhang, Ya HaAbstract:Escherichia coli GlpG is an integral membrane protein that belongs to the widespread rhomboid protease family. Rhomboid proteases, like site-2 protease (S2P) and γ-secretase, are unique in that they cleave the transmembrane domain of other membrane proteins. Here we describe the 2.1 A resolution Crystal Structure of the GlpG core domain. This Structure contains six transmembrane segments. Residues previously shown to be involved in catalysis, including a Ser–His dyad, and several water molecules are found at the protein interior at a depth below the membrane surface. This putative active site is accessible by substrate through a large ‘V-shaped’ opening that faces laterally towards the lipid, but is blocked by a half-submerged loop Structure. These observations indicate that, in intramembrane proteolysis, the scission of peptide bonds takes place within the hydrophobic environment of the membrane bilayer. The Crystal Structure also suggests a gating mechanism for GlpG that controls substrate access to its hydrophilic active site. Rhomboid, γ-secretase and related membrane proteins function specifically within the membrane: many signalling proteins undergo intramembrane proteolysis to become activated, and others are converted to poorly soluble and amyloidal peptide fragments. The Crystal Structure of rhomboid has now been determined, revealing how it utilizes water molecules from outside of the membrane to cleave membrane-embedded protein substrates. This mechanism is likely to be shared by other proteins that catalyse similar reactions. Mutations in one of them, presenilin, are linked to familial Alzheimer's disease. The first description of the Crystal Structure of an intramembrane protease suggests a model where the substrate enters through a gated opening, unfolds, and becomes cleaved inside the membrane-embedded protease.
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Crystal Structure of a rhomboid family intramembrane protease
Nature, 2006Co-Authors: Yongcheng Wang, Yingjiu ZhangAbstract:Escherichia coli GlpG is an integral membrane protein that belongs to the widespread rhomboid protease family. Rhomboid proteases, like site-2 protease (S2P) and gamma-secretase, are unique in that they cleave the transmembrane domain of other membrane proteins. Here we describe the 2.1 A resolution Crystal Structure of the GlpG core domain. This Structure contains six transmembrane segments. Residues previously shown to be involved in catalysis, including a Ser-His dyad, and several water molecules are found at the protein interior at a depth below the membrane surface. This putative active site is accessible by substrate through a large 'V-shaped' opening that faces laterally towards the lipid, but is blocked by a half-submerged loop Structure. These observations indicate that, in intramembrane proteolysis, the scission of peptide bonds takes place within the hydrophobic environment of the membrane bilayer. The Crystal Structure also suggests a gating mechanism for GlpG that controls substrate access to its hydrophilic active site.
Seungwu Han - One of the best experts on this subject based on the ideXlab platform.
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training machine learning potentials for Crystal Structure prediction using disordered Structures
Physical Review B, 2020Co-Authors: Changho Hong, Jeong Min Choi, Wonseok Jeong, Sungwoo Kang, Kyeongpung Lee, Jisu Jung, Yong Youn, Seungwu HanAbstract:Prediction of the stable Crystal Structure for multinary (ternary or higher) compounds with unexplored compositions demands fast and accurate evaluation of free energies in exploring the vast configurational space. The machine-learning potential such as the neural network potential (NNP) is poised to meet this requirement but a dearth of information on the Crystal Structure poses a challenge in choosing training sets. Herein we propose constructing the training set from density functional theory (DFT)--based dynamical trajectories of liquid and quenched amorphous phases, which does not require any preceding information on material Structures except for the chemical composition. To demonstrate suitability of the trained NNP in the Crystal Structure prediction, we compare NNP and DFT energies for ${\mathrm{Ba}}_{2}{\mathrm{AgSi}}_{3}$, ${\mathrm{Mg}}_{2}{\mathrm{SiO}}_{4}$, ${\mathrm{LiAlCl}}_{4}$, and ${\mathrm{InTe}}_{2}{\mathrm{O}}_{5}\mathrm{F}$ over experimental phases as well as low-energy Crystal Structures that are generated theoretically. For every material, we find strong correlations between DFT and NNP energies, ensuring that the NNPs can properly rank energies among low-energy Crystalline Structures. We also find that the evolutionary search using the NNPs can identify low-energy metastable phases more efficiently than the DFT-based approach. By proposing a way to developing reliable machine-learning potentials for the Crystal Structure prediction, this work paves the way to identifying unexplored multinary phases efficiently.
Ya Ha - One of the best experts on this subject based on the ideXlab platform.
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Crystal Structure of a rhomboid family intramembrane protease
Nature, 2006Co-Authors: Yongcheng Wang, Yingjiu Zhang, Ya HaAbstract:Escherichia coli GlpG is an integral membrane protein that belongs to the widespread rhomboid protease family. Rhomboid proteases, like site-2 protease (S2P) and γ-secretase, are unique in that they cleave the transmembrane domain of other membrane proteins. Here we describe the 2.1 A resolution Crystal Structure of the GlpG core domain. This Structure contains six transmembrane segments. Residues previously shown to be involved in catalysis, including a Ser–His dyad, and several water molecules are found at the protein interior at a depth below the membrane surface. This putative active site is accessible by substrate through a large ‘V-shaped’ opening that faces laterally towards the lipid, but is blocked by a half-submerged loop Structure. These observations indicate that, in intramembrane proteolysis, the scission of peptide bonds takes place within the hydrophobic environment of the membrane bilayer. The Crystal Structure also suggests a gating mechanism for GlpG that controls substrate access to its hydrophilic active site. Rhomboid, γ-secretase and related membrane proteins function specifically within the membrane: many signalling proteins undergo intramembrane proteolysis to become activated, and others are converted to poorly soluble and amyloidal peptide fragments. The Crystal Structure of rhomboid has now been determined, revealing how it utilizes water molecules from outside of the membrane to cleave membrane-embedded protein substrates. This mechanism is likely to be shared by other proteins that catalyse similar reactions. Mutations in one of them, presenilin, are linked to familial Alzheimer's disease. The first description of the Crystal Structure of an intramembrane protease suggests a model where the substrate enters through a gated opening, unfolds, and becomes cleaved inside the membrane-embedded protease.
