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The Two PK_a‘s of Aspartate-85 and Control of Thermal Isomerization and Proton Release in the Arginine-82 to Lysine Mutant of Bacteriorhodopsin

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Biochemistry 1995年第27期34.0卷 8820-8834页

作者： Balashov, Sergei P. Govindjee, Rajni Imasheva, Eleonora S. Misra, Saurav Ebrey, Thomas G. Feng, Yan Crouch, Rosalie K. Menick, Donald R. Department of Cell and Structural Biology Center for Biophysics and Computational Biology University of Illinois at Urbana-Champaign Urbana Illinois 61801 United States Departments of Biochemistry and Molecular Biology Ophthalmology and Medicine Medical University of South Carolina Charleston South Carolina 29425 United States

To explore the role of Arg82 in the catalysis of proton transfer in bacteriorhodopsin, we replaced Arg82 with Lys, which is also positively charged at neutral pH but has an intrinsic pK_a of about 1.7 pH units lower than that of Arg. In the R82K mutant expressed in Halobacterium salinarium, we found the following: (1) The pK_a of the purple-to-blue transition at low pH (which reflects the pK_a Asp85) is 3.6 ±0.1. At high pH a second inflection in the blue-to-purple transition with pK_a = 8.0 is found. The complex titration behavior of Asp85 indicates that the pK_a of Asp85 depends on the protonation state of another amino acid residue, X’, which has a pK_a = 8.0 in R82K. The fit of the experimental data to a model of two interacting residues shows that deprotonation of X’ at high pH causes a shift in the p of Asp85 from 3.7 to 6.0. In turn, protonation of Asp85 decreases the pK_a of X’ by 2.3 pH units. This suggests that X’ can release a proton upon formation of the M intermediate and the concomitant protonation of Asp85 in the photocycle. (2) The rate constant of dark adaptation, k_da, is proportional to the fraction of blue membrane between pH 2 and 10, indicating that thermal isomerization proceeds through the transient protonation of Asp85. The pH dependence of k_da shows that two groups with pK_a1 = 3.9 and pK_a2 = 8.0 control the rate of dark adaptation in R82K. The 1.7 pH unit shift in pk_a2 in R82K compared to the wild type (WT) (pk_a2 = 9.7) supports the hypothesis that X’ is Arg82 in WT and Lys82 in R82K (or at least that these groups are the principal part of a cluster of residues that constitute X'). (3) Under steady state illumination, the efficiency of proton transport in R82K incorporated in phosphatidylcholine vesicles is at least 40% of that in the WT. A flash-induced transient signal of the pH-sensitive dye pyranine is s

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PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures

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Journal of molecular biology 2025年 168963页

作者： Vallat, Brinda Webb, Benjamin M. Zalevsky, Arthur Tangmunarunkit, Hongsuda Sekharan, Monica R. Voinea, Serban Shafaeibejestan, Aref Sagendorf, Jared Hoch, Jeffrey C. Kurisu, Genji Morris, Kyle L. Velankar, Sameer Kesselman, Carl Burley, Stephen K. Berman, Helen M. Sali, Andrej Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine Rutgers The State University of New Jersey Piscataway 08854 NJ United States Rutgers Cancer Institute Rutgers The State University of New Jersey New Brunswick 08901 NJ United States Research Collaboratory for Structural Bioinformatics Protein Data Bank Department of Bioengineering and Therapeutic Sciences Quantitative Biosciences Institute (QBI) Department of Pharmaceutical Chemistry University of California San Francisco. San Francisco 94157 CA United States Information Sciences Institute Viterbi School of Engineering University of Southern California Los Angeles CA United States Biological Magnetic Resonance Data Bank Department of Molecular Biology and Biophysics University of Connecticut Farmington 06030-3305 CT United States Protein Data Bank Japan Institute for Protein Research Osaka University Osaka Suita 565-0871 Japan Electron Microscopy Data Bank European Molecular Biology Laboratory European Bioinformatics Institute Cambridge Hinxton CB10 1SD United Kingdom Protein Data Bank in Europe European Molecular Biology Laboratory European Bioinformatics Institute Cambridge Hinxton CB10 1SD United Kingdom Research Collaboratory for Structural Bioinformatics Protein Data Bank San Diego Supercomputer Center University of California La Jolla 92093 CA United States Department of Chemistry and Chemical Biology Rutgers The State University of New Jersey Piscataway 08854 NJ United States Rutgers Artificial Intelligence and Data Science (RAD) Collaboratory Rutgers The State University of New Jersey Piscataway 08854 NJ United States Department of Quantitative and Computational Biology University of Southern California Los Angeles 90089 CA United States

Structures of many large biomolecular assemblies are now being determined using integrative approaches. In these approaches, information derived from multiple experimental and computational methods is combined to compute three-dimensional structures of multi-protein complexes and other macromolecular machines. A standalone prototype data resource for integrative structures called PDB-Dev was built, based on recommendations of the Integrative and Hybrid Methods (IHM) Task Force of the Worldwide Protein Data Bank (wwPDB). This effort included developing data standards and software tools for collecting, curating, validating, visualizing, archiving, and disseminating integrative structures that span diverse spatiotemporal scales and conformational states. Mechanisms have been created to validate integrative structures based on the experimental data underpinning them. Building upon this foundational framework, PDB-Dev has been further expanded to handle large dynamic macromolecular systems and integrative structures that combine, for example, experimental restraints with atomic coordinates computed by machine learning algorithms. Data standards and supporting tools have also been extended to capture information about biomolecular dynamics, such as conformational transitions and related kinetic data derived from biophysical methods. Recently, PDB-Dev was unified with the PDB archive and rebranded as PDB-IHM (***), further promoting FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data stewardship for integrative structural biology. © 2025 The Author(s)

关键词： IHMCIF integrative modeling PDB PDBx/mmCIF structure validation

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BPS2025 - Exploring the interaction between Kv2.1 and auxiliary AMIGO subunits using computational and experimental approaches

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Biophysical Journal 2025年第3期124卷 602a-602a页

作者： Adrian Koretsky Ana I. Fernández-Mariño Vanessa Leone Xiaofeng Tan Lucy R. Forrest Kenton Swartz National Institute of Neurological Disorders and Stroke National Institutes of Health Bethesda MD USA Molecular Physiology and Biophysics Section National Institute of Neurological Disorders and Stroke National Institutes of Health Bethesda MD USA Computational Structural Biology Section National Institute of Neurological Disorders and Stroke National Institutes of Health Bethesda MD USA National Institutes of Health Bethesda MD USA

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GOAT

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Applied Bioinformatics 2012年第4期4卷 281-283页

作者： Xu, Qikai Shaulsky, Gad Graduate Program in Structural and Computational Biology and Molecular Biophysics Baylor College of Medicine Houston USA Department of Molecular and Human Genetics Baylor College of Medicine Houston USA

Understanding the composition of gene lists that result from high-throughput experiments requires elaborate processing of gene annotation lists. In this article we present GOAT (Gene Ontology Analysis Tool), a tool based on the statistical software ‘R’ for analysing Gene Ontology™ (GO) term enrichment in gene lists. Given a gene list, GOAT calculates the enrichment and statistical significance of every GO term and generates graphical presentations of significantly enriched terms. GOAT works for any organism with a genome-scale GO annotation and allows easy updates of ontologies and annotations.

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Imaging Ice Embedded Single Particles With A 16 Megapixel CCD Camera

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Microscopy and Microanalysis 2003年第S2期9卷 962-963页

作者： Christopher R. Booth Donghua Chen Steven J. Ludtke Wah Chiu Program in Structural and Computational Biology and Molecular Biophysics National Center for Macromolecular Imaging Verna and Marrs McLean Department of Biochemistry and Molecular Biology Baylor College of Medicine Houston Texas 77030 USA

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Going Deeper in Cryo Electron Tomography with Neural Networks

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Microscopy and Microanalysis 2017年第S1期23卷 814-815页

作者： Muyuan Chen Wei Dai Stella Y. Sun Michael F. Schmid Wah Chiu Steven J. Ludtke Graduate Program in Structural and Computational Biology and Molecular Biophysics Baylor College of Medicine Houston TX Verna Marrs and McLean Department of Biochemistry and Molecular Biology Baylor College of Medicine Houston TX

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Simple and robust 3D MINFLUX excitation with a variable phase plate

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Light(Science & Applications) 2024年第7期13卷 1354-1363页

作者： Takahiro Deguchi Jonas Ries European Molecular Biology Laboratory Cell Biology and BiophysicsHeidelbergGermany. Max Perutz Labs Vienna Biocenter Campus(VBC)ViennaAustria. University of Vienna Center for Molecular BiologyDepartment of Structural and Computational BiologyViennaAustria. University of Vienna Faculty of PhysicsViennaAustria

MINFLUX has achieved extraordinary resolution in superresolution imaging and single fluorophore *** is based on localizing single fluorophores by rapid probing with a patterned beam that features a local intensity *** implementations,however,are complex and expensive and are limited in speed and ***,we show that a combination of an electro-optical modulator with a segmented birefringent element such as a spatial light modulator produces a variable phase plate for which the phase can be scanned on the MHz *** or top-hat phase patterns generate high-contrast compact excitation point-spread functions for MINFLUX localization in the x,y,and z-direction,respectively,which can be scanned across a fluorophore within a microsecond,switched within 60 microseconds and alternated among different excitation *** discuss how to compensate for non-optimal performance of the components and present a robust 3D and multi-color MINFLUX excitation module,which we envision as an integral component of a high-performance and cost-effective open-source MINFLUX.

关键词： excitation phase switched

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Statistical measures on residue-level protein structural properties

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Journal of structural and Functional Genomics 2011年第2期12卷 119-136页

作者： Huang, Yuanyuan Bonett, Stephen Kloczkowski, Andrzej Jernigan, Robert Wu, Zhijun Program on Bioinformatics and Computational Biology Iowa State University Ames IA 50014 United States Summer REU Program on Computational Systems Biology Iowa State University Ames IA 50014 United States Department of Biochemistry Biophysics and Molecular Biology Iowa State University Ames IA 50014 United States Department of Mathematics Iowa State University Ames IA 50014 United States

The atomic-level structural properties of proteins, such as bond lengths, bond angles, and torsion angles, have been well studied and understood based on either chemistry knowledge or statistical analysis. Similar properties on the residue-level, such as the distances between two residues and the angles formed by short sequences of residues, can be equally important for structural analysis and modeling, but these have not been examined and documented on a similar scale. While these properties are difficult to measure experimentally, they can be statistically estimated in meaningful ways based on their distributions in known proteins structures. Residue-level structural properties including various types of residue distances and angles are estimated statistically. A software package is built to provide direct access to the statistical data for the properties including some important correlations not previously investigated. The distributions of residue distances and angles may vary with varying sequences, but in most cases, are concentrated in some high probability ranges, corresponding to their frequent occurrences in either α-helices or β-sheets. Strong correlations among neighboring residue angles, similar to those between neighboring torsion angles at the atomic-level, are revealed based on their statistical measures. Residue-level statistical potentials can be defined using the statistical distributions and correlations of the residue distances and angles. Ramachandran-like plots for strongly correlated residue angles are plotted and analyzed. Their applications to structural evaluation and refinement are demonstrated. With the increase in both number and quality of known protein structures, many structural properties can be derived from sets of protein structures by statistical analysis and data mining, and these can even be used as a supplement to the experimental data for structure determinations. Indeed, the statistical measures on various types of residue d

关键词： Protein structural analysis Residue-level structural properties Statistical methods Statistical potentials structural bioinformatics structural correlation plots structural databases

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Dormancy heterogeneity among Arabidopsis thaliana seeds is linked to individual seed size

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Plant Communications 2024年第2期5卷 215-227页

作者： Michal Krzyszton Sebastian P.Sacharowski Veena Halale Manjunath Katarzyna Muter Grzegorz Bokota Ce Wang Dariusz Plewczynski Tereza Dobisova Szymon Swiezewski Laboratory of Seeds Molecular Biology Institute of Biochemistry and BiophysicsPAS02-106 WarsawPoland Laboratory of Functional and Structural Genomics Centre of New TechnologiesUniversity of WarsawWarsawPoland Laboratory of Bioinformatics and Computational Genomics Faculty of Mathematics and Information ScienceWarsaw University of TechnologyWarsawPoland Labdeers Ltd. 680-01 BoskoviceCzech Republic

Production of morphologically and physiologically variable seeds is an important strategy that helps plants to survive in unpredictable natural ***,the model plant Arabidopsis thaliana and most agronomically essential crops produce visually homogenous *** automated phenotype analysis,we observed that small seeds in Arabidopsis tend to have higher primary and secondary dormancy levels than large *** analysis revealed distinct gene expression profiles between large and small *** seeds have higher expression of translation-related genes implicated in germination *** contrast,small seeds have elevated expression of many positive regulators of dormancy,including a key regulator of this process,the DOG1 *** in DOG1 expression are associated with differential production of its alternative cleavage and polyadenylation isoforms;in small seeds,the proximal poly(A)site is selected,resulting in a short mRNA ***,single-seed RNA sequencing analysis demonstrated that large seeds resemble DOG1 knockout mutant ***,on the single-seed level,expression of genes affected by seed size is correlated with expression of genes that position seeds on the path toward *** results demonstrate an unexpected link between seed size and dormancy phenotypes in a species that produces highly homogenous seed pools,suggesting that the correlation between seed morphology and physiology is more widespread than initially assumed.

关键词： seed size dormancy DOG1 Arabidopsis

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Investigation of RNA-RNA Interactions Using the RISE Database

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Current Protocols in Bioinformatics 2018年第1期64卷 e58/1-e58/1页

作者： Ju, Yanyan Gong, Jing Yang, Yucheng T. Zhang, Qiangfeng Cliff MOE Key Laboratory of Bioinformatics Beijing Advanced Innovation Center for Structural Biology Center for Synthetic and Systems Biology Tsinghua-Peking Joint Center for Life Sciences School of Life Sciences Tsinghua University Beijing China Department of Molecular Biophysics and Biochemistry Yale University New Haven CT United States Program in Computational Biology and Bioinformatics Yale University New Haven CT United States

RNA-RNA interactions (RRIs) are essential to understanding the regulatory mechanisms of RNAs. Mapping RRIs in vivo in a transcriptome-wide manner remained challenging until the recent development of several sequencing-based technologies. However, RRIs generated from large-scale studies had not been systematically collected and analyzed before. This article introduces RISE, a database of the RNA Interactome from Sequencing Experiments. RISE provides a comprehensive collection of RRIs in human, mouse, and yeast, derived from transcriptome-wide sequencing experiments, as well as targeted sequencing studies and other public databases/datasets. To facilitate better understanding of the biological roles of these RRIs, RISE also offers rich functional annotations involving RNAs, and an interactive interface to explore the analysis results. Here, we provide a brief description of the RISE website and a step-by-step protocol for using RISE to study RRIs. © 2018 by John Wiley & Sons, Inc. © 2018 John Wiley & Sons, Inc.

关键词： interaction RISE RNA RNA structure RNA-RNA sequencing experiments

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