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Structural biology

About: Structural biology is a research topic. Over the lifetime, 2206 publications have been published within this topic receiving 126070 citations.


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Journal ArticleDOI
15 Jan 2020
TL;DR: It is shown that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases.
Abstract: This is a review of relevant Raman spectroscopy (RS) techniques and their use in structural biology, biophysics, cells, and tissues imaging towards development of various medical diagnostic tools, drug design, and other medical applications. Classical and contemporary structural studies of different water-soluble and membrane proteins, DNA, RNA, and their interactions and behavior in different systems were analyzed in terms of applicability of RS techniques and their complementarity to other corresponding methods. We show that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases. In particular, the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS), which would help to further the development of protein structural crystallography and would result in a number of novel high-resolution structures of membrane proteins—drug targets; and, structural studies of photoactive membrane proteins (rhodopsins, photoreceptors, etc.) for the development of new optogenetic tools. Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed. All of these techniques have been extensively developed during recent several decades. A number of interesting applications of CARS, resonant, and surface-enhanced Raman spectroscopy methods are also discussed.

25 citations

BookDOI
15 Jun 2011
TL;DR: The P. pastoris Expression System Successful Large-Scale Expression of Membrane Proteins Using P. pastors as a Biotechnological Tool and Future Perspectives are presented.
Abstract: Preface INTRODUCTION Expression Solubilization and Structural Methods Abbreviations PART I: Expression Systems BACTERIAL SYSTEMS Introduction Understanding the Problem Vector/Promoter Types T7 Expression System Tunable T7 Expression Systems Other Useful Membrane Protein Expression Strains Clone Stability Media Types Fusion Partners/Membrane Targeting Peptides Chaperone Overexpression Cautionary Notes Related to Chaperone Overexpression Emerging Role of Quality Control Proteases Tag Selection Potential Expression Yield Strategies to Overcome Protein Instability MEMBRANE PROTEIN EXPRESSION IN SACCHAROMYCES CEREVISIAE Introduction Getting Started Special Considerations Case Studies Conclusions EXPRESSION SYSTEMS: PICHIA PASTORIS Introduction A (Brief) Summary on the (Long) History of P. pastoris Introducing P. pastoris as a Biotechnological Tool: Its (Extended) Strengths and (Limited) Weaknesses Basics of the P. pastoris Expression System Successful Large-Scale Expression of Membrane Proteins Using P. pastoris Guidelines for Optimizing Membrane Protein Expression in P. pastoris Using GPCRs as Models Conclusions and Future Directions HETEROLOGOUS PRODUCTION OF ACTIVE MAMMALIAN G-PROTEIN-COUPLED RECEPTORS USING BACULOVIRUS-INFECTED INSECT CELLS Introduction Experimental Conclusions and Future Perspectives MEMBRANE PROTEIN EXPRESSION IN MAMMALIAN CELLS Introduction Mammalian Systems Case Studies Conclusions MEMBRANE PROTEIN PRODUCTING USING PHOTOSYNTHETIC BACTERIA: A PRACTICAL GUIDE Introduction Preparation of Expression Constructs Transfer of Plasmid DNA to Rhodobacter via Conjugal Mating Small-Scale Screening for Expression and Localization of Target Protein in Rhodobacter Large-Scale Culture Detergent Solubilization and Chromatographic Purification of Expressed Membrane Proteins Protein Identification and Assessment of Purity Preparations of Specialized Rhodobacter Membranes Appendix: Media and Buffer Formulations PART II: Protein-Specific Considerations PERIPHERAL MEMBRANE PROTEIN PRODUCTION FOR STRUCTURAL AND FUNCTIONAL STUDIES Introduction Case Studies of Peripheral Membrane Proteins Conclusions EXPRESSION OF G-PROTEIN-COUPLED RECEPTORS Introduction Bacterial Expression of GPCRs Expression of GPCrs in Inclusion Bodies and Refolding Expression of GPCrs in Yeast Expression of GPCrs in Insect Cells Expression of GPCrs in Mammalian Cell Lines Expression of GPCrs in Retina Rod Cells Expression of GPCrs in a Cell-Free System Stabilization of GPCrs during Solubilization and Purification Conclusions STRUCTURAL BIOLOGY OF MEMBRANE PROTEINS Introduction Folding and Structural Analysis of Membrane Proteins Test Cases PART III: Emerging Methods and Approaches ENGINEERING INTEGRAL MEMBRANE PROTEINS FOR EXPRESSION AND STABILITY Introduction Engineering Higher Expression Engineering Higher Stability Conclusions EXPRESSION AND PURIFICATION OF G-PROTEIN-COUPLED RECEPTORS FOR NUCLEAR MAGNETIC RESONANCE STRUCTURAL STUDIES Introduction: G-Protein-Coupled Receptor Superfamily CXCR1 GPCR Structures NMR Studies of GPCRs Expression Systems Cloning of CXCR1 into pGEX2a Expression of CXCR1 Purification Refolding and Reconstitution Binding and Activity Measurements NMR Spectra SOLUBILIZATION, PURIFICATION, AND CHARACTERIZATION OF INTEGRAL MEMBRANE PROTEINS Introduction Solubilization of IMPs IMP Purification Characterization of Solubilized IMPs STABILIZING MEMBRANE PROTEINS IN DETERGENT AND LIPID SYSTEMS Introduction Choice of Detergent: Solubilization versus Stability Mitigating Protein Denaturation Making or Selecting a Stable Protein Conclusions RAPID OPTIMIZATION OF MEMBRANE PROTEIN PRODUCTION USING GREEN FLUORESCENT PROTEIN-FUSIONS AND LEMO21(DE3) Introduction Main Protocol Materials Expression and Isolation of GFP-His8 Conclusions

25 citations

Journal ArticleDOI
03 Sep 2021
TL;DR: The most widely used membrane mimetics in structural and functional studies of integral membrane proteins (IMPs) are detergents, liposomes, bicelles, nanodiscs/Lipodisqs, amphipols, and lipidic cubic phases as discussed by the authors.
Abstract: Integral membrane proteins (IMPs) fulfill important physiological functions by providing cell–environment, cell–cell and virus–host communication; nutrients intake; export of toxic compounds out of cells; and more. However, some IMPs have obliterated functions due to polypeptide mutations, modifications in membrane properties and/or other environmental factors—resulting in damaged binding to ligands and the adoption of non-physiological conformations that prevent the protein from returning to its physiological state. Thus, elucidating IMPs’ mechanisms of function and malfunction at the molecular level is important for enhancing our understanding of cell and organism physiology. This understanding also helps pharmaceutical developments for restoring or inhibiting protein activity. To this end, in vitro studies provide invaluable information about IMPs’ structure and the relation between structural dynamics and function. Typically, these studies are conducted on transferred from native membranes to membrane-mimicking nano-platforms (membrane mimetics) purified IMPs. Here, we review the most widely used membrane mimetics in structural and functional studies of IMPs. These membrane mimetics are detergents, liposomes, bicelles, nanodiscs/Lipodisqs, amphipols, and lipidic cubic phases. We also discuss the protocols for IMPs reconstitution in membrane mimetics as well as the applicability of these membrane mimetic-IMP complexes in studies via a variety of biochemical, biophysical, and structural biology techniques.

25 citations

Journal ArticleDOI
TL;DR: It is confirmed that Cas2 proteins have pH-dependent nuclease activity against double-stranded DNAs, and indirect structural evidence for their conformational changes is provided, supporting the hypothesis that conformational switching is important for catalysis.

25 citations

Journal ArticleDOI
TL;DR: Crystal structure of the tubulin carboxypeptidase complex between vasohibin and SVBP, combined with mutagenesis, reveals the residues responsible for substrate recognition and cleavage.
Abstract: The cyclic enzymatic removal and ligation of the C-terminal tyrosine of α-tubulin generates heterogeneous microtubules and affects their functions. Here we describe the crystal and solution structure of the tubulin carboxypeptidase complex between vasohibin (VASH1) and small vasohibin-binding protein (SVBP), which folds in a long helix, which stabilizes the VASH1 catalytic domain. This structure, combined with molecular docking and mutagenesis experiments, reveals which residues are responsible for recognition and cleavage of the tubulin C-terminal tyrosine.

25 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
202335
202272
2021149
2020154
2019152
2018140