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1st International Conference on Bioinformatics (BIOINFORMATICS 2010)

作者： Cantoni, Virginio Gatti, Riccardo Lombardi, Luca Univ Pavia Dept Comp Engn & Syst Sci Via Ferrata 1 Pavia Italy

ISBN: (纸本)9789896740191

The morphological complementarities of molecular surfaces provides insights for the identification and evaluation of binding sites. A quantitative characterization of these sites is an initial step towards protein based drug design. The final goal of the activity here presented is to provide a method that allows the identification of sites of possible protein-protein and protein-ligand interaction on the basis of the geometrical and topological structure of protein surfaces. The goal is to discover complementary regions (that is with concave and convex segments that match each others) among different molecules. In particular, we are considering the first step of this process: the segmentation of the protein surface in protuberances and cavities through an approach based on an analysis of the molecule Convex Hull and on the Distance Transform.

关键词： protein structure analysis protein-protein interaction Surface labeling Convex hull Distance transform

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protein structure analysis and Validation with X-Ray Crystallography

Protein Structure Analysis and Validation with X-Ray Crystal...

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作者： Anastassios C. Papageorgiou Nirmal Poudel Jesse Mattsson

X-ray crystallography is the main technique for the determination of protein structures. About 85% of all protein structures known to date have been elucidated using X-ray crystallography. Knowledge of the three-dimensional structure of proteins can be used in various applications in biotechnology, biomedicine, drug design, and basic research and as a validation tool for protein modifications and ligand binding. Moreover, the requirement for pure, homogeneous, and stable protein solutions in crystallizations makes X-ray crystallography beneficial in other fields of protein research as well. Here, we describe the technique of X-ray protein crystallography and the steps involved for a successful three-dimensional crystal structure determination.

关键词： protein structure analysis Crystallization structure Determination X-ray Crystallography Statistical Calculation Molecular Replacement Data collection X-rays

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protein structure-sensitive analysis by Normal Pulse Voltammetry

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ELECTROanalysis 2016年第11期28卷 2884-2889页

作者： Cernocka, Hana Palecek, Emil CAS Inst Biophys Vvi Kralovopolska 135 Brno 61265 Czech Republic

Earlier we showed that constant current chronopotentiometric stripping (CPS) at mercury-containing electrodes reflects changes in proteins, such as denaturation, single amino acid exchange or protein damage by physical and chemical agents. Here we attempted to compare performance of the galvanostatic CPS with the potentiostatic normal pulse voltammetry (NPV). We have found that repeated 50ms or longer NPV pulses denature the surface-attached protein. Using shorter pulses and adapting other NPV settings we have been able to obtain a good resolution of native (folded) and denatured (unfolded) bovine serum albumin. On the other hand, partial denaturation of the surface-attached native bovine serum albumin during the potential scanning may prevent detection of small conformational changes in the protein.

关键词： Normal pulse voltammetry Constant current chronopotentiometry protein structure analysis Hanging mercury drop electrode Catalytic hydrogen evolution

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Voltammetric and chronopotentiometric protein structure-sensitive analysis

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ELECTROCHIMICA ACTA 2017年 224卷 211-219页

作者： Cernocka, Hana Palecek, Emil CAS Vvi Inst Biophys Kralovopolska 135 Brno 61265 Czech Republic

Previously we showed that constant current chronopotentiometric stripping (CPS) is convenient for protein analysis based on the ability of some amino acid residues to catalyze hydrogen evolution on mercury-containing electrodes. This method showed a remarkable sensitivity to changes in protein structures, including protein denaturation and even small protein damage. Here we used normal pulse voltammetric stripping (NPVS) with bare and dithiothreitol-modified hanging mercury drop electrode. We found that NPV pulses denatured the surface-attached protein but we showed conditions under which this method was able to distinguish native and denatured proteins with sensitivity approaching that of CPS. Using NPVS it was possible to follow bovine serum albumin (BSA) thermal denaturation as well as to investigate the effect of NPV pulses on the structure of the surface-attached protein. In addition to BSA we studied several proteins, such as human serum albumin, ovalbumin, urease, aldolase, concanavalin A, histone and vasopressin peptide. Our results suggest that CPS remains the method-of choice for studies of changes in protein structure and of biochemical processes, such as DNA-protein specific binding, lectin-glycoprotein interactions, detection of protein damage, etc., while voltammetric methods, such as NPVS may suit better for investigation of the processes which proteins undergo at the electrode surface. (C) 2016 Elsevier Ltd. All rights reserved.

关键词： protein structure analysis Normal pulse voltammetry and constant current chronopotentiometry Bare and thiol-modified hanging mercury drop electrodes Hydrogen evolution reaction catalyzed by proteins

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Comparative protein structure analysis with Bio3D-Web

Comparative Protein Structure Analysis with Bio3D-Web

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作者： Barry J. Grant Lars Skjærven Xin-Qiu Yao

Bio3D-web is an online application for the interactive analysis of sequence-structure-dynamics relationships in user-defined protein structure sets. Major functionality includes structure database searching, sequence and structure conservation assessment, inter-conformer relationship mapping and clustering with principal component analysis (PCA), and flexibility prediction and comparison with ensemble normal mode analysis (eNMA). Collectively these methods allow users to start with a single sequence or structure and characterize the structural, conformational, and internal dynamic properties of homologous proteins for which there are high-resolution structures available. Functionality is also provided for the generation of custom PDF, Word, and HTML analysis reports detailing all user-specified analysis settings and corresponding results. Bio3D-web is available at http://***/bio3d/webapps, as a Docker image https://***/r/bio3d/bio3d-web/, or downloadable source code https://***/Grantlab/bio3d-web. less

关键词： protein structure analysis structure Determination Principal Component analysis Multiple Sequence Alignment structure Visualization protein Engineering Molecular Dynamics Simulation Sequence Alignment analysis Sequence analysis structure analysis DNA Ligation protein dynamics protein flexibility Sequence-structure-function relationships

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protein structure Validation and analysis with X-Ray Crystallography

Protein Structure Validation and Analysis with X-Ray Crystal...

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作者： Anastassios C. Papageorgiou Jesse Mattsson

X-ray crystallography is the main technique for the determination of protein structures. About 85 % of all protein structures known to date have been elucidated using X-ray crystallography. Knowledge of the three-dimensional structure of proteins can be used in various applications in biotechnology, biomedicine, drug design, and basic research and as a validation tool for protein modifications, ligand binding, and structural authenticity. Moreover, the requirement for pure, homogeneous, and stable protein solutions in crystallizations makes X-ray crystallography beneficial in other fields of protein research as well. Here, we describe the technique of X-ray protein crystallography and the steps involved for a successful three-dimensional crystal structure determination. less

关键词： protein structure analysis Crystallization structure Determination Molecular Replacement protein Model Validation X-ray Crystallography Statistical Calculation Data collection X-rays

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analysis of Oncogene protein structure Using Small World Network Concept

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CURRENT BIOINFORMATICS 2020年第7期15卷 732-740页

作者： Kumari, Neetu Verma, Anshul Banaras Hindu Univ Dept Comp Sci Varanasi Uttar Pradesh India

Background: The basic building block of a body is protein which is a complex system whose structure plays a key role in activation, catalysis, messaging and disease states. Therefore, careful investigation of protein structure is necessary for the diagnosis of diseases and for the drug designing. protein structures are described at their different levels of complexity: primary (chain), secondary (helical), tertiary (3D), and quaternary structure. Analyzing complex 3D structure of protein is a difficult task but it can be analyzed as a network of interconnection between its component, where amino acids are considered as nodes and interconnection between them are edges. Objective: Many literature works have proven that the small world network concept provides many new opportunities to investigate network of biological systems. The objective of this paper is analyzing the protein structure using small world concept. Methods: protein is analyzed using small world network concept, specifically where extreme condition is having a degree distribution which follows power law. For the correct verification of the proposed approach, dataset of the Oncogene protein structure is analyzed using Python programming. Results: protein structure is plotted as network of amino acids (Residue Interaction Graph (RIG)) using distance matrix of nodes with given threshold, then various centrality measures (i.e., degree distribution, Degree-Betweenness correlation, and Betweenness-Closeness correlation) are calculated for 1323 nodes and graphs are plotted. Conclusion: Ultimately, it is concluded that there exist hubs with higher centrality degree but less in number, and they are expected to be robust toward harmful effects of mutations with new functions.

关键词： Small world network concepts protein structure analysis oncogene protein degree distribution centrality measures amino acid

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Getting to the core of protein pharmaceuticals - Comprehensive structure analysis by mass spectrometry

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EUROPEAN JOURNAL OF PHARMACEUTICS AND BIOPHARMACEUTICS 2015年 93卷 95-109页

作者： Leurs, Ulrike Mistarz, Ulrik H. Rand, Kasper D. Univ Copenhagen Dept Pharm DK-2100 Copenhagen Denmark

protein pharmaceuticals are the fastest growing class of novel therapeutic agents, and have been a major research and development focus in the (bio)pharmaceutical industry. Due to their large size and structural diversity, biopharmaceuticals represent a formidable challenge regarding analysis and characterization compared to traditional small molecule drugs. Any changes to the primary, secondary, tertiary or quaternary structure of a protein can potentially impact its function, efficacy and safety. The analysis and characterization of (structural) protein heterogeneity is therefore of utmost importance. Mass spectrometry has evolved as a powerful tool for the characterization of both primary and higher order structures of protein pharmaceuticals. Furthermore, the chemical and physical stability of protein drugs, as well as their pharmacokinetics are nowadays routinely determined by mass spectrometry. Here we review current techniques in primary, secondary and tertiary structure analysis of proteins by mass spectrometry. An overview of established top-down and bottom-up protein analyses will be given, and in particular the use of advanced technologies such as hydrogen/deuterium exchange mass spectrometry (HDX-MS) for higher-order structure analysis will be discussed. Modification and degradation pathways of protein drugs and their detection by mass spectrometry will be described, as well as the growing use of mass spectrometry to assist protein design and biopharmaceutical development. (C) 2015 Elsevier B.V. All rights reserved.

关键词： Pharmaceutical analysis protein pharmaceuticals Biopharmaceuticals protein structure analysis Mass spectrometry Hydrogen/deuterium exchange mass spectrometry

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Genetic and protein structure prediction analyses identify a rare pathogenic PKD1 variant causing autosomal dominant polycystic kidney disease

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CEN CASE REPORTS 2025年 1-6页

作者： Shiiya, Takamitsu Watanabe, Hirofumi Aida, Ryo Otsuka, Tadashi Kaseda, Ryohei Yamamoto, Suguru Kaneko, Yoshikatsu Goto, Shin Narita, Ichiei Niigata Univ Kidney Res Ctr Grad Sch Med & Dent Sci Div Clin Nephrol & Rheumatol 1-757 Asahimachi DoriChuo Ku Niigata Niigata 9518510 Japan

Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common monogenic kidney disorders. The diagnosis of ADPKD requires imaging findings showing multiple kidney cysts or genetic testing, in cases where a family history is unknown. We report a patient diagnosed with ADPKD based on the identification of a rare PKD1 variant. The patient was a 41-year-old female in whom cysts and calcification in the kidneys were incidentally detected. Whole-exome sequencing identified a rare PKD1 variant (NM_001009944.3: c.11557G > A/p.E3853K). protein structure prediction of the PKD1-PKD2 complex showed that the variant may be pathogenic, leading to the diagnosis of autosomal dominant polycystic kidney disease. A detailed family history revealed that her relatives also had ADPKD, further supporting the diagnosis of ADPKD. Comprehensive genetic analysis and protein structure prediction led to the diagnosis of ADPKD and the identification of rare causative genes. These methods are useful for diagnosing hereditary kidney diseases of unknown etiologies.

关键词： Autosomal dominant polycystic kidney disease PKD1 PKD2 protein structure analysis Whole-exome sequencing

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protein Folding at Atomic Resolution: analysis of Autonomously Folding Supersecondary structure Motifs by Nuclear Magnetic Resonance

Protein Folding at Atomic Resolution: Analysis of Autonomous...

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作者： Lorenzo Sborgi Abhinav Verma Mourad Sadqi Eva Alba Victor Muñoz

The study of protein folding has been conventionally hampered by the assumption that all single-domain proteins fold by an all-or-none process (two-state folding) that makes it impossible to resolve folding mechanisms experimentally. Here we describe an experimental method for the thermodynamic analysis of protein folding at atomic resolution using nuclear magnetic resonance (NMR). The method is specifically developed for the study of small proteins that fold autonomously into basic supersecondary structure motifs, and that do so in the sub-millisecond timescale (folding archetypes). From the NMR experiments we obtain hundreds of atomic unfolding curves that are subsequently analyzed leading to the determination of the characteristic network of folding interactions. The application of this approach to a comprehensive catalog of elementary folding archetypes holds the promise of becoming the first experimental approach capable of unraveling the basic rules connecting protein structure and folding mechanism. less

关键词： protein structure analysis NMR Proton NMR Triple Resonance NMR Circular Dichroism Data analysis protein folding protein stability Folding mechanisms Folding interaction networks

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