Current Protocols in Protein Science最新文献_第5页

In Situ Imaging of Tryptic Peptides by MALDI Imaging Mass Spectrometry Using Fresh-Frozen or Formalin-Fixed, Paraffin-Embedded Tissue 使用新鲜冷冻或福尔马林固定石蜡包埋组织的MALDI成像质谱法原位成像胰蛋白酶肽

Current Protocols in Protein Science Pub Date : 2018-08-16 DOI: 10.1002/cpps.65

Peggi M. Angel, Kim Norris-Caneda, Richard R. Drake

引用次数: 19

Computational Prediction of Carbohydrate-Binding Proteins and Binding Sites 碳水化合物结合蛋白和结合位点的计算预测

Current Protocols in Protein Science Pub Date : 2018-08-14 DOI: 10.1002/cpps.75

Huiying Zhao, Ghazaleh Taherzadeh, Yaoqi Zhou, Yuedong Yang

{"title":"Computational Prediction of Carbohydrate-Binding Proteins and Binding Sites","authors":"Huiying Zhao, Ghazaleh Taherzadeh, Yaoqi Zhou, Yuedong Yang","doi":"10.1002/cpps.75","DOIUrl":"10.1002/cpps.75","url":null,"abstract":"Protein-carbohydrate interaction is essential for biological systems, and carbohydrate-binding proteins (CBPs) are important targets when designing antiviral and anticancer drugs. Due to the high cost and difficulty associated with experimental approaches, many computational methods have been developed as complementary approaches to predict CBPs or carbohydrate-binding sites. However, most of these computational methods are not publicly available. Here, we provide a comprehensive review of related studies and demonstrate our two recently developed bioinformatics methods. The method SPOT-CBP is a template-based method for detecting CBPs based on structure through structural homology search combined with a knowledge-based scoring function. This method can yield model complex structure in addition to accurate prediction of CBPs. Furthermore, it has been observed that similarly accurate predictions can be made using structures from homology modeling, which has significantly expanded its applicability. The other method, SPRINT-CBH, is a de novo approach that predicts binding residues directly from protein sequences by using sequence information and predicted structural properties. This approach does not need structurally similar templates and thus is not limited by the current database of known protein-carbohydrate complex structures. These two complementary methods are available at https://sparks-lab.org. © 2018 by John Wiley & Sons, Inc.","PeriodicalId":10866,"journal":{"name":"Current Protocols in Protein Science","volume":"94 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpps.75","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36396048","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Sequence Similarity Searching 序列相似性搜索

Current Protocols in Protein Science Pub Date : 2018-08-13 DOI: 10.1002/cpps.71

Gang Hu, Lukasz Kurgan

引用次数: 48

Isolation of Antibodies to Heparan Sulfate on Glypicans by Phage Display 用噬菌体展示法分离硫酸肝素抗体

Current Protocols in Protein Science Pub Date : 2018-08-09 DOI: 10.1002/cpps.66

Heungnam Kim, Mitchell Ho

引用次数: 14

One-Dimensional Electrophoresis Using Nondenaturing Conditions 非变性条件下的一维电泳

Current Protocols in Protein Science Pub Date : 2018-08-09 DOI: 10.1002/cpps.73

Sean R. Gallagher

{"title":"One-Dimensional Electrophoresis Using Nondenaturing Conditions","authors":"Sean R. Gallagher","doi":"10.1002/cpps.73","DOIUrl":"10.1002/cpps.73","url":null,"abstract":"Electrophoresis is used to separate complex mixtures of proteins (e.g., from cells, subcellular fractions, column fractions, or immunoprecipitates), to investigate subunit composition, track post-translational modifications, and verify identity and homogeneity of protein samples. It can also serve to purify proteins for use in further applications. In polyacrylamide gel electrophoresis, proteins migrate in response to an electrical field through pores in a polyacrylamide gel matrix; pore size decreases with increasing acrylamide concentration. Nondenaturing or “native” electrophoresis—i.e., electrophoresis in the absence of denaturants such as detergents and urea—is an often-overlooked technique for determining the native size, subunit structure, and optimal separation of a protein. Because mobility depends on the size, shape, and intrinsic charge of the protein, nondenaturing electrophoresis provides a set of separation parameters distinctly different from mainly size-dependent denaturing sodium dodecyl sulfate—polyacrylamide gel electrophoresis and charge-dependent isoelectric focusing. Two protocols are presented below. Continuous PAGE is highly flexible, permitting cationic and anionic electrophoresis over a full range of pH. The discontinuous procedure is limited to proteins negatively charged at neutral pH but provides high resolution for accurate size calibration.","PeriodicalId":10866,"journal":{"name":"Current Protocols in Protein Science","volume":"94 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpps.73","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36383666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

In Situ Imaging of N-Glycans by MALDI Imaging Mass Spectrometry of Fresh or Formalin-Fixed Paraffin-Embedded Tissue 新鲜或福尔马林固定石蜡包埋组织的MALDI成像质谱法原位成像n-聚糖

Current Protocols in Protein Science Pub Date : 2018-08-03 DOI: 10.1002/cpps.68

Richard R. Drake, Thomas W. Powers, Kim Norris-Caneda, Anand S. Mehta, Peggi M. Angel

{"title":"In Situ Imaging of N-Glycans by MALDI Imaging Mass Spectrometry of Fresh or Formalin-Fixed Paraffin-Embedded Tissue","authors":"Richard R. Drake, Thomas W. Powers, Kim Norris-Caneda, Anand S. Mehta, Peggi M. Angel","doi":"10.1002/cpps.68","DOIUrl":"10.1002/cpps.68","url":null,"abstract":"Glycosylation of cell surface, secreted, and circulating proteins is one of the most common types of post-translational modification. These modifications occur most commonly as one of three major classes: N-linked glycosylation on asparagine residues, O-linked glycosylation on serine or threonine residues, or as glycosaminoglycan oligosaccharide polymers on serine. Specifically, for N-linked glycans, an endoglycosidase enzyme, peptide N-glycosidase F (PNGase F), cleaves the attached oligosaccharides between the asparagine and first sugar. A method to analyze released N-glycans and map them to specific locations within a tissue is presented here. The PNGase F is applied by solvent sprayer as a molecular layer on frozen or formalin-fixed tissues and all released N-glycans in a given region of tissue are detected using matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (MALDI-IMS). Using the described MALDI-IMS protocol, at least 40 or more individual N-glycans can be mapped to tissue histopathology and extracted for further structural analysis approaches. © 2018 by John Wiley & Sons, Inc.","PeriodicalId":10866,"journal":{"name":"Current Protocols in Protein Science","volume":"94 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpps.68","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36369087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 66

Delivery of Fluorescent Probes Using Streptolysin O for Fluorescence Microscopy of Living Cells 利用链溶素O递送荧光探针用于活细胞荧光显微镜

Current Protocols in Protein Science Pub Date : 2018-07-30 DOI: 10.1002/cpps.60

Kai Wen Teng, Pin Ren, Paul R. Selvin

引用次数: 8

Analysis of Protein Phosphorylation Using Phos-Tag Gels 利用Phos-Tag凝胶分析蛋白质磷酸化

Current Protocols in Protein Science Pub Date : 2018-07-25 DOI: 10.1002/cpps.64

Zoltan Nagy, Shane Comer, Albert Smolenski

引用次数: 30

Screening of Detergents for Stabilization of Functional Membrane Proteins 稳定功能性膜蛋白的洗涤剂的筛选

Current Protocols in Protein Science Pub Date : 2018-07-18 DOI: 10.1002/cpps.59

Guillaume Lenoir, Thibaud Dieudonné, Anaïs Lamy, Maylis Lejeune, José-Luis Vazquez-Ibar, Cédric Montigny

引用次数: 7

Using Fluorescence Anisotropy for Ligand Binding Kinetics of Membrane Proteins 利用荧光各向异性研究膜蛋白的配体结合动力学

Current Protocols in Protein Science Pub Date : 2018-07-16 DOI: 10.1002/cpps.63

Kirsten N. Swonger, Anne S. Robinson

引用次数: 6