PPT-Lecture 08 PROTEIN SEQUENCE

ANALYSIS PROTEIN DATABASES PROTEIN SEQUENCE MOTIFDOMAIN FOLDINDING PROPERTIES TOOLS httptwexpasyorg httpwwwebiacukToolspfaiprscan httpwwwncbinlmnihgovStructurecddwrpsbcgi. A. ll?. Using SystemVerilog UVM Sequences for Fun and Profit. by. Rich Edelman and Raghu Ardeishar. Verification Technologists. Mentor Graphics. Questa Verification Platform. thefreedictionary.com/fairest . Sequence:. Edman degradation. Mass spectrometry. Secondary structure:. Circular Dichroism. FTIR. Tertiary, quaternary structure:. NMR. X-ray crystallography. Protein sequencing approaches depend on what is known and what is the goal. mzIdentML. ProteinDetectionList. ProteinAmbiguityGroup. id=“PAG1”. ProteinDetectionHypothesis. id=“PDH1” . dbseq_ref. =“dbseq_Q05421|CP2E1_MOUSE”. . anchor protein. ProteinAmbiguityGroup. Lian Yang. 2. ; . Baozhen Shan. 1. ; . Bin Ma. 2. 1. Bioinformatics Solutions Inc, Canada . 2. University of Waterloo, Canada. Problem. . Complete protein sequence coverage. antibody confirmation. Gustavo Caetano - . Anolles. 1. PowerPoint by Casey . Hanson. Protein Sequence, Structure, and Function | Gustavo Caetano - Anolles | 2015. Exercise. In this exercise we will be doing the following:. Sequence:. Edman degradation. Mass spectrometry. Secondary structure:. Circular Dichroism. FTIR. Tertiary, quaternary structure:. NMR. X-ray crystallography. Protein sequencing approaches depend on what is known and what is the goal. Exercise – Project Layout. G. eneral remarks – recap: Report 60pts, Exam 40 . pts. , weekly presentations of each group, one bad presentation allowed, groups of 3-4 students. Contact & Questions: . A nutrient found in all living things. It contains nitrogen and is responsible for the formation, maintenance, and repair of the body’s tissues/ It can also be used for energy. CHNO. Amino acids . Sequence, Sequence on the Wall, Who’s the Fairest of Them A ll? Using SystemVerilog UVM Sequences for Fun and Profit by Rich Edelman and Raghu Ardeishar Verification Technologists Mentor Graphics Questa Verification Platform Proteins are major components of all cellular systems. Proteins consist of one or more linear polymers called polypeptides. Proteins are linear and never branched. Different AA’s are linked together via . Concepts. Introduction to Biostatistics and Bioinformatics. Sequence . Database Searching. This Lecture. Stuart M. Brown, Ph.D.. Center for Health Informatics and Bioinformatics. NYU School of Medicine. for . life.. . The importance of proteins was recognized by chemists in the early 19th century, including Swedish chemist . Jöns. Jacob Berzelius. , who in 1838 coined the term . protein. , a word derived from the Greek . Hsin. -Yu Chang. www.ebi.ac.uk. Classifying . proteins into families and . identifying . protein homologues can help scientists . to . characterise. unknown proteins. . . . Greider. and Blackburn discovered telomerase in 1984 and were awarded Nobel prize in 2009. Which model organism they used for this study ? . COVID19 is a pandemic across the world. It is caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The Surface/Spike Glycoprotein of SARS-CoV-2, which plays a key role in the receptor recognition and cell membrane fusion process, is composed of two subunits, S1 and S2. In the present work we have searched for Surface/Spike glycoprotein in the NCBI protein database and origin from “India”, the search hit out 192 protein sequences as on 20 June 2020. Further, the sequences were aligned using Surface/Spike glycoprotein from Wuhan-China Origin and on the basis of the sequence length of 1273, the sequences were screened. Out of 192 input protein sequences, 177 sequences were complete in the length of 1273 amino-acids. Comparing all the sequences via sequence alignment mode in MEGA-X, exhibited a complex diversified outcome and reported 32 sequences. The protein sequence id QKI28685.1 was identified as a root and 31 protein sequences as a mutant/variant. QKI28685.1 was subjected to 3D protein structure modelling. As no full-length structural template was identified in the database. Automated homology modelling, Swiss-Model server and threading based I-Tasser were considered for the structure determination. Swiss-Model reported a partial structure from amino acid length 27 to 1146. A full-length structure is obtained from the I-Tasser server. The structures were analyzed using the ProSA and Ramachandran plot. 31 identified mutations were manually incorporated in the protein structure and a total of 31 mutants were created. Further, these proteins are in a process to study and understand the structural changes and their impact on the protein-protein interaction and protein-drug interaction..