PPT-Protein structure prediction and design

VBC603 PG 30122020 Protein Strucuture Sequence Structure and Function What determines fold Anfinsens experiments in 1957 demonstrated that proteins can fold spontaneously into their native conformations under physiological conditions This implies that primary structure does indeed determine folding or 3D . Why do we want to know protein structure?. Classification. Functional Prediction. What is protein structure?. Primary - chains of amino acids. Secondary - interaction between groups of amino acids. Tertiary - the organization in three dimensions of all the atoms in a polypeptide. What can we compare?. 3D shapes (RMSD). Atomic motions (B-value, RMSF). Solvent accessibilities (SASA). AMIGOS - Reads an RNA PDB file and outputs a complete table of torsion angle calculations.. APBS - Software for evaluating the electrostatic properties of . Brian Kuhlman. University of North Carolina, Chapel Hill. Outline: Three Protein Design Stories . Using Flexible Backbone Design for the Complete Redesign of a Protein Core . Designing the Structure and Sequence of a Protein-Binding Peptide. Beyond protein structure. Miguel . Andrade. Faculty of Biology, . Johannes Gutenberg University . Institute of Molecular Biology. Mainz, Germany. a. ndrade@uni-mainz.de. Transmembrane helices. N-terminal signals. Avdesh Mishra, . Md. . Tamjidul. . Hoque. {amishra2, . thoque. }@uno.edu. Presented By: Avdesh Mishra. Department of Computer Science. Protein structure in its native state gains lowest free energy. Miguel . Andrade. Faculty of Biology, . Johannes Gutenberg University . Institute of Molecular Biology. Mainz, Germany. a. ndrade@uni-mainz.de. X-ray crystallography . (103,988 . in PDB). need crystals. Advisor: Dr. Chen . Keasar. Arie Barsky, Nadav Nuni. Protein folding problem. Proteins are responsible for constructing and operating the organism, and are made of chains of amino-acids. Protein folding problem. przewidywania struktury białek Magdalena Mozolewska Instytut Podstaw Informatyki PAN Importance • In most cases function of the proteins depends strictly on their structure: • denatured enzymes computer science, mathematics, information technology and statistics. to analyze the biological data like . genomics, Protein structure prediction, . Pharmaco-phore. modeling , toxicity prediction and drug designing.. VBC-603. P.G.. 02.01.2021. Knowledge Based Approaches. Homology Modelling. Need homologues of known protein structure. Backbone modelling. Side chain modelling . Fail in absence of homology. Threading Based Methods. Question. Why design novel proteins? . what can be gained by the design and characterization of novel proteins? . Can we design 3D protein structures that have never been observed?. Are the 3D structures that have not been observed in nature unattainable, or just . Prediction . Wang Yang. 2014.1.3. Outline. Molecular. . Co-evolution . phenomenon. A. pplications . of Co-evolution . in . protein structure prediction and PPI prediction.. Co-evolution measurement: . Some of the slides are adapted from Dr. Dong Xu’s lecture notes. Why secondary structure prediction?. Accurate secondary structure prediction can be an important information for the tertiary structure prediction. Secondary structures. Tertiary structures. MTYKLILNGKTKGETTTEAVDAATAEKVFQYANDNGVDGEWTYTE. helices. strands. loops. Three dimensional packing of secondary structures. Protein Structures. Protein structures.