PPT-Visualizing Protein Structures

What we hope to learn The basic building blocks amino acids Secondary structure Forces that drive folding Motifs or supersecondary structure Domains Finding out more about structures. SUMI SINGH. (sxs5729). Levels of Protein Structure. 2. Thanks to: Frank . Lloyd . Wright for graphics. WOOD, BRICK etc. . . material/building blocks . AMINO ACIDS. *****************************************************************. 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. 4 Steps to Visualizing. Read the text. . Picture the information in your brain . Plan how to draw it on paper. . Draw and label the picture on paper. . Simple Practice. Visualize . the animal described below.. Alexey Onufriev, . Virginia Tech. www.cs.vt.edu/~onufriev. Proteins play key roles in a living system. Three (out of many many) examples of protein functions. Catalysis:. Almost all chemical reactions in a living cell are catalyzed by protein enzymes.. Day 3 - SAMS Program. Will . Foran. Sam Sanford . Objectives. What is the Central Dogma?. DNA Translation. Exercise 1 - DNA Transcription. RNA Translation. Exercise 2 - RNA Translation . Proteins. Protein Structure Analysis. Alexey Onufriev, . Virginia Tech. www.cs.vt.edu/~onufriev. Proteins play key roles in a living system. Three (out of many many) examples of protein functions. Catalysis:. Almost all chemical reactions in a living cell are catalyzed by protein enzymes.. loops (coil). Bovine . carboxypeptidase. A. Figure 6-28. Tertiary . structures . may contain . common patterns, or motifs, of secondary structures (= . supersecondary. structures) . βαβ. β. -hairpins. What to Know. What are some protein functions?. General principles for protein folding. General structural features of globular and structural proteins. Know the 4 common globular protein motifs. Understand how protein structures are stabilized and why some portions of proteins are marginally stable. loops (coil). Bovine . carboxypeptidase. A. Figure 6-28. Tertiary . structures . may contain . common patterns, or motifs, of secondary structures (= . supersecondary. structures) . βαβ. β. -hairpins. by . Sadhana S. definition. Protein structure prediction/protein . modelling. is the prediction of the three-dimensional structure of protein from its amino acid sequence. i.e., the prediction of its folding & its. Program for today:. - . Structures. . from. . p. rotein. X-. ray. . crystallography. - . Statistics. . of. . protein. . structures. - Statistical . potentials. 1. V10. Processing of Biological Data. Virginia Tech. www.cs.vt.edu/~onufriev. Gene is protein. ’. s blueprint, genome is life. ’. s blueprint . Gene. Genome. DNA. Protein. Gene. Gene. Gene. Gene. Gene. Gene. Gene. Gene. Gene. Gene. Gene. Secondary structures. Tertiary structures. MTYKLILNGKTKGETTTEAVDAATAEKVFQYANDNGVDGEWTYTE. helices. strands. loops. Three dimensional packing of secondary structures. Protein Structures. Protein structures.