PPT-V10 – Protein structures

Program for today Structures from p rotein X ray crystallography Statistics of protein structures Statistical potentials 1 V10 Processing of Biological Data. 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. 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.. . for . bioinformatics . Robbie P. Joosten. Netherlands Cancer Institute. Autumnschool. 2013. S. tructures . in . bioinformatics. Understand biology. Direct . interpretation. Data mining. Homology . 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. Proteins account for more than 50% of the dry mass of most cells. Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances. 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. . 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. 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.