PPT-Protein structure prediction and design- II

VBC603 PG 02012021 Knowledge Based Approaches Homology Modelling Need homologues of known protein structure Backbone modelling Side chain modelling Fail in absence of homology Threading Based Methods. SUMI SINGH. (sxs5729). Levels of Protein Structure. 2. Thanks to: Frank . Lloyd . Wright for graphics. WOOD, BRICK etc. . . material/building blocks . AMINO ACIDS. *****************************************************************. 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. 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. and Secondary Levels. The . secondary structure . of a protein describes the structure that forms when amino acids form hydrogen bonds between the atoms in the backbone and atoms on the same or another peptide chain.. 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. 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. Contains . carbon, hydrogen. , oxygen, and nitrogen. Remember carbohydrates and lipids contain carbon, hydrogen, and oxygen – SO protein adds . nitrogen. Some proteins also contain sulfur, iron. , copper, phosphorus, or . 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. - 2 - Abstract Background Accurate identification of protein domain boundaries is useful for protein structure determination and prediction. However, predicting protein domain boundaries from a sequ 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. 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. This has proved to be a very challenging problem. It has aptly been described as the second half of the genetic code, and as the three-dimensional code, as opposed to the one-dimensional code involved in nucleotide/amino acid sequence. . Swanand. Gore & Gerard . Kleywegt. PDBe. – EBI. May 7. th. 2010, 9-10 am. Macromolecular Crystallography Course. Outline. Structural Biology and Bioinformatics. Databases in Structural Bioinformatics. Secondary structures. Tertiary structures. MTYKLILNGKTKGETTTEAVDAATAEKVFQYANDNGVDGEWTYTE. helices. strands. loops. Three dimensional packing of secondary structures. Protein Structures. Protein structures.