PPT-Computational Design of Protein Structures and Interfaces

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 ProteinBinding Peptide. CAFFREY SHYAMAL SOMAROO JASON D HUGHES JULIAN MINTSERIS AND ENOCH S HUANG Pfizer Discovery Technology Center Cambridge Massachusetts 02139 US Bioinformatics Program and Biomedical Engineering Department Boston U niversity Boston Massachusetts 02215 Given a set of real numbers, output a sequence, . (. l. 1. , … , . l. i. , … , . l. n. ). , . where . l. i. . ≤ . l. i+1. . for . i. = . 1 … n-1 .. Naive Algorithm. For index . i. =1 .. . INTERACTIONS. Chapter 6. Patrick . Hutto. Dongjin Kim. John . Difante. Lee Hailey. Introduction. Pre-1990s – efficient and effective interfaces . was . main goal. GUI advances, Internet, cell phones, . 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. Given a set of real numbers, output a sequence, . (. l. 1. , … , . l. i. , … , . l. n. ). , . where . l. i. . ≤ . l. i 1. . for . i. = . 1 … n-1 .. Naive Algorithm. For index . i. =1 .. . Jianlin Cheng, PhD. Department of EECS. University of Missouri, Columbia. Spring, 2019. The Genomic Era. Collins, Venter, Human Genome, 2000. DNA Sequencing Revolution. Scientists. Government. Company. VBC-603. P.G.. 30.12.2020. Protein . Strucuture. Sequence, Structure and Function. What determines fold?. Anfinsen’s 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 3-D . Interface . types. highlight the main design and research issues for each of the different interfaces. Consider which interface is best for a given application or activity. www.id-book.com. 2. 1. Command-based. 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 . Program for today:. - . Structures. . from. . p. rotein. X-. ray. . crystallography. - . Statistics. . of. . protein. . structures. - Statistical . potentials. 1. V10. Processing of Biological Data. Hao. . Zheng. Comp . Sci. & . Eng. U of South Florida . 1. Memory-Mapping Interface. 2. Each component has an unique address in the system address space.. Memory Mapped Interfaces. 3. Memory Mapped Interfaces. Secondary structures. Tertiary structures. MTYKLILNGKTKGETTTEAVDAATAEKVFQYANDNGVDGEWTYTE. helices. strands. loops. Three dimensional packing of secondary structures. Protein Structures. Protein structures.