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Lecture 8 Nonribosomal Code & Protein Design 1 Nonribosomal Peptide Synthetase (nrps) Enzyme
| Content Provider | Semantic Scholar |
|---|---|
| Abstract | Protein redesign plays an important role in the realization of novel molecular functions and drug design. In this lecture, we introduce a novel algorithm for protein redesign problem, which combines a statistical mechanics-derived ensemble-based approach to computing the binding constant with the speed and completeness of a branch-and-bound pruning algorithm [1]. Nonribosomal peptide synthetase (NRPS) enzymes, usually produced by microorganisms like bacteria and fungi, complement the traditional ribosomal peptide synthesis pathway. They are also the sources of hundreds of peptide-like products with pharmaceutical properties, including natural antibiotics, antifungals, antivirals, anticancer therapeutics, immunosup-pressants, and siderophores. Enzymes of the NRPS pathway have multiple domains with individual functions acting in an assembly-line fashion. It is commonly believed that the substrate specificity of the NRPS enzymes is dictated primarily by the " gatekeeper " adeny-lation (A), and recent evidence also indicates that the condensation (C), thiolation (T), and epimerization (E) domains may carry some specificity as well. Previous NRPS enzyme redesign methods can be divided into two main techniques, domain-swapping and active site modification through site-directed mutagenesis. Domain-swapping techniques modify NRPS enzymes by swapping an adenylation domain of an existing NRPS enzyme for an adenylation domain from a second, different NRPS enzyme. Active site modification through site-directed mutagenesis utilizes structural information of the GrsA-PheA enzyme. From sequence alignment of GrsA-PheA with 160 other known adenylation domains, a " signature sequence " was derived for each adenylation domain by extracting those residues that align with the structurally determined substrate binding pocket of the GrsA-PheA crystal structure. 2 Methods First, [1] developed an ensemble scoring method K * to model the protein-ligand binding in a single mutation. Since it is not currently possible to compute exact partition functions for complex molecular species, K * approximates these partition functions with the use of rotamerically-based conformational ensembles. When applying K * to a protein-ligand system, a number of choices must be made with respect to ensemble generation and single-structure scoring, where single-structure scoring |
| File Format | PDF HTM / HTML |
| Alternate Webpage(s) | http://www.cs.duke.edu/brd/Teaching/Bio/asmb/current/Notes2/online/Lecture8.pdf |
| Alternate Webpage(s) | http://www.cs.duke.edu/~brd/Teaching/Bio/asmb/current/Notes2/online/Lecture8.pdf |
| Language | English |
| Access Restriction | Open |
| Content Type | Text |
| Resource Type | Article |
