Explorations into protein structure with the knob-socket model - CORE CORE Search Search Services Access to raw data API Dataset FastSync Content discovery Recommender Discovery Managing content Repository dashboard Support FAQs About About CORE Blog Contact us Explorations into protein structure with the knob-socket model By Keith Jeffrey Fraga Abstract Protein sequences contain the information in order for a protein to fold to a unique compact, three-dimensional native structure. The forces that drive protein structures to form compact folds are largely dominated by burial of hydrophobic amino acids, which results in non-specific packing of amino acid side-chains. The knob-socket model attempts to organize side-chain packing into tetrahedral packing motifs. This tetrahedral motif is characterized with a three residues on the same secondary structure forming the base of the tetrahedron packing with a side-chain from a separate secondary structure. The base of the motif is termed the socket, and the other side-chain is called the knob. Here, we focus on extending the knob-socket model to understand tertiary and quaternary structure. First, single knobs sometimes pack into more than one socket in real structures. We focus on understanding the topology and amino acid preferences of these tertiary packing surfaces. The main results from the study of tertiary packing surfaces is that they have a preferred handedness, some interactions are ancillary to the packing interaction, there are specific amino preferences for specific positions in packing surfaces, and there is no relationship between side-chain rotamer of the knob packing into the tertiary packing surface. Next, we examine the application of the knob-socket to irregular and mixed packing in protein structure. The main conclusions from these efforts show canonical packing modes between secondary structures and highlight the important of coil secondary structure in providing many of the knobs for packing. Third, we investigate protein quaternary structure with a clique analysis of side-chain interactions. We identify a possible pseudo knob-socket interaction, and compare knob-socket interactions between tertiary and quaternary structure. Lastly, we discuss the workflow used in CASP12 to predict side-chain contacts and atomic coordinates of proteins Topics: Molecular biology, Biochemistry, Bioinformatics, Pure sciences, Biological sciences, Coil interactions, Knob socket analysis, Protein packing, Protein structure prediction, Protein-protein interactions, Tertiary structure, Chemicals and Drugs, Chemistry, Medical Pharmacology, Medicinal-Pharmaceutical Chemistry, Medicine and Health Sciences, Pharmaceutical Preparations, Pharmacy and Pharmaceutical Sciences, Physical Sciences and Mathematics Publisher: Scholarly Commons Year: 2016 OAI identifier: oai:scholarlycommons.pacific.edu:uop_etds-1263 Provided by: Scholarly Commons Download PDF: Sorry, we are unable to provide the full text but you may find it at the following location(s): https://scholarlycommons.pacif... (external link) https://scholarlycommons.pacif... (external link) To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request. Suggested articles Useful links Blog Services About CORE Contact us Cookies Privacy notice Writing about CORE? Discover our research outputs and cite our work. CORE is a not-for-profit service delivered by the Open University and Jisc.
