2026-09-18T20:10:25Zhttps://dspace.mit.edu/server/oai/request

oai:dspace.mit.edu:1721.1/478802022-01-13T07:54:15Zcom_1721.1_7582com_1721.1_7581col_1721.1_131022

Amy E. Keating. Gutwin, Karl N. (Karl Nickolai) Massachusetts Institute of Technology. Dept. of Biology. Massachusetts Institute of Technology. Department of Biology 2009-10-01T15:57:47Z 2009-10-01T15:57:47Z 2009 2009 http://hdl.handle.net/1721.1/47880 433096679 Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2009. Page 224 blank. Includes bibliographical references. The alpha-helical coiled coil is a protein sequence and structural motif that consists of two or more helices in a parallel or antiparallel orientation supercoiling around a central axis. Coiled coils have been observed in a wide range of protein families, and many studies have focused on their sequence and structural diversity over the past half-century. In particular, the observation that coiled coils can be involved in determining protein-protein interactions and protein architectures has prompted the developments of methods to predict the structure of a coiled-coil complex from sequence information alone. In this thesis, I discuss the development of a structurally annotated database of coiled-coil sequence useful for training statistics-based methods of coiled-coil structure prediction. This database was used to retrain and stringently cross-validate the Multicoil method of predicting coiled-coil oligomerization state. In addition, I describe recent work using implicit and explicit structure models to predict dimeric coiled-coil orientation and alignment. Improvements to existing models, insight into coiled-coil structure determinants, and the future of coiled-coil prediction are also discussed. by Karl N. Gutwin. Ph.D. 224 p. eng Massachusetts Institute of Technology M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. http://dspace.mit.edu/handle/1721.1/7582 Biology. Computational prediction of coiled-coil interaction structure specificity Thesis application/pdf false Publication unknown unknown <Publication xmlns="https://www.openaire.eu/cerif-profile/1.1/" id="0f8461d8-adbd-446d-b836-fd989fc033b1"> <Type xmlns="https://www.openaire.eu/cerif-profile/vocab/COAR_Publication_Types">http://purl.org/coar/resource_type/c_1843</Type> <Language>eng</Language> <Title>Computational prediction of coiled-coil interaction structure specificity</Title> <PublishedIn> <Publication> </Publication> </PublishedIn> <PublicationDate>2009</PublicationDate> <Authors> <Author> <DisplayName>Gutwin, Karl N. (Karl Nickolai)</DisplayName> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> </Authors> <Editors> </Editors> <Publishers> <Publisher> <DisplayName>Massachusetts Institute of Technology</DisplayName> <OrgUnit /> </Publisher> </Publishers> <License>http://dspace.mit.edu/handle/1721.1/7582</License> <Keyword>Biology.</Keyword> <Abstract>The alpha-helical coiled coil is a protein sequence and structural motif that consists of two or more helices in a parallel or antiparallel orientation supercoiling around a central axis. Coiled coils have been observed in a wide range of protein families, and many studies have focused on their sequence and structural diversity over the past half-century. In particular, the observation that coiled coils can be involved in determining protein-protein interactions and protein architectures has prompted the developments of methods to predict the structure of a coiled-coil complex from sequence information alone. In this thesis, I discuss the development of a structurally annotated database of coiled-coil sequence useful for training statistics-based methods of coiled-coil structure prediction. This database was used to retrain and stringently cross-validate the Multicoil method of predicting coiled-coil oligomerization state. In addition, I describe recent work using implicit and explicit structure models to predict dimeric coiled-coil orientation and alignment. Improvements to existing models, insight into coiled-coil structure determinants, and the future of coiled-coil prediction are also discussed.</Abstract> <Access xmlns="http://purl.org/coar/access_right" > </Access> </Publication>