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Protein Structural Analysis: Α-Helices and Their Interactions

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Protein Structural Analysis: Α-Helices and Their Interactions Protein Structural Analysis: a-helices and their interactions by Frances Mary Genevieve Pearl Biomolecular and Structural Modelling Unit, Department of Biochemistry and Molecular Biology, University College London, Gower Street, London. WCIE 6BT This thesis is submitted in fulfilment of the requirements for the degree of Doctor of Philosophy from the University of London March 1998 ProQuest Number: U643156 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest. ProQuest U643156 Published by ProQuest LLC(2016). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. Microform Edition © ProQuest LLC. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 Abstract Abst r a c t Helices are fundamental building blocks of many protein structures, and interactions between them play a crucial role in stabilising a protein’s fold. This work updates and enhances the current knowledge of the nature of these interactions using the 3-dimensional coordinates of protein structures deposited in the Protein Data Bank. Having defined rigorous criteria for identifying regular a-helices, the geometric and physical properties of helix-helix interactions were studied. In contrast with previous studies, a systematic analysis of a large dataset of helix-helix interactions was undertaken. These interactions were divided into different geometric types, which were found to exhibit different physical properties. However, the range of interaction within each class was still very broad. Having studied the gross features of helix-helix interactions, an analysis of the residue packing at the interface was undertaken. Established manual methods were used to designate the packing classes of 36 highly interacting helix pairs from 11 proteins. These methods were found to be inappropriate for use with extensive amounts of data. Clearly an automatic method that allowed identification of previously undescribed packings would be desirable. Towards this end, contact maps and distance matrices were chosen as simple representations of helix-helix interactions amenable to automated computational analyses. Helix pairs with conserved packing interfaces within a set of globin structures were automatically clustered. However, those from a more general set of proteins failed to cluster. This led to a reassessment of the helix packing models. Although some helix interactions fit the idealised models, most are somewhat irregular. The helix packing we observe is driven solely by energetic considerations - to minimise free energy and generate an energetically stable globular protein. From this study it is clear that predicting a helix packing interaction in the absence of other contacts is unlikely to be successful. Page 2 Acknowledgements A cknowledgements Firstly, I’d like to thank my supervisor, Prof Janet Thornton and my husband Prof Laurence Pearl for their help, guidance and encouragement during the last six and a half years. For scientific advice, technical help, patience and friendship I am particularly indebted to Roman Laskowski, to Christine Orengo, and to Mark Williams. Other colleagues I would like to thank for their help and support are David Jones, Martin Jones, Christine Mason, Malcolm Mac Arthur, Andrew Martin, John Mitchell, Gail Hutchinson, Tim Slidel, Helen Stirk and Andrew Wallace. Finally, I would like to thank all the members of my family, and the others that helped contribute to ’child care’ to enable this thesis to be written. This work was supported by a Medical Research Council, Human Genome grant 1991-1994. Page 3 Dedication To Michael and Henry Page 4 Contents C o n te n ts Title p age ............................................................................................................................1 Abstract ............................................................................................................................2 Acknowledgements.......................................................................................................... 3 D edication......................................................................................................................... 4 Contents ............................................................................................................................5 List of Figures................................................................................................................11 List of Tables...................................................................................................................14 C h a p t e r 1: I ntroduction - T h e r o l e o f a-HELiCES in p r o t e i n s 16 1.1 An Introduction to protein structure .............................................. 17 1.1.1 Amino acid s ................................................................................20 1.1.2 Primary structure ......................................................................20 1.1.2.i Conformation of the residues .......................... 20 1.1.2.Ü Allowed conformational space and the Ramachandran P lot ...........................................21 1.1.2.Û7 Side chain conformations ..................................23 1.1.3 Secondary structure ................................................................... 24 1.13.f Helices ............................................................... 25 1.1.3.» S h eets..................................................................29 1.1.3.Û7 p-tums ................................................................30 1.1.3./V Coil .................................................................... 31 1.1.4 Supersecondary stru ctu re ......................................................... 31 1.1.4.f aa-coiled coil ................................................... 31 1.1.4.» aa-tum s .............................................................33 1.1.4./» a a -h a irp in s........................................................ 34 1.1.4./V aa-com er ...........................................................34 1.1.4.V EF-hand .............................................................35 1.1.4.V/ Helix-tum-helix .................................................35 1.1.4.V// Helix-loop-Helix .................................................35 1.1.5 Tertiary Structure ......................................................................36 1.1.6 Structural D om ains ................................................................... 36 1.1.6./ Mainly-a c la s s ...................................................38 1.1.6.// Mainly-P c la s s ...................................................41 1.1.6./// a-P c la s s .............................................................41 1.1.7 Quaternary Structure .................................................... 41 1.2 Structural determination .................................................................... 42 1.2.1 X-ray crystallography .............................................................. 42 1.2.1./ Basic theory ........................................................42 1.2.1.// R esolution .......................................................... 45 1.2.1./// R-factor ............................................................... 46 1.2.2 N M R ............................................................................................ 46 Page 5 Contents 1.3 Thesis objectives and outline ...........................................................48 C h a p t e r 2: A n a l y s is o f a-HELicES .....................................................................50 2.1 Selection of a non-homologous data set ......................................... 50 2.2 Calculation of single helix properties ............................................55 2.2.1 M ethods ...................................................................................... 57 2.2.2 Definition of helices ................................................................ 57 2.2.3 Assignment of a-helices .........................................................59 2.2.4 Derivation of axial v ecto rs ...................................................... 60 2.2.5 Geometrical properties m easured ............................................ 62 2.2.6 Physical properties measured ................................................. 63 2.2.6./ Hydrophobicity .................................................63 2.2.6.// Hydrophobic moment .......................................63 2.2.6./// Accessibility ......................................................65 2.2.6./V Accessibility moment .............................. 6 8 2.3 Results - Analysis of single helix properties .................................. 69 2.3.1 Helix le n g th ............................................................................... 69 2.3.2 Helix id e ality .............................................................................69 2.3.3 Helix ideality as a function of helix length ...........................71 2.3.3./ Calculation of standard Ca-Ca virtual torsion angles .................................................... 71 2.3.3.// Helix ideality in short a-h elices......................72 2.3.3./// Helix ideality in longer helices
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