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Theses Digitisation: This Is a Digitised Version of the Original Print Thesis. Copyright and Moral https://theses.gla.ac.uk/ Theses Digitisation: https://www.gla.ac.uk/myglasgow/research/enlighten/theses/digitisation/ This is a digitised version of the original print thesis. Copyright and moral rights for this work are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This work cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given Enlighten: Theses https://theses.gla.ac.uk/ [email protected] The Geometry of Hydrogen-Bonds and Carbonyl-Carbonyl Interactions Between Tra/is-Amides in Proteins and Small Molecules William John Buddy Submitted for the degree of Doctor of Philosophy Division of Biochemistry and Molecular Biology Faculty of Biomedical and Life Sciences UNIVERSITY o / GLASGOW April 2005 ProQuest Number: 10391071 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 com plete 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 10391071 Published by ProQuest LLO (2017). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States C ode Microform Edition © ProQuest LLO. ProQuest LLO. 789 East Eisenhower Parkway P.Q. Box 1346 Ann Arbor, Ml 48106- 1346 ^GLASGOW UNIVERSHT LIBRARY: Abstract The geometries, at the level of atoms or groups of atoms, of interactions and motifs found in crystal structures in the Protein Data Bank (PDB) and the Cambridge Structural Database (CSD) are analysed. The bulk of the thesis examines electrostatic interactions that occur between trans secondary amide groups, or peptide groups as they are known in proteins. The two types considered are N-H "0=C hydrogen-bonds and carbonyl-carbonyl interactions. Additionally, a chapter investigates specific hydrogen-bonded motifs, known as asx- and ST-tums, that commonly occur within protein structures. The geometry of hydrogen-bonds between trans secondary amide groups (i.e. peptide groups) has been studied extensively in proteins, and to a lesser extent in the CSD. They are a subset of the general case of N-H-'0=C hydrogen-bonds. Previous analyses of the CSD have shown a tendency for N-H’”0=C hydrogen-bonds to exhibit lone-pair directionality, where the hydrogen atom is near to the plane of the lone-pairs of the carbonyl oxygen atom, and the H - 0=C angle approaches 120°. For trans secondary amides the in-plane preference is also obseiwed, but the H*--0=C angle is greater, averaging about 150°. Here, an examination of the CSD allows elucidation of four factors that together account for this difference in H-”0=C : 1. A smaller proportion of trans secondary amide carbonyl oxygens accept more than one hydrogen-bond than do carbonyl oxygens in general. 2. N-H"-0=C bonds often occur in ‘ring’ motifs with relatively constrained geometries and H”-0=C values near 120°. These cannot be formed by trans secondary amides. 3. Chains of hydrogen-bonds between trans secondary amides, with large H---0=C values, often extend throughout the crystal lattice. 4. The steric accessibility of trans secondary amide carbonyl oxygens is less than for carbonyl oxygens in general. It has been suggested that electrostatic interactions between carbonyl groups affect hydrogen-bond geometry in a-helix and p-sheet, influence the twist of p-sheet, encourage polarization of carbonyl groups in a-helix, and explain the propensity of asparagine and aspartate residues in unusual regions of the Ramachandran plot. The carbonyl groups of ketones in the CSD frequently interact with each other, and commonly occur in three geometric motifs, that can be described as antiparallel, parallel, or perpendicular. At optimal geometry the antiparallel motif has energetic favourability approaching that of a medium-strength hydrogen-bond. Here it is shown that, after hydrogen-bonding has been taken into consideration, carbonyl-carbonyl interactions between trans secondary amides in the CSD also occur in these three motifs, and with a surprisingly similar propensity: 48% occur in the antiparallel arrangement (cf. 49% of those between ketones). Furthermore, interactions between main-chain carbonyl groups in a 454-chain subset of the PDB are identified. For each carbonyl-carbonyl interaction, its geometry, local secondary structure, and local hydrogen-bonding, are considered. The three motifs present in the CSD are not found to be representative of the geometries present in the PDB. However, other favourable carbonyl-carbonyl interaction motifs are observed. These occur in a variety of situations with respect to secondary structure and hydrogen-bonding, and are prevalent at the C-termini of a-lielices. They are shown to contribute to the stability of common C-termini capping conformations, one being the Schellman loop, the other being the case where a pro line terminates the helix. The hydro gen-bonded p-tum is a small, well characterised, protein motif defined by a hydrogen-bond between the main-chain carbonyl group of one residue and the main-chain N-H group of another three residues ahead in the polypeptide chain. There are four common types, distinguished by geometry: I, I', II, and If. In Asx- and ST-turns, the side-chain carbonyl of an asparagine, aspartate, serine, or tlireonine residue hydrogen-bonds with the main-chain N-H of a residue two ahead in the chain, such that they structurally mimic the p-tum. Asx-tums have previously been categorized into four classes and ST-tums into three categories, based on side-chain rotamer types and the conformation of the central residue of each turn. Here it is shown that the four classes of asx-tum are geometrically equivalent to the four types of hydrogen-bonded p-turn, and that the three categories of ST-tum are geometrically equivalent to three of the four types of hydrogen-bonded p-tum. It is proposed that asx- and ST-tums be named using the type I, II, r and IF p-tum nomenclature. Using this nomenclature, the frequency of occurrence of both asx- and ST-tums is: type IF > type I > type II > type F, whereas for p-tums it is type I > type II > type F > type IF. It is found that the type II Asx- or ST-turn is the same as a previously identified hydrogen-bonded motif called the Asx- or ST-nest. To the memory o f my brother, James. Acknowledgments Thanks to: Prof James Milner-White, my supeiMsor in Glasgow, for his constant guidance and encouragement throughout. Willem Nissink, my supervisor at the Cambridge Crystallographic Data Centre (CCDC), for his consistent support in all aspects of the work. Frank Allen, executive director o f the CCDC, for electing to spend so much valuable time on my project, for critical appraisals o f the text, and for providing, at crucial stages, his carefully considered advice on the overall direction of the work. Also, the staff o f the CCDC, particularly Sam Motherwell for all o f his help with the steric accessibility section. He provided the RPluto data, along with much helpful advice. Robin Taylor for stimulating discussions regarding hydrogen-bond geometry. The BBSRC and CCDC for funding. The protein crystallography group at the University o f Glasgow, both for scientific and social support. Particularly: Alastair McEwen, Alan Riboldi-Tunnicliffe, Neil Paterson, and Adrian Lapthorn. Zoe Gokhale for coding the identification and characterisation program for intraprotein carbonyl-carbonyl interactions. Gilleain Torrance for assistance with other aspects of the intraprotein carbonyl-carbonyl interaction section. Stuart Mackayfor IT support and his friendship, but particularly for tolerating and responding to my endless wails of, "my computer's broken!" and, "why, why, why doesn't it work?". My friends, whether back home in Northern Ireland, here in Glasgow, or elsewhere, for providing distraction and escape when most needed. Lastly, and most importantly, my parents and my sister, for always being there when I need them, and for their persistent love and attention, even in my darkest moods. Contents Page 1 Abbreviations, Tables and Figures 1 2 Introduction 2.1 Outline 2.2 General 2.3 Hydrogen-bonding between tr«rt5-amide groups 2.3.1 Context 2.3.2 Small molecule studies 9 2.3.3 Protein studies 11 2.4 Carbonyl-carbonyl interactions between trans-amide groups 2.4.1 Context 13 2.4.2 Small molecule studies 13 2.4.3 Protein studies 15 2.5 Mimicry of P-turns by Asx- and ST-turns 2.5.1 Context 17 2.5.2 P-tums 17 2.5.3 Asx-tums and ST-tums 18 2.5.4 Nests 20 Hydrogen-bonding between trans-amide groups; Factors affecting hydrogen-bond geometry 3.1 Brief introduction and outline 21 3.2 Materials and methods 3.2.1 Database searches 22 3.2.2 Statistical correction for angular data 23 3.3 Results & Discussion 3.3.1 Hydrogen-bonds between trans-amide groups 24 3.3.2 Comparison with other hydrogen-bonded systems 26 3.3.3 Hydrogen-bonded chains 29 3.3.4 Multiple hydrogen-bonds 31 3.3.5 Ring motifs 33 3.3.6 Tliree-centered hydrogen-bonds 37 3.3.7 Summary of factors affecting H- -0=C angle 39 3.3.8 Other Aspects
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