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3 results on '"Macromolecules--Structure"'

1. Comparing chemistry to outcome: the development of a chemical distance metric, coupled with clustering and hierarchal visualization applied to macromolecular crystallography

Author

Gaetano T. Montelione, Amanda M. Ruby, Thomas D. Grant, Andrew E. Bruno, Jayaraman Seetharaman, John F. Hunt, Edward H. Snell, and Joseph R. Luft

Subjects
lcsh:Medicine, Bioinformatics, Crystallography, X-Ray, law.invention, Polyethylene Glycols, Crystal, Bacteroides fragilis, law, Catalytic Domain, Cluster Analysis, Crystallization, Macromolecules--Structure, lcsh:Science, 0303 health sciences, Multidisciplinary, Crystallography, Chemistry, Physics, Hydrogen-Ion Concentration, Condensed Matter Physics, Macromolecular Crystallography, Metric (mathematics), Physical Sciences, Crystallographic Techniques, Biological system, Macromolecule, Research Article, Macromolecular Substances, 030303 biophysics, X-Ray Crystallography, Structural Characterization, Research and Analysis Methods, Crystals, Phosphates, 03 medical and health sciences, Similarity (network science), Bacterial Proteins, Computational Techniques, Solid State Physics, Cluster analysis, 030304 developmental biology, lcsh:R, Sodium, Models, Theoretical, Hierarchical clustering, Visualization, Crystal Growth, Chemical Properties, Potassium, lcsh:Q, Crystal Structure Refinement
Abstract

Many bioscience fields employ high-throughput methods to screen multiple biochemical conditions. The analysis of these becomes tedious without a degree of automation. Crystallization, a rate limiting step in biological X-ray crystallography, is one of these fields. Screening of multiple potential crystallization conditions (cocktails) is the most effective method of probing a proteins phase diagram and guiding crystallization but the interpretation of results can be time-consuming. To aid this empirical approach a cocktail distance coefficient was developed to quantitatively compare macromolecule crystallization conditions and outcome. These coefficients were evaluated against an existing similarity metric developed for crystallization, the C6 metric, using both virtual crystallization screens and by comparison of two related 1,536-cocktail high-throughput crystallization screens. Hierarchical clustering was employed to visualize one of these screens and the crystallization results from an exopolyphosphatase-related protein from Bacteroides fragilis, (BfR192) overlaid on this clustering. This demonstrated a strong correlation between certain chemically related clusters and crystal lead conditions. While this analysis was not used to guide the initial crystallization optimization, it led to the re-evaluation of unexplained peaks in the electron density map of the protein and to the insertion and correct placement of sodium, potassium and phosphate atoms in the structure. With these in place, the resulting structure of the putative active site demonstrated features consistent with active sites of other phosphatases which are involved in binding the phosphoryl moieties of nucleotide triphosphates. The new distance coefficient, CDcoeff, appears to be robust in this application, and coupled with hierarchical clustering and the overlay of crystallization outcome, reveals information of biological relevance. While tested with a single example the potential applications related to crystallography appear promising and the distance coefficient, clustering, and hierarchal visualization of results undoubtedly have applications in wider fields.

Published
2014

2. Supramolecular architecture of multi-dimensional frameworks in crystalline adducts of hexamethylenetetramine with hexacyanoferrates and metal pseudohalides.

Author

Xue, Feng., Chinese University of Hong Kong Graduate School. Division of Chemistry., Xue, Feng., and Chinese University of Hong Kong Graduate School. Division of Chemistry.

Abstract

by Feng Xue., Thesis (M.Phil.)--Chinese University of Hong Kong, 1996., Includes bibliographical references (leaves 76-84)., ACKNOWLEDGMENTS --- p.I, p.II, TABLE OF CONTENTS --- p.III, LIST OF TABLES --- p.V, LIST OF FIGURES --- p.VI, Chapter CHAPTER 1: --- INTRODUCTION --- p.1, Chapter 1. --- supramolecular chemistry --- p.1, Chapter 2. --- Infinite multi-dimensional architecture --- p.10, Chapter 3. --- Chemistry of pseudohalides --- p.15, Chapter 4. --- Chemistry of hexamethylenetetramine --- p.20, Chapter 5. --- Objectives of the present research --- p.24, Chapter CHAPTER 2: --- EXPERIMENTAL --- p.25, Chapter 1. --- Preparation --- p.25, Chapter 1.1 --- Materials --- p.25, Chapter 1.2 --- Preparation of the compounds --- p.25, Chapter 2. --- X-ray crystallography --- p.26, Chapter CHAPTER 3: --- DESCRIPTION OF CRYSTAL STRUCTURES --- p.28, Chapter 1. --- isostructural compounds K2[FEII(CN)6] ´Ø 2[(CH2)6n4H] ´Ø 4H2 O(1) and K2[FEIII(CN)6] ´Ø [(CH2)6N4H] ´Ø [(CH2)6N4] ´Ø 4H2O (2) --- p.28, Chapter 2. --- Crystal structure of NA2[FEIII(CN)6] ´Ø [(CH2)6N4H] ´Ø [(CH2)6N4] ´Ø 5H2O (3) --- p.33, Chapter 3. --- Crystal structure of K3[FEIII(CN)6] ´Ø 2[(CH2)6N4] ´Ø 4H2O (4) --- p.37, Chapter 4. --- Crystal Structure of ferricyanic acid-HMT adduct H3[FEIII(CN)6] ´Ø 2[(CH2)6N4] ´Ø 2H2O (5) --- p.43, Chapter 5. --- "Crystal structure of cadmium chloride-HMT adduct, Cd2[C6H12N4H2]Cl6´Ø 3H2O (6)" --- p.48, Chapter 6. --- "Crystal structure of cadmium bromide-HMT adduct, CdBr2 ´Ø 2[(CH2)6N4] ´Ø 2H2O (7)" --- p.53, Chapter 7. --- "Crystal structure of cadmium iodide-HMT adduct, 3CdI2 ´Ø 2[(CH2)6N4] ´Ø 4H2O (8)" --- p.57, Chapter 8. --- Crystal structure of cadmium thiocyanate-HMT adduct Cd(SCN)2 ´Ø 1(CH2)6N4] ´Ø MeOH (9) --- p.61, Chapter 9. --- Crystal structure of cobalt cyanate-HMT adduct Co(NCO)2 ´Ø [(CH2)6N4] ´Ø 2H2O (10) --- p.67, Chapter CHAPTER 4: --- SUMMARY AND DISCUSSIONS --- p.72, REFERENCES --- p.76, TABLE A1 Crystallographic data for compounds 1 ~5 --- p.85, TABLE A2 Crystallographic data for compounds 6~10 --- p.86, APPENDIX 1 Atomic Coordinates (Ax 104) and Equivalent Isotropic Thermal Parameters (A 2x103) --- p.87, APPENDIX 2 Anisotropic thermal parameters (A2x 103) --- p.92, APPENDIX 3 H-atom coordinates (x 104) and isotropic thermal parameters (A2x 103) --- p.96, http://library.cuhk.edu.hk/record=b5895724, Use of this resource is governed by the terms and conditions of the Creative Commons “Attribution-NonCommercial-NoDerivatives 4.0 International” License (http://creativecommons.org/licenses/by-nc-nd/4.0/)

Published
1996

3. Functional dendrimers: synthesis and applications.

Author

Mak, Chi Ching., Chinese University of Hong Kong Graduate School. Division of Chemistry., Mak, Chi Ching., and Chinese University of Hong Kong Graduate School. Division of Chemistry.

Abstract

by Chi Ching Mak., Thesis (Ph.D.)--Chinese University of Hong Kong, 1995., Includes bibliographical references (leaves 122-130)., Contents --- p.i, Acknowledgments --- p.iii, p.iv, Abbreviations --- p.v, List of publications originated from this thesis --- p.vi, Chapter I --- Introduction to Dendrimer Chemistry, Chapter I-1 --- Background --- p.1, Chapter I-2 --- Comparison of Dendrimer and Linear Polymer --- p.6, Chapter I-3 --- Synthesis --- p.8, Chapter I-3-1 --- Divergent-growth Approach --- p.8, Chapter I-3-2 --- Convergent-growth Approach --- p.10, Chapter I-3-3 --- Accelerated Approach --- p.11, Chapter II --- Functional Dendrimers --- p.14, Chapter III --- Optically Active Dendrimers, Chapter III-1 --- Background --- p.18, Chapter III-2 --- Architecture of Tartaric Acid-based Optically Active Dendrimers --- p.23, Chapter III-3 --- Results and Discussion --- p.24, Chapter III-3-1 --- Syntheses and Structure Elucidations of all (L)-Tartaric Acid-based Dendrimers 41 and 42 --- p.24, Chapter III-3-2 --- Syntheses and Structure Elucidations of Optically Active Layer-block Dendrimers 43 and 44 --- p.29, Chapter III-3-3 --- Structure-Optical Rotation Relationships --- p.33, Chapter III-3-4 --- "Syntheses and Characterization of Higher Generation, Optically Active Dendritic Fragments" --- p.37, Chapter III-3-5 --- Conclusions --- p.43, Chapter IV --- Catalytic Dendrimers, Chapter IV-1 --- Background --- p.44, Chapter IV-2 --- Syntheses and Characterization of Dendritic Bis(oxazoline) Copper(II) Catalyst --- p.47, Chapter IV-2-1 --- Architecture --- p.47, Chapter IV-2-2 --- Syntheses of the Bis(oxazoline) Core Precursors --- p.49, Chapter IV-2-3 --- Syntheses of the Achiral Dendritic Sectors --- p.51, Chapter IV-2-4 --- Syntheses of Dendritic Ligands --- p.52, Chapter IV-3 --- Kinetics and Selectivity of Dendritic Bis(oxazoline)-Copper(II) Complex Catalyzed Diels-Alder Reaction --- p.55, Chapter IV-3-1 --- Introduction --- p.55, Chapter IV-3-2 --- Reaction Mechanism and Reactivity Kinetics --- p.56, Chapter IV-3-3 --- Substrate Selectivity --- p.63, Chapter IV-4 --- Syntheses and Properties of Optically Active Dendritic Bis(oxazoline) Ligands and Their Copper(II) Complexes Catalysts --- p.65, Chapter IV-4-1 --- Background --- p.65, Chapter IV-4-2 --- Syntheses and Characterization of Chiral Dendritic Bis(oxazoline) Ligands 109-112 --- p.67, Chapter IV-4-3 --- Chiroptical Properties --- p.72, Chapter IV-4-4 --- Enantioselectivity of the Metal-catalyzed Diels-Alder Reaction --- p.73, Chapter IV-4-5 --- Conclusions --- p.74, Chapter V --- Summary --- p.75, Chapter VI --- Experimental --- p.77, References --- p.122, Spectra --- p.131, http://library.cuhk.edu.hk/record=b5888848, Use of this resource is governed by the terms and conditions of the Creative Commons “Attribution-NonCommercial-NoDerivatives 4.0 International” License (http://creativecommons.org/licenses/by-nc-nd/4.0/)

Published
1996

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