DOCSLIB.ORG

Functional Behavior of Molecular Baskets and Structure-Activity Studies on Trapping Organophosphorus Nerve Agents in Water

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Functional Behavior of Molecular Baskets and Structure-Activity Studies on Trapping Organophosphorus Nerve Agents in Water Functional Behavior of Molecular Baskets and Structure-Activity Studies on Trapping Organophosphorus Nerve Agents in Water DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Yian Ruan Graduate Program in Chemistry The Ohio State University 2014 Dissertation Committee: Jovica D. Badjic, Advisor Christopher M. Hadad Jon R. Parquette Copyright by Yian Ruan 2014 Abstract Molecular recognition is exploited by nature to carry out delicately regulated reactions and form precisely organized structures in living organisms. Enzymes promote reactions by preorganizing substrates and stabilizing transition states in an active site via covalent and non-covalent interactions. Receptor proteins and antibodies can respond selectively to stimuli and trigger subsequent activities. These protein-substrate interactions have been great inspirations for chemists in the design of synthetic receptors as hosts and the study of their molecular recognition properties. Investigation of recognition behaviors can help decipher sub-cellular processes. Moreover, some artificial host-guest complexes have found applications in catalysis, sensing, imaging and drug delivery systems. The Badjic group has developed a family of host molecules called molecular baskets to study the effect of gating on molecular recognition. These baskets possess a cavity formed by a benzene base and phthalimide side walls. Pyridine-based gates close the basket via hydrogen bonds or metal chelation. Tuning the electronic and steric characteristics of gates affects the rate of guests entering and departing the basket. ii With all the knowledge about molecular gating, questions arise as to whether these gates can be applied to other platforms and how the mechanism of gating will be affected. A new quinoxaline containing platform was synthesized, which gave a more spacious basket 2.1 (see Chapter 2). Amidopyridine gates were installed and shown to close the basket by forming a seam of intramolecular hydrogen bonds. The recognition characteristics of both smaller basket 1.7 and bigger 2.1 were quantified in different solvents and the apparent guest binding (Ka) was found to be inversely proportional to the affinity of bulk solvents populating each host (Ks). Mechanisms of gate operations were also investigated for both baskets. Results suggested two competing pathways, determined by the population of basket’s inner space. All previous recognition studies of molecular basket were carried out in organic solvents; however, creating similar hosts in aqueous media is desirable, as water is the media for all biological reactions. Water-soluble synthetic receptors are excellent tools to study more complicated processes in nature. In an effort to mimic butyrylcholinesterase (BuChE) and paraoxonase-1 (PON1) enzymes as bioscavengers of organophosphorus compounds, water soluble cup-shaped basket 3.1 was developed. The basket with histamine residues (see Chapter 3) was first prepared and is able to trap organophosphonates whose shape and size correspond to chemical warfare agents of G type. A series of organophosphonates were found to bind the basket with different affinities. Experimental and computational studies indicated that the cavity can expand to accommodate more sizable guests, suggesting an induced-fit model of recognition. iii Subsequently, baskets 4.1−4.7 with amino acids at the rim (see Chapter 4) were synthesized and solubilized in water at physiological pH. They were found to trap dimethyl methylphosphonate (DMMP), akin to sarin in size, and steric interactions at the rim had a great impact on the binding affinity. These results are important toward creating effective supramolecular sensors and degradation catalysts of nerve agents. iv Dedication This document is dedicated to my family. v Acknowledgments I would like to first thank my advisor, Dr. Jovica Badjic, for his excellent guidance and all the help for my graduate school career. His enthusiasm for research and attitude towards science has great influence on me. I would also like to thank Dr. Baoyu Wang and other group members for all the insightful discussion and suggestions. Special thanks to Dr. Christopher Hadad and his group members for their excellent computational work as well as inspiring suggestions. I also want to thank Dr. Tanya Young, Dr. Chunhua Yuan and Dr. Tapas Mal for their help with NMR experiments, and Dr. Vicki Wysocki and Yang Song for their work on mass spectrometry. I would like to express my gratitude to all my friends and family. My deepest appreciation goes to my mother, who has been always caring and supportive through the years. I was constantly inspired by her persistence and optimism even in the hardest of times. Finally, I want to thank my husband, Huayang Liu, whose love and encouragement allowed me to finish this journey. vi Vita 1986................................................................Born-Beijing, China 2008................................................................B.S. Chemistry and Biology, Tsinghua University, China 2008 to present ..............................................Graduate Research and Teaching Associate, Department of Chemistry and Biochemistry, The Ohio State University Publications Yian Ruan, Erdin Dalkilic, Paul W. Peterson, Aroh Pandit, Arif Dastan, Jason D. Brown, Shane M. Polen, Christopher M. Hadad, and Jovica D. Badjic, Trapping of Organophosphorus Chemical Nerve Agents in Water with Amino Acid Functionalized Baskets, Chem. Eur. J., 2014, in press. Yian Ruan, Bao-Yu Wang, Jeremy Erb, Shigui Chen, Christopher M. Hadad, and Jovica D. Badjic, On the Role of Guests in Enforcing the Mechanism of Action of Gated Baskets, Org. Biomol. Chem., 2013, 11, 7667-7675. (Cover Article) Yian Ruan, Taha A. Hashem, Ryan J. Yoder, Veselin Maslak, Christopher M. Hadad and Jovica D. Badjić, The Prospect of Selective Recognition of Nerve Agents with Modular Basket-like Hosts. A Structure-Activity Study of the Entrapment of a Series of Organophosphonates in Aqueous Media, J. Phys. Chem. B, 2013, 117, 3240 - 3249. Shigui Chen, Yian Ruan, Jason D. Brown, Judith Gallucci, Veselin Maslak, Christopher M. Hadad and Jovica D. Badjic, The Assembly of Amphiphilic Baskets in Stimuli- Responsive Vesicles. Developing a strategy for the Detection of Organophosphorus Chemical Nerve Agents, J. Am. Chem. Soc., 2013, 135 (40), 14964–14967. vii Keith Hermann, Stephen Sardini, Yian Ruan, Ryan Yoder, Chakraborty Mrinal, Shubam Vyas, Christopher M. Hadad and Jovica D. Badjić, Method for the Preparation of Derivatives of Heptiptycene: Toward Dual-Cavity Baskets, J. Org. Chem., 2013, 78, 2984 - 2991. Jovica D. Badjic, Sandra Stojanovic, Yian Ruan, Kinetically and Thermodynamically Controlled Syntheses of Covalent Molecular Capsules. Advances in Physical Organic Chemistry, 2011, 45, 1-35. (Book Chapter) Pei-Yuan Jin, Peng Jin, Yi-An Ruan, Yong Ju, and Yu-Fen Zhao, Synthesis of Some Novel 1,2,3-Triazole-Fused Oligonucleoside and Oligosaccharide Analogs, Synlett, 2007, 19, 3003-3006. Fields of Study Major Field: Chemistry viii Table of Contents Abstract ............................................................................................................................... ii Dedication ........................................................................................................................... v Acknowledgments.............................................................................................................. vi Vita .................................................................................................................................... vii List of Tables .................................................................................................................... xii List of Figures .................................................................................................................. xiv List of Abbreviations ................................................................................................... xxviii Chapter 1 : Molecular Baskets and Host-guest Chemistry ................................................. 1 1.1 Introduction ................................................................................................... 1 1.2 Molecular baskets and gating ........................................................................ 8 1.3 Molecular encapsulation in aqueous solution ............................................. 16 1.4 Conclusion ................................................................................................... 20 Chapter 2 : On the Role of Guests in Enforcing the Mechanism of Action of Gated Baskets .............................................................................................................................. 22 2.1 Introduction ................................................................................................. 22 2.2 Design and preparation of basket ................................................................ 24 ix 2.3 Encapsulation thermodynamics................................................................... 32 2.4 Conformation dynamics and P/M racemization mechanisms ..................... 36 2.5 Conclusion ................................................................................................... 43 Chapter 3 : The Prospect of Selective Recognition of Nerve Agents with Modular Basket- like Hosts. A Structure-Activity Study of the Entrapment of
Load more

Recommended publications
  • Latest Stable Copy and Install It With: Chmod+X Chimera- *.Bin&&./Chimera- *.Bin
    Tangram Suite Documentation Release 0.0.8 InsiliChem Mar 26, 2019 General instructions 1 What is Tangram Suite 3 2 How to install Tangram Suite5 3 General usage 7 4 FAQ & Known issues 9 5 List of Tans 11 6 Tangram BondOrder 13 7 Tangram QMSetup 15 8 Tangram DummyAtoms 17 9 Tangram GAUDIView 19 10 Tangram MMSetup 21 11 Tangram NCIPlot 23 12 Tangram NormalModes 25 13 Tangram OrbiTraj 27 14 Tangram PLIP 29 15 Tangram PoPMuSiCGUI 31 16 Tangram PropKaGUI 33 17 Tangram ReVina 35 18 Tangram SubAlign 37 19 Tangram TalaDraw 39 i ii Tangram Suite Documentation, Release 0.0.8 It’s composed of several independent graphical interfaces and commands for UCSF Chimera. General instructions 1 Tangram Suite Documentation, Release 0.0.8 2 General instructions CHAPTER 1 What is Tangram Suite In progress 3 Tangram Suite Documentation, Release 0.0.8 4 Chapter 1. What is Tangram Suite CHAPTER 2 How to install Tangram Suite 2.1 Install the full Tangram Suite (recommended) 1 - If you don’t have UCSF Chimera installed, download the latest stable copy and install it with: chmod+x chimera- *.bin&&./chimera- *.bin 2 - Download the latest installer from the releases page (Linux and MacOS only) and run it with: bash tangram-*.sh 2.2 Using the conda meta-package Instead of using the Bash installer, you can use conda (if you are already using it) to create a new environment with the tangram metapackage, which will handle all the dependencies. While in alpha, both insilichem channels are needed (the main one and also the dev label): conda create-n tangram-c insilichem/label/dev-c insilichem-c omnia-c rdkit-c ,!conda-forge tangram 2.3 Updating extensions Each extension will check if there’s a new release available every time you launch it.
    [Show full text]
  • UCSF Chimera Was Developed by the Computer Graphics Laboratory at the University of California, San Francisco, Under Support of NIH Grant P41-RR01081
    matrixcopy apply the transformation matrix of one model to another tcolor color using texture map colors UCSF Chimera matrixget write the current transformation matrices to a ®le texture de®ne texture maps and associated colors QUICK REFERENCE GUIDE June 2007 matrixset read and apply transformation matrices from a ®le thickness move the clipping planes in opposite directions minimize energy-minimize structures turn rotate about the X, Y, or Z axis mmaker (matchmaker) align models in sequence, then in 3D vdw* display van der Waals (VDW) surface modelcolor set color at the model level vdwde®ne* set VDW radii Commands modeldisplay* set display at the model level vdwdensity set VDW surface dot density *reverse function Äcommand available move translate along the X, Y, or Z axis version show copyright information and Chimera version movie capture image frames and assemble them into a movie viewdock start ViewDock and load docking results 2dlabels create arbitrary text labels and place them in 2D namesel name and save the current selection wait suspend command processing until motion has stopped ac enable accelerators (keyboard shortcuts) neon create a shadowed stick/tube image (not on Windows) window adjust the view to contain the speci®ed atoms addaa add an amino acid to a peptide C-terminus objdisplay* display graphical objects windowsize adjust the dimensions of the graphics window addcharge assign partial charges to atoms open* read structures and data, execute command ®les write save a molecule model as a PDB ®le addh add hydrogens pdbrun
    [Show full text]
  • Isomerism in Organic Compounds
    DEPARTMENT OF ORGANIC CHEMISTRY PHARMACEUTICAL FACULTY SEMMELWEIS UNIVERSITY László Szabó − Gábor Krajsovszky ISOMERISM IN ORGANIC COMPOUNDS Budapest 2017 © László Szabó © Gábor Krajsovszky ISBN 978-963-12-9206-0 Publisher: Dr. Gábor Krajsovszky 2 Acknowledgements The Author is thankful to dr. Ruth Deme assistant lecturer for drawing the structural formulas, as well as to Mrs. Zsuzsanna Petró-Karátson for the typewriting of the text part. The Author is thankful to dr. Péter Tétényi for the translation of the manuscript to English language. Dr. Gábor Krajsovszky 3 ISOMERISM IN ORGANIC COMPOUNDS Isomers are the compounds with the same qualitative and quantitative composition of elements, therefore their relative molecular weights and general formulas are identical, but their structures – including in the 3D arrangement – are different. The compounds propyl chloride and propane are not isomers, since their qualitative composition of elements are different. The compounds propane and propene are not isomers, although they are built from the same elements, but with different quanti- tative composition of elements. The compounds propene and cyclohexane are not isomers, although they are built from the same elements, with the same ratio of ele- ments, their relative molecular weights are different. However, the compounds butane and isobutane are isomers, since they have the same general formula, but their 3D arrangement is different. Only one compound or many compounds may have the same general formulas. For example, methane (a linear saturated
    [Show full text]
  • 3D-Printing Models for Chemistry
    3D-Printing Models for Chemistry: A Step-by-Step Open-Source Guide for Hobbyists, Corporate ProfessionAls, and Educators and Student in K-12 and Higher Education Poster Elisabeth Grace Billman-Benveniste+, Jacob Franz++, Loredana Valenzano-Slough+* +Department of Chemistry, Michigan Technological University, ++Department of Mechanical Engineering, Michigan Technological University *Corresponding Author References 1. “LulzBot TAZ 5.” LulzBot, 14 Aug. 2018, www.lulzbot.com/store/printers/lulzbot-taz-5 2. Gaussian 16, Revision B.01, Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Petersson, G. A.; Nakatsuji, H.; Li, X.; Caricato, M.; Marenich, A. V.; Bloino, J.; Janesko, B. G.; Gomperts, R.; Mennucci, B.; Hratchian, H. P.; Ortiz, J. V.; Izmaylov, A. F.; Sonnenberg, J. L.; Williams-Young, D.; Ding, F.; Lipparini, F.; Egidi, F.; Goings, J.; Peng, B.; Petrone, A.; Henderson, T.; Ranasinghe, D.; ZakrzeWski, V. G.; Gao, J.; Rega, N.; Zheng, G.; Liang, W.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; HasegaWa, J.; Ishida, M.; NakaJima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Throssell, K.; Montgomery, J. A., Jr.; Peralta, J. E.; Ogliaro, F.; Bearpark, M. J.; Heyd, J. J.; Brothers, E. N.; Kudin, K. N.; Staroverov, V. N.; Keith, T. A.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A. P.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Millam, J. M.; Klene, M.; Adamo, C.; Cammi, R.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Farkas, O.; Foresman, J. B.; Fox, D. J. Gaussian, Inc., Wallingford CT, 2016. 3.
    [Show full text]
  • Development and Application of a Computational Platform for Complex Molecular Design Jaime Rodríguez-Guerra Pedregal
    ADVERTIMENT. Lʼaccés als continguts dʼaquesta tesi queda condicionat a lʼacceptació de les condicions dʼús establertes per la següent llicència Creative Commons: http://cat.creativecommons.org/?page_id=184 ADVERTENCIA. El acceso a los contenidos de esta tesis queda condicionado a la aceptación de las condiciones de uso establecidas por la siguiente licencia Creative Commons: http://es.creativecommons.org/blog/licencias/ WARNING. The access to the contents of this doctoral thesis it is limited to the acceptance of the use conditions set by the following Creative Commons license: https://creativecommons.org/licenses/?lang=en Development and Application of a Computational Platform for Complex Molecular Design a dissertation submitted by Jaime Rodríguez-Guerra Pedregal & directed by Prof. Dr. Jean-Didier Maréchal in fulfillment of the requirements for the degree of Doctor of Biotechnology Tutor: Prof. Dr. Jordi Joan Cairó Badillo Department of Chemical, Biological and Environmental Engineering Universitat Autònoma de Barcelona July 2018 Development and Application of a Computational Platform for Complex Molecular Design a dissertation submitted by & recommended for acceptance by advisor Jaime Rodríguez-Guerra Pedregal Prof. Dr. Jean-Didier Maréchal Tutor: Prof. Dr. Jordi Joan Cairó Badillo Department of Chemical, Biological and Environmental Engineering Universitat Autònoma de Barcelona July 2018 ©2018 – Jaime Rodríguez-Guerra Pedregal Licensed as Creative Commons BY-NC-ND Attribution-NonCommercial-NoDerivs In the beginning, there was nothing. And God said «Let there be light». And there was light. There was still nothing, but you could see it a lot better. —WoodyAllen. Development and Application of a Computational Platform for Complex Molecular Design by Jaime Rodríguez-Guerra Pedregal Abstract In this dissertation, a series of novel computational modeling tools is reported.
    [Show full text]
  • Hands-On Tutorials of Autodock 4 and Autodock Vina
    Hands-on tutorials of AutoDock 4 and AutoDock Vina Pei-Ying Chu (朱珮瑩) Supervisor: Jung-Hsin Lin (林榮信) Research Center for Applied Sciences, Academia Sinica 2018 Frontiers in Computational Drug Design, Academia Sinica, March 16-20, 2018 AutoDock http://autodock.scripps.edu AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock 4 is free and is available under the GNU General Public License. 2 AutoDock Vina http://vina.scripps.edu/ Because the scoring functions used by AutoDock 4 and AutoDock Vina are different and inexact, on any given problem, either program may provide a better result. AutoDock Vina is available under the Apache license, allowing commercial and 3 non-commercial use and redistribution. http://autodock.scripps.edu/downloads These programs were installed on VM. 4 http://mgltools.scripps.edu/ AutoDockTools (ADT) is developed to help set up the docking. ADT is included in MGLTools packages. 5 In general, each docking (AutoDock 4 and/or AutoDock Vina) requires: 1. structure of the receptor (protein), in pdbqt format 2. structure of the ligand (small molecule, drug, etc.) in pdbqt format 3. docking and grid parameters (search space) PDBQT format is very similar to PDB format but it includes partial charges ('Q') and AutoDock 4 (AD4) atom types ('T'). • Preparing the ligand involves ensuring that its atoms are assigned the correct AutoDock4 atom types, adding Gasteiger charges if necessary, merging non-polar hydrogens, detecting aromatic carbons if any, and setting up the 'torsion tree'.
    [Show full text]
  • H2O2 and NH 2 OH
    Int. J. Mol. Sci. 2006 , 7, 289-319 International Journal of Molecular Sciences ISSN 1422-0067 © 2006 by MDPI www.mdpi.org/ijms/ A Quest for the Origin of Barrier to the Internal Rotation of Hydrogen Peroxide (H 2O2) and Fluorine Peroxide (F 2O2) Dulal C. Ghosh Department of Chemistry, University of Kalyani, Kalyani-741235, India Email: [email protected], Fax: +91-33 25828282 Received: 2 July 2006 / Accepted: 24 July 2006 / Published: 25 August 2006 Abstract: In order to understand the structure-property relationship, SPR, an energy- partitioning quest for the origin of the barrier to the internal rotation of two iso-structural molecules, hydrogen peroxide, H 2O2, and fluorine peroxide, F 2O2 is performed. The hydrogen peroxide is an important bio-oxidative compound generated in the body cells to fight infections and is an essential ingredient of our immune system. The fluorine peroxide is its analogue. We have tried to discern the interactions and energetic effects that entail the nonplanar skew conformation as the equilibrium shape of the molecules. The physical process of the dynamics of internal rotation initiates the isomerization reaction and generates infinite number of conformations. The decomposed energy components faithfully display the physical process of skewing and eclipsing as a function of torsional angles and hence are good descriptors of the process of isomerization reaction of hydrogen peroxide (H 2O2) and dioxygen difluoride (F 2O2) associated with the dynamics of internal rotation. It is observed that the one-center, two-center bonded and nonbonded interaction terms are sharply divided in two groups. One group of interactions hinders the skewing and favours planar cis/trans forms while the other group favours skewing and prefers the gauche conformation of the molecule.
    [Show full text]
  • Mai Muuttunut Pilit Muut Aidi Mini
    MAIMUUTTUNUT US009963689B2 PILIT MUUT AIDI MINI (12 ) United States Patent ( 10 ) Patent No. : US 9 ,963 , 689 B2 Doudna et al. ( 45) Date of Patent: May 8 , 2018 ( 54 ) CASI CRYSTALS AND METHODS OF USE FOREIGN PATENT DOCUMENTS THEREOF WO WO 2013 / 126794 AL 8 / 2013 ( 71 ) Applicant: The Regents of the University of wo WO 2013 / 142578 A19 / 2013 California , Oakland , CA (US ) WO WO 2013 / 176772 A1 11/ 2013 ( 72 ) Inventors : Jennifer A . Doudna , Oakland , CA OTHER PUBLICATIONS (US ) ; Samuel H . Sternberg , Oakland , McPherson , A . Current Approaches to Macromolecular Crystalli CA (US ) ; Martin Jinek , Oakland , CA zation . European Journal of Biochemistry . 1990 . vol . 189 , pp . (US ) ; Fuguo Jiang , Oakland , CA (US ); 1 - 23 . * Emine Kaya , Oakland , CA (US ) ; Kundrot, C . E . Which Strategy for a Protein Crystallization Project ? Cellular Molecular Life Science . 2004 . vol . 61, pp . 525 - 536 . * David W . Taylor, Jr. , Oakland , CA Benevenuti et al. , Crystallization of Soluble Proteins in Vapor (US ) Diffusion for X - ray Crystallography , Nature Protocols , published on - line Jun . 28 , 2007 , 2 ( 7 ) : 1633 - 1651. * ( 73 ) Assignee : THE REGENTS OF THE Cudney R . Protein Crystallization and Dumb Luck . The Rigaku UNIVERSITY OF CALIFORNIA , Journal. 1999 . vol. 16 , No . 1 , pp . 1 - 7 . * Drenth , “ Principles of Protein X - Ray Crystallography ” , 2nd Edi Oakland , CA (US ) tion , 1999 Springer - Verlag New York Inc ., Chapter 1 , p . 1 - 21. * Moon et al . , “ A synergistic approach to protein crystallization : ( * ) Notice : Subject to any disclaimer , the term of this Combination of a fixed -arm carrier with surface entropy reduction ” , patent is extended or adjusted under 35 Protein Science , 2010 , 19 : 901 -913 .
    [Show full text]
  • UCSF Chimera[Mdash]A Visualization System for Exploratory Research And
    UCSF Chimera—A Visualization System for Exploratory Research and Analysis ERIC F. PETTERSEN, THOMAS D. GODDARD, CONRAD C. HUANG, GREGORY S. COUCH, DANIEL M. GREENBLATT, ELAINE C. MENG, THOMAS E. FERRIN Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, California 94143-2240 Received 24 February 2004; Accepted 6 May 2004 DOI 10.1002/jcc.20084 Published online in Wiley InterScience (www.interscience.wiley.com). Abstract: The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1605–1612, 2004 Key words: molecular graphics; extensibility; visualization; multiscale modeling; sequence alignment Introduction had not anticipated.
    [Show full text]
  • Molecular Dynamics (MD) for Cancer Control Protocol
    Molecular Dynamics (MD) for Cancer control Protocol Claudio Nicolini ( [email protected] ) Claudio Ando Nicolini's Lab, NanoWorld, USA; HC Professor Nanobiotechnology, Lomonosov Moscow State University, Russia; Foreign Member Russian Academy of Sciences; President NWI Fondazione EL.B.A. Nicolini; Editor-in-Chief NWJ, Santa Clara, USA Marine Bozdaganyan Claudio Ando Nicolini's Lab, NanoWorld, USA; Lomonosov Moscow State University (MSU), Moscow, Russia; Fondazione EL.B.A. Nicolini Nicola Luigi Bragazzi Claudio Ando Nicolini's Lab, NanoWorld, USA Philippe Orekhov Claudio Ando Nicolini's Lab, NanoWorld, USA Eugenia Pechkova Claudio Ando Nicolini's Lab, NanoWorld, USA Method Article Keywords: Langmuir-Blodgett (LB)-based crystallography Posted Date: March 15th, 2016 DOI: https://doi.org/10.1038/protex.2016.016 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/13 Abstract In the present protocol, we describe how molecular dynamics \(MD) can be applied for studying Langmuir-Blodgett \(LB)-based crystal proteins. MD can therefore play a major role in nanomedicine, as well as in personalized medicine. Introduction The computer simulation of dynamics in molecular systems is widely used in molecular physics, biotechnology, medicine, chemistry and material sciences to predict physical and mechanical properties of new samples of matter. In the molecular dynamics method there is a polyatomic molecular system in which all atoms are interacting like material points, and behavior of the atoms is described by the equations of classical mechanics. This method allows doing simulations of the system of the order of 106 atoms in the time range up to 1 microsecond.
    [Show full text]
  • Eduardo's Guide for 3D Printing Proteins Using Chimera for 3D Printing
    Eduardo’s Guide for 3D Printing Proteins Eduardo da Veiga Beltrame – [email protected] - www.munfred.com ​ ​ ​ Using Chimera for 3D Printing UCSF Chimera is a free and open source molecular visualizer. In this tutorial we’ll show how Chimera can be used to generate 3D printable molecular models for FDM/FFF desktop 3D printers. You can download Chimera at https://www.cgl.ucsf.edu/chimera/. ​ ​ Finding PDB Files First, you need the coordinate file of the molecule you want to print. The files containing the atoms coordinates for a molecule are called .pdb files (for protein data bank). These structures are determined using an array of techniques such as x-ray crystallography and nuclear magnetic resonance, and when they are published they are also deposited in databases and become freely available for download. The biggest such database is the Protein Data Bank, and if you are interested it's worth a visit: www.rcsb.org ​ If you’re looking for cool structures and some explanations, the molecule of the month PDB articles at http://pdb101.rcsb.org/ are a good way to start browsing. They are ​ ​ written by David Goodsell, who is awesome. If you can't find your molecule, if it's not on the PDB it's probably because nobody knows it's structure yet. If what you want is some small molecule, you can try searching for the structure online, or can draw it using Avogadro, a free and open source molecule editor you can get at www.avogadro.cc. ​ ​ Visualizing and Exporting Models Once you have your PDB file, you can render it on a molecular visualizer.
    [Show full text]
  • Visualizing Protein Structures-Tools and Trends
    Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 12 January 2020 Visualizing protein structures - tools and trends 1,2 3 1,2 X. Martinez ,​ M. Chavent ,​ M. Baaden ​ ​ ​ 1) CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005, Paris, France 2) Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, Paris, France 3) Institut de Pharmacologie et de Biologie Structurale IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France Abstract Molecular visualisation is fundamental in the current scientific literature, textbooks and dissemination materials, forming an essential support for presenting results, reasoning on and formulating hypotheses related to molecular structure. Visual exploration has become easily accessible on a broad variety of platforms thanks to advanced software tools that render a great service to the scientific community. These tools are often developed across disciplines bridging computer science, biology and chemistry. Here we first describe a few Swiss Army knives geared towards protein visualisation for everyday use with an existing large user base, then focus on more specialised tools for peculiar needs that are not yet as broadly known. Our selection is by no means exhaustive, but reflects a diverse snapshot of scenarios that we consider informative for the reader. We end with an account of future trends and perspectives. Keywords Molecular Graphics, Protein visualization, Software tools, Virtual reality Introduction Many parts of science rely on a visualization-driven cycle of experimentation, reasoning, conjecture and validation, even more so in relation with structural biology and biophysics. Molecular visualization (1) in particular is now broadly used in many contexts, with the purpose of illustration in the scientific literature or the aim to gain insight about primary research data.
    [Show full text]