DOCSLIB.ORG

X-Ray Scattering of Helix, Analysis of Structure of Fibrous Proteins, Effect of Inter Molecular Packing

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
X-Ray Scattering of Helix, Analysis of Structure of Fibrous Proteins, Effect of Inter Molecular Packing Module 30 X-ray Scattering of helix, analysis of structure of fibrous proteins, effect of inter molecular packing Learning Objectives Introduction Helix X-ray fibre diffraction Theory of X-ray fibre diffraction Humidity and Molecular orientation Introduction: 30.1. The Discovery of X-rays: Wilhelm Conrad Röntgen, a German Scientist, while conducting a number of experiments on cathode rays in 1895 (cathode ray is emanation of electrons from the cathode end of a vacuum-pumped glass tube) observed a new form of radiation other than cathode rays. This new form of radiation was named as X-rays by him. Fig 30.1: Wilhelm Conrad Röntgen 30.2. X-ray Diffraction: The properties of X-rays were studied by various scientists. In 1912, a group of physicists at the University of Munich were interested in both crystallography and the behaviour of X-rays. P. P. Ewald and A. Sommerfeld were studying the passage of light waves through crystals. At a colloquium, discussing some of this work, Max von Laue, pointed out that if the wavelength of the radiation became as small as the distance between the atoms in the crystal, a diffraction pattern should result. There was some evidence that, X-rays might have wavelength in this range, and W. Friedrich agreed to make an experimental test. An X-ray beam passed through a crystal of copper sulphate gave a definite diffraction pattern. 30.3. Helix: Helix is a smooth curve in a three dimensional space satisfying the condition that the tangent to the curve at any point makes a constant angle with the fixed line called axis. This axis is called helical axis. One can give numerous examples for helix. Common examples for helix are spiral staircase, and a spring (Fig 30.2). Fig 30.2: Spring - a basic model for Helix The helix can be classified into two categories: left handed helix and right handed helix. If the helix is advancing in the positive Z-direction and if the direction of the chain is in clockwise direction, then the helix is said to be right handed helix. If the direction of the chain is in the anti- clockwise direction, then the helix is said to be left handed helix. The above said definition and examples are for continuous helix. In the biological macromolecular system numerous biomolecules favour helical structures. In the molecular system, the atoms or molecules are arranged at equal distance from the helical axis. If the molecular chain forming helix is due to a single chain, the helix is called single helix. If two chains are involved in the helical structure, the helix is called double helix. If the helix is formed by three molecular chains, the helix is called triple helix. A chain molecule is the one, which has continuous covalent linkage. Alpha helix in protein structure is an example for single helix. The structure of DNA and Xanthan gum polysaccharide (a bacterial polysaccharide produced by xanthomonas campestris) are double helical structures. In the double helical structures, the chain can run in parallel direction or in antiparallel direction. In DNA, the chains are in the opposite directions and in Xanthan gum polysaccharide, the chains are in the parallel direction. Collagen and Xylem favour triple helical structures. In these triple helical structures, the chains are running in the same direction. X-ray fibre diffraction is the primary tool used to deduce the three dimensional structure of helical molecules. Fig 30.3: Types of Helices 30.4. X-ray Fiber Diffraction: X-ray fiber diffraction is the powerful tool which is used to study the three dimensional structure polymeric chain molecules which fail to form single crystals. However, the long chain molecule can allow orientation in a particular direction, preferably along the chain direction. The orientated molecules when allowed to diffract the x-rays in a direction perpendicular to the orientated direction, the recorded diffraction pattern can be used to deduce the helical structure. To enhance the chain orientation and chain packing, different techniques can be used. A stress can be applied to the fibrous structure which in turn will enhance the orientation. Fibre orientation can also be enhanced by applying mechanical stress in humidity environment. This technique is extensively used in X-ray fibre diffraction on polysaccharides and other fibrous proteins. 30.5. Theory of X-ray fibre diffraction There are fundamental differences between single crystal and fibre diffraction analysis. Much less order and regularity is present in the fiber than in the crystal, as a result of which less information will be obtained from the fibre diffraction pattern. Since the number of observed bragg reflections from single crystal X-ray diffraction experiment exceed far than the number of atoms in the molecular structure, one can find details of the structure with a high probability of correctness with such a surfeit of data. On the otherhand, in a poorly resolved fibre diagram, there may be only five to fifty distinguishable reflections in all, and these more often are diffused and ill-formed. As a result, if one already knows the nature of the subunits from which the fibre is constructed one can use X-ray data to determine how these subunits are arranged, but one cannot hope to solve fibrous protein structure in the complete absence of any assumptions as to compositions. Fibrous molecules are long chain polymers which need not show true structural repeats at finite intervals. For example, the short repeat distance of the collagen framework is about 30 Å, there is clear evidence that the exact aminoacid sequence in adjacent 30 Å segment differ considerably. The co-operative effect of that portion of the structure which does repeat contributes to the diffraction pattern and therefore represents an averaged structure. Hence, although one can discover the framework of the collagen structure by x-ray analysis, one cannot determine the exact aminoacid sequence. In fibrous proteins, the orderliness of aggregation of structural units is less than in the crystalline globular proteins. Stretching or rolling fibres or stroking films can align the polypeptide chain axis of the crystalline domains roughly in parallel, and to a lesser degree to make their orientation about these axis similar. In the most usual phase of a stretched fibre, however, the crystallites will be ordered along the fibre axis but we have random orientations about this axis. The effect on the diffraction pattern is therefore to smear out each spot into a ring around the fibre axis direction. The two- dimensional x-ray photograph obtained can be thought of as being roughly an axial slice through this rotated pattern. Because of this rotation effect, information about the entire pattern will be contained on this single photograph. Another difficulty is caused due to the alternation of crystalline and disordered regions in fibre. Only that fraction of the total material which is crystalline will contribute to the diffraction pattern, and the remaining amorphous material will produce an objectionable diffused background scattering. 30.6. X-ray diffraction of helical fibers: Fig 30.4: Geometrical representation of layer lines for fibre diffraction. For the interpretation of X-ray diagrams of fibres, an important unifying structural concept was first introduced by Michael Polanyi, namely that of layer-planes (LP) and layer-lines (LL) in reciprocal space. The concept is most easily explained with a simple model frequently used in the standard teaching of elementary diffraction theory. Assume a single linear, regular “polymer” consisting of identical “atoms” or point scatterers occupying equidistant positions 푧푗 = 푗푃 on the z- axis, where j is an integer and P is the polymer repeat period. For normal incidence, the scattering amplitude in 2 2 푖푞.푟푗 |퐴(푞)| = |∑푗 푓푗(푞)푒 | (30.1) reduces to 2휋 2휋 퐴(푞) = 푓(푞) ∑ 푒푖푞푧푗푃 = 푓(푞) ∑+∞ 훿(푞 − 1 ) (30.2) 푗 푃 1=−∞ 푍 푃 Where, we have made use of the identity (the fundamental relation for diffraction by ordered structures) +∞ 2휋푖푛푥 +∞ ∑푛=−∞ 푒 = ∑푚=−∞ 훿(푥 − 푚) (30.3) the exponential in the left-hand side is represented by a point on the unit circle in Gauss plane of complex numbers. If x is not an integer, the summation over n produces an infinite number of such points distributed evenly over the circle; by judiciously grouping the points, the sum is seen to vanish. On the other hand, if x is any integer m, all terms on the left are equal to 1 and the sum is then infinite. The vertical component 푞푧 of the transfer wave vector is therefore quantized to integer multiples of 2π/P. Eq. 30.2 expresses the familiar fact that the Fourier transform of a vertical set of points separated by P is a set of horizontal planes separated by 2π/P in reciprocal space. These planes of equation 푞푧 = 2πl/P are called layer planes and are labelled by the integer l. Now for elastic scattering, relevant for the diffraction of monochromatic X-rays, the allowed wave vector 푘푓 of X-ray which is scattered, in addition to lying on one of the layer planes, but also lies on Ewald sphere (ES), that is a sphere in reciprocal space of radius|푘푓| = |푘푖|.The intersections of the latter by the former are latitudes on the sphere and constitute the bases of cones with a common apex at the sphere centre (Fig.30.4). These conical surfaces intersect the observation screen along the loci of nonzero diffracted intensity. Such conical sections are hyperbolae called layer lines. Due to the finite radius of the Ewald sphere, the distance between the layer lines is chirped, that is it increases towards higher-l (Fig.30.4).
Load more

Recommended publications
  • Atomic Modeling of Proteins Via Small Angle X-Ray Scattering (SAXS)
    Atomic modeling of proteins via Small Angle X-ray Scattering (SAXS) Susan Tsutakawa SIBYLS Beamline. Advanced Light Source Synchrotron, Lawrence Berkeley Natl Lab Six Take Home Messages on What can SAXS do for you? X-ray Scattering by Small Angle X-ray Scattering electrons provides distances measures all electron pair between electrons. distances in a protein in solution Atomic models can be quantitatively compared with SAXS data Atomic models are more SAXS can validate protein powerful than shape structure predictions because they can be tested. SAXS can reveal protein conformations occurring in solution at the atomic level If I could ask for any scientific app, what would it be? Accurate and reliable protein structure prediction For proteins with no known orthologs, structure predictions currently are not reliable. Amino Acid Protein Prediction Structure Prediction Sequence Server SIBYLS SAXS data I propose that Beamline input of SAXS data 12.3.1 can improve protein structure algoriths. As in crystallography, SAXS uses elastic scattering of X-rays, where the X-rays are scattered by an electron without a change in energy. Scattered X- rays constructively or destructively combine with each other. The X-ray scattering provides information on the distance between electrons. In SAXS, the intramolecular distances In Crystallography, these electrons are are constant; the scattering is related to each in crystallographic coherent, and the amplitudes are symmetry. added. SAXS is a distance method, measuring all electron pair distances. Scattering Curve Electron Pair Distance Histogram Fourier dmax Intensity (q) Intensity SAXS sample 30 ul q (Å-1) Protein 1-3 mg/ml Exact Buffer Distance information can validate an atomic model – as exemplified by validation of the May, 1953 model of DNA by fiber diffraction GeneticalImplications of the structure of Deoxyribonucleic Acid WatsonJ.D.
    [Show full text]
  • Small Angle X-Ray Scattering Experiments of Monodisperse Samples Close to the Solubility Limit
    Small angle x-ray scattering experiments of monodisperse samples close to the solubility limit Erik W. Martina, Jesse B. Hopkinsb, Tanja Mittaga1 a Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis TN b The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 1Corresponding author: email address: [email protected] Abstract The condensation of biomolecules into biomolecular condensates via liquid-liquid phase separation (LLPS) is a ubiquitous mechanism that drives cellular organization. To enable these functions, biomolecules have evolved to drive LLPS and facilitate partitioning into biomolecular condensates. Determining the molecular features of proteins that encode LLPS will provide critical insights into a plethora of biological processes. Problematically, probing biomolecular dense phases directly is often technologically difficult or impossible. By capitalizing on the symmetry between the conformational behavior of biomolecules in dilute solution and dense phases, it is possible to infer details critical to phase separation by precise measurements of the dilute phase thus circumventing complicated characterization of dense phases. The symmetry between dilute and dense phases is found in the size and shape of the conformational ensemble of a biomolecule – parameters that small-angle x-ray scattering (SAXS) is ideally suited to probe. Recent technological advances have made it possible to accurately characterize samples of intrinsically disordered protein regions at low enough concentration to avoid interference from intermolecular attraction, oligomerization or aggregation, all of which were previously roadblocks to characterizing self-assembling proteins. Herein, we describe the pitfalls inherent to measuring such samples, the details required for circumventing these issues and analysis methods that place the results of SAXS measurements into the theoretical framework of LLPS.
    [Show full text]
  • Solution Small Angle X-Ray Scattering : Fundementals and Applications in Structural Biology
    The First NIH Workshop on Small Angle X-ray Scattering and Application in Biomolecular Studies Open Remarks: Ad Bax (NIDDK, NIH) Introduction: Yun-Xing Wang (NCI-Frederick, NIH) Lectures: Xiaobing Zuo, Ph.D. (NCI-Frederick, NIH) Alexander Grishaev, Ph.D. (NIDDK, NIH) Jinbu Wang, Ph.D. (NCI-Frederick, NIH) Organizer: Yun-Xing Wang (NCI-Frederick, NIH) Place: NCI-Frederick campus Time and Date: 8:30am-5:00pm, Oct. 22, 2009 Suggested reading Books: Glatter, O., Kratky, O. (1982) Small angle X-ray Scattering. Academic Press. Feigin, L., Svergun, D. (1987) Structure Analysis by Small-angle X-ray and Neutron Scattering. Plenum Press. Review Articles: Svergun, D., Koch, M. (2003) Small-angle scattering studies of biological macromolecules in solution. Rep. Prog. Phys. 66, 1735- 1782. Koch, M., et al. (2003) Small-angle scattering : a view on the properties, structures and structural changes of biological macromolecules in solution. Quart. Rev. Biophys. 36, 147-227. Putnam, D., et al. (2007) X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Quart. Rev. Biophys. 40, 191-285. Software Primus: 1D SAS data processing Gnom: Fourier transform of the I(q) data to the P(r) profiles, desmearing Crysol, Cryson: fits of the SAXS and SANS data to atomic coordinates EOM: fit of the ensemble of structural models to SAXS data for disordered/flexible proteins Dammin, Gasbor: Ab initio low-resolution structure reconstruction for SAXS/SANS data All can be obtained from http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html MarDetector: 2D image processing Igor: 1D scattering data processing and manipulation SolX: scattering profile calculation from atomic coordinates Xplor/CNS: high-resolution structure refinement GASR: http://ccr.cancer.gov/staff/links.asp?profileid=5546 Part One Solution Small Angle X-ray Scattering: Basic Principles and Experimental Aspects Xiaobing Zuo (NCI-Frederick) Alex Grishaev (NIDDK) 1.
    [Show full text]
  • Bridging the Solution Divide: Comprehensive Structural Analyses of Dynamic RNA, DNA, and Protein Assemblies by Small-Angle X-Ray
    Available online at www.sciencedirect.com Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering Robert P Rambo1 and John A Tainer1,2 Small-angle X-ray scattering (SAXS) is changing how we macromolecules with functional flexibility and intrinsic perceive biological structures, because it reveals dynamic disorder, which occurs in functional regions and interfaces macromolecular conformations and assemblies in solution. [1,2]. Therefore, as structural biology evolves, it will SAXS information captures thermodynamic ensembles, need to provide structural insights into larger macromol- enhances static structures detailed by high-resolution ecular assemblies that display dynamics, flexibility, and methods, uncovers commonalities among diverse disorder. macromolecules, and helps define biological mechanisms. SAXS-based experiments on RNA riboswitches and ribozymes Solution structures from X-ray scattering and on DNA–protein complexes including DNA–PK and p53 For noncoding functional RNAs and intrinsically disor- discover flexibilities that better define structure–function dered proteins, defining their shapes and conformational relationships. Furthermore, SAXS results suggest space in solution marks a critical step toward understand- conformational variation is a general functional feature of ing their functional roles. Facilitating this goal are ab initio macromolecules. Thus, accurate structural analyses will bead-modeling algorithms for interpreting small-angle X- require a comprehensive approach that assesses both ray scattering (SAXS) data. These ab initio models flexibility, as seen by SAXS, and detail, as determined by X-ray represent low-resolution shapes and contribute signifi- crystallography and NMR. Here, we review recent SAXS cantly to interpretation of flexible systems in solution, computational tools, technologies, and applications to nucleic particularly for protein–DNA complexes.
    [Show full text]
  • Novel Ligands Targeting the DNA/RNA Hybrid and Telomeric Quadruplex As Potential Anticancer Agents
    This electronic thesis or dissertation has been downloaded from the King’s Research Portal at https://kclpure.kcl.ac.uk/portal/ Novel Ligands Targeting the DNA/RNA Hybrid and Telomeric Quadruplex as Potential Anticancer Agents Islam, Mohammad Kaisarul Awarding institution: King's College London The copyright of this thesis rests with the author and no quotation from it or information derived from it may be published without proper acknowledgement. END USER LICENCE AGREEMENT Unless another licence is stated on the immediately following page this work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International licence. https://creativecommons.org/licenses/by-nc-nd/4.0/ You are free to copy, distribute and transmit the work Under the following conditions: Attribution: You must attribute the work in the manner specified by the author (but not in any way that suggests that they endorse you or your use of the work). Non Commercial: You may not use this work for commercial purposes. No Derivative Works - You may not alter, transform, or build upon this work. Any of these conditions can be waived if you receive permission from the author. Your fair dealings and other rights are in no way affected by the above. Take down policy If you believe that this document breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 10. Oct. 2021 Novel Ligands Targeting the DNA/RNA Hybrid and Telomeric Quadruplex as Potential Anticancer Agents A dissertation submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy Mohammad Kaisarul Islam Institute of Pharmaceutical Sciences School of Biomedical Sciences King’s College London Supervisors Professor David E.
    [Show full text]
  • Recent Methods for Purification and Structure Determination Of
    International Journal of Molecular Sciences Review Recent Methods for Purification and Structure Determination of Oligonucleotides Qiulong Zhang 1,3,4,†, Huanhuan Lv 1,3,4,†, Lili Wang 1,3,4, Man Chen 1,3,4, Fangfei Li 1,3,4, Chao Liang 1,3,4, Yuanyuan Yu 1,3,4, Feng Jiang 1,2,3,4,*, Aiping Lu 1,3,4,* and Ge Zhang 1,3,4,* 1 Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China; [email protected] (Q.Z.); [email protected] (H.L.); [email protected] (L.W.); [email protected] (M.C.); [email protected] (F.L.); [email protected] (C.L.); [email protected] (Y.Y.) 2 The State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China 3 Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China 4 Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China * Correspondence: [email protected] (F.J.); [email protected] (A.L.); [email protected] (G.Z.); Tel.: +86-513-8210-6970 (F.J.); +852-3411-2456 (A.L.); +852-3411-2958 (G.Z.); Fax: +86-513-8210-6970 (F.J.); +852-3411-2461 (A.L. & G.Z.) † These authors contributed equally to this work. Academic Editor: Mateus Webba da Silva Received: 25 November 2016; Accepted: 14 December 2016; Published: 18 December 2016 Abstract: Aptamers are single-stranded DNA or RNA oligonucleotides that can interact with target molecules through specific three-dimensional structures.
    [Show full text]
  • ACA 2011 - Transactions Time Resolved Photochemistry Electron Density Bruker AXS
    American Crystallographic Association Number 4 Winter 2010 ACA 2011 - Transactions Time Resolved Photochemistry Electron Density Bruker AXS 3 Year Warranty on IµS APEX DUO - Dual Wavelength Perfected The Most Versatile System for Small Molecule Crystallography The APEX DUO combines the highest intensity Microfocus sealed tube sources for Mo and Cu radiation with the most sensitive CCD detector for crystallography. The APEX DUO allows collection of charge density quality data with Mo radiation and exploits all the advantages of Cu wavelength for absolute structure determination and diffraction experiments on ever smaller organic crystals. Data from both wavelengths can be collected successively in one experiment and switching between wavelengths is fully automated, fast and without user intervention. Crystallography think forward www.bruker-axs.com APEX Duo_ACA_1-2010.indd 1 1/8/2010 9:55:19 AM American Crystallographic Association www.AmerCrystalAssn.org Table of Contents 2 President’s Column 3 Notes from Council 4 From the Editor's Desk On the cover- see page 43 Acta F Showcases Structural Genomics Index of Advertisers 5-6 Awards to Crystallographers 7-8 Memories of Jim Stewart (1931 -2010) 9-10 ACA Living History - David Sayre 11 Science as Art / Art as Science 14 ACA 2010 - Crystallography World of Wonders 15 19th Annual BHT Regional Meeting 16 6th Meeting of the Argentinian Crystallograpic Assn. 18 High Pressure Single-Crystal Diffraction 19 Puzzle Corner 20-23 Book Reviews 24-27 Election Results for ACA Offices - 2011 Contributors to this Issue 28 ACA Corporate Members 29-37 2010 ACA Travel Award Winners 38-39 Contributors to ACA Award Funds 40-42 ACA 2011 - New Orleans - Preview 43 Calls for ACA Nominations - Travel Funds Available What's on the Cover 44 Calendar Announcing: ACA 2011 Small Molecule Course Contributions to ACA RefleXions may be sent to either of the Editors: Please address questions pertaining to advertisements, membership inquiries, or use of the ACA mailing list to: Connie (Chidester) Rajnak ......................
    [Show full text]
  • Homology Modeling (Comparative Modeling) Structure Prediction
    Cyrus Bench Homology: A highly automated, cloud-enabled, powerful, and user-friendly homology modeling pipeline using RosettaCM White Paper Lucas G. Nivón, Ryan Gomoto, and Yifan Song November, 2017 Author Affiliations: Cyrus Biotechnology, Inc. 500 Union Street Suite 320, Seattle WA 98101. Corresponding Author: Yifan Song, [email protected] or [email protected]. Abstract We describe a new protein structure prediction tool, Cyrus Bench Homology, offering the RosettaCM package on very large, cloud-based computational resources, and presented to users via an easy-to-use web application. Among recent protein structure homology modeling methods, RosettaCM has emerged as the best-performing tool by various metrics in blinded comparisons. However, in practice RosettaCM depends on a variety of external software to complete its standard pipeline for processing homology models and requires large computing resources to achieve top performance. These software and computational requirements have made a full RosettaCM pipeline very difficult to set up outside of large institutions that can provide thousands of CPUs and coordinate software licensing. Cyrus Bench Homology (available at cyrusbio.com) implements the full RosettaCM pipeline for homology prediction, with all software dependencies and computational resources auto-configured. We provide a practical summary of how to use Cyrus Bench Homology, describe the underlying algorithms with an emphasis on recent improvements and key intellectual antecedents, highlight the results of scientific testing, and apply this tool in a variety of examples. Many software tools for homology modeling explicitly aim for accessibility while sacrificing overall accuracy. Cyrus Bench Homology is novel in offering the most accurate structure prediction tool in a very easy-to-use package accessible to any bench scientist.
    [Show full text]
  • Cryo-Transmission Electron Microscopy Structure of a Gigadalton Peptide Fiber of De Novo Design
    Cryo-transmission electron microscopy structure of a gigadalton peptide fiber of de novo design Thomas H. Sharpa,b, Marc Bruninga,1, Judith Mantellb,c,1, Richard B. Sessionsb,1, Andrew R. Thomsona,1, Nathan R. Zaccaib,1, R. Leo Bradyb, Paul Verkadeb,c,d,2, and Derek N. Woolfsona,b,2 aSchool of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom; bSchool of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom; cWolfson Bioimaging Facility, University of Bristol, Bristol BS8 1TD, United Kingdom; and dSchool of Physiology and Pharmacology, University of Bristol, Bristol BS8 1TD, United Kingdom Edited by David Baker, University of Washington, Seattle, WA, and approved July 6, 2012 (received for review November 21, 2011) Nature presents various protein fibers that bridge the nanometer of α-helical coiled coils, remain relatively poorly described at to micrometer regimes. These structures provide inspiration for the the assembly, molecular, and atomic levels (7–9). de novo design of biomimetic assemblies, both to address difficul- From a more-applied perspective, interest in peptide- and pro- ties in studying and understanding natural systems, and to provide tein-based fibrous biomaterials has increased recently because routes to new biomaterials with potential applications in nano- these materials have potential applications in biotechnology and technology and medicine. We have designed a self-assembling fi- synthetic biology—for example, as scaffolds for 3D cell culture, ber system, the SAFs, in which two small α-helical peptides are tissue engineering, and templating the assembly of functional in- programmed to form a dimeric coiled coil and assemble in a con- organic materials (10–13).
    [Show full text]
  • PROTEIN STRUCTURE and FUNCTION, from a COLLOIDAL to a MOLECULAR VIEW" by HAROLD A
    Carlsberg Res. Commun. Vol. 49, p. 1-55, 1984 PROTEIN STRUCTURE AND FUNCTION, FROM A COLLOIDAL TO A MOLECULAR VIEW" by HAROLD A. SCHERAGA Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853, USA Presented as the 7th Linderstrom-Lang Lecture at the Carlsberg Laboratory, Copenhagen, on lOth May, 1983 Keywords: Hydrodynamic properties, internal interactions, ribonuclease, synthetic polypep- tides, conformational changes, protein folding, conformational energy calculations, structural elements of proteins, enzyme-substrate complexes 1. INTRODUCTION opment of theoretical methods to use these Forty years ago, proteins were described in experimental distance constraints, together with terms of ellipsoids of revolution in order to empirical potential energy functions, to gain an account for their hydrodynamic properties. understanding as to how interatomic inter- With the determination of the amino acid sequ- actions dictate the structural features of proteins ence of insulin (290) and other proteins, it and to try to compute the three-dimensional became meaningful to discuss protein structure structures of polypeptides and proteins in solu- and function in terms of the interatomic inter- tion. At the same time, both theoretical and actions within the protein molecule. Various experimental methods were used to elucidate physical chemical methods were developed and the pathway(s) of folding from a nascent poly- applied to elucidate such interactions. Many of peptide chain to the three-dimensional structure the pairwise interactions deduced from such of the native protein. The same theoretical and studies were found to exist, e.g. in bovine pan- experimental methods have also been applied to creatic ribonuclease A (303), when the X-ray study the biological function of the folded (na- crystal structure was subsequently determined tive) protein, e.g.
    [Show full text]
  • Strukturelle Analyse Der Dynamischen Konformationsänderung Des Prion-Proteins in Proteinmissfaltungskrankheiten
    Strukturelle Analyse der dynamischen Konformationsänderung des Prion-Proteins in Proteinmissfaltungskrankheiten DISSERTATION zur Erlangung des akademischen Grades des Doktors der Naturwissenschaften (Dr. rer. nat.) Eingereicht im Fachbereich Chemie der Fakultät für Mathematik, Informatik und Naturwissenschaften an der Universität Hamburg vorgelegt von Anne Sommer Hamburg 2015 Die praktischen Arbeiten wurden im Zeitraum von Februar 2010 bis September 2014 in der Nachwuchsgruppe von Dr. Lars Redecke im Laboratorium für Strukturbiologie von Infektion und Entzündung der Universitäten Hamburg und Lübeck sowie am Institut für Biochemie und Molekularbiologie des Fachbereichs Chemie der Universität Hamburg in den Laboratorien der Arbeitsgruppe von Prof. Dr. Christian Betzel durchgeführt. 1. Gutachter: Prof. Dr. Ch. Betzel 2. Gutachter: Prof. Dr. B. Meyer Tag der Disputation: 07.08.2015 I. Inhaltsverzeichnis I I. Inhaltsverzeichnis II. Abkürzungsverzeichnis ...................................................................................................... V III. Zusammenfassung ........................................................................................................... IX IV. Summary ........................................................................................................................... XI 1. Einleitung .............................................................................................................................. 1 1.1. Prionen-Erkrankungen ...................................................................................................
    [Show full text]
  • Synchrotron Radiation X-Ray Diffraction Techniques Applied to Insect Flight Muscle
    International Journal of Molecular Sciences Review Synchrotron Radiation X-ray Diffraction Techniques Applied to Insect Flight Muscle Hiroyuki Iwamoto Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan; [email protected]; Tel.: +81-791-58-2506 Received: 26 April 2018; Accepted: 5 June 2018; Published: 13 June 2018 Abstract: X-ray fiber diffraction is a powerful tool used for investigating the molecular structure of muscle and its dynamics during contraction. This technique has been successfully applied not only to skeletal and cardiac muscles of vertebrates but also to insect flight muscle. Generally, insect flight muscle has a highly ordered structure and is often capable of high-frequency oscillations. The X-ray diffraction studies on muscle have been accelerated by the advent of 3rd-generation synchrotron radiation facilities, which can generate brilliant and highly oriented X-ray beams. This review focuses on some of the novel experiments done on insect flight muscle by using synchrotron radiation X-rays. These include diffraction recordings from single myofibrils within a flight muscle fiber by using X-ray microbeams and high-speed diffraction recordings from the flight muscle during the wing-beat of live insects. These experiments have provided information about the molecular structure and dynamic function of flight muscle in unprecedented detail. Future directions of X-ray diffraction studies on muscle are also discussed. Keywords: insect flight muscle; X-ray diffraction; synchrotron radiation; X-ray microbeam; time-resolved measurement 1. Introduction Like light microscopy and electron microscopy, X-ray diffraction is one of the techniques used to resolve the fine structure of objects by using the scattering of electromagnetic waves or electron beams.
    [Show full text]