Physics of RNA and Viral Assembly
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Measurement and Interpretation of Diffuse Scattering in X-Ray Diffraction for Macromolecular Crystallography
Measurement and Interpretation of Diffuse Scattering in X-Ray Diffraction for Macromolecular Crystallography Workshop at the 2017 NSLS-II and CFN Users’ Meeting, Brookhaven National Laboratory, Upton, NY, May 15, 2017 Organizers: Michael Wall, [email protected] (LANL), Robert Sweet, [email protected] (NSLS-II, BNL), Nozomi Ando, [email protected] (Princeton University), James S. Fraser, [email protected] (University of California, San Francisco), George N. Phillips, Jr., [email protected] (Rice University) X-ray diffraction from macromolecular crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering reflects the mean electron density in the unit cells of the crystal. The diffuse scattering arises from correlations in the variations of electron density that may occur from one unit cell to another, and therefore contains information about collective motions in proteins. Leading researchers in diffuse scattering gathered May 15, 2017 for a one-day workshop at the NSLS-II Users’ Meeting. A major focus of the workshop was to provide a roadmap to the acquisition of reliable data by surveying measurement methods and discussing the increase in measurement accuracy enabled by improved detectors, experimental methods, and data integration. Another major focus was to survey examples of information that can be extracted about the behavior of biomolecules that would guide the thinking of biochemists and biologists. A number of talks addressed the measurement of diffuse-scattering data and advances in the modeling of the data in terms of conformational variation. Below we give a short synopsis of each talk, and at the end an analysis of the results of the workshop in total. -
Downloading Our Newsletter
Department of Chemistry Biochemistry& NEWSLETTER In This Issue Page Chair’s Message................2 Jorge Torres Discovers Key Role for a Motor Awards...........................2-5 Protein in Cancer Cell Proliferation Seaborg Symposium........6-7 Happenings....................7-10 Biochemistry Professor high-throughput genetic Distinguished Lectures....11-14 Jorge Torres discovered that screen that knocked the Research.......................15-17 suppressing STARD9, a proteins out one by one to In Memoriam................17-19 newly identified protein see how that affected involved in regulating cell spindle function. Calendar.........................19 division, could be a novel “The idea was to find strategy for fighting certain something that arrested the Spring 2012 cancers, as it stops malignant cells while they were Volume 31 - Number 2 cells from dividing and trying to divide and causes them to die quickly. injured them in such a way that cell death occurred quickly,” The study was published in Torres said. “We were looking for a way to attack the cancer the December 9, 2011 issue cells as they were dividing.” of Cell. From the screens, Torres and his team selected the most During the five-year promising protein. This was STARD9, a kinesin-like protein Jorge Torres study, designed to seek — a sort of molecular motor — that functions to form a targets for anti-cancer stable mitotic spindle. therapies, Torres and co-workers found that depleting “When STARD9 is depleted in the cancer cells, the STARD9 also helped the commonly used chemotherapy chromosomes attempt to align for transmission into the drug Taxol work more effectively against cancers such as daughter cells but fail,” he said. -
DNA Ejection from Bacteriophage: Towards a General Behavior for Osmotic Suppression Experiments Martin Castelnovo, Alex Evilevitch
DNA ejection from bacteriophage: towards a general behavior for osmotic suppression experiments Martin Castelnovo, Alex Evilevitch To cite this version: Martin Castelnovo, Alex Evilevitch. DNA ejection from bacteriophage: towards a general behavior for osmotic suppression experiments. European Physical Journal E: Soft matter and biological physics, EDP Sciences: EPJ, 2007, 24, pp.9-18. 10.1140/epje/i2007-10205-5. hal-00196724 HAL Id: hal-00196724 https://hal.archives-ouvertes.fr/hal-00196724 Submitted on 13 Dec 2007 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. DNA ejection from bacteriophage: towards a general behavior for osmotic suppression experiments M. Castelnovo∗ and A. Evilevitch† (Dated: December 18, 2007) We present in this work in vitro measurements of the force ejecting DNA from two distinct bacteriophages (T5 and λ) using the osmotic ejection suppression technique. Our datas are analyzed by revisiting the current theories of DNA packaging in spherical capsids. In particular we show that a simplified analytical model based on bending considerations only is able to account quantitatively for the experimental findings. Physical and biological consequences are discussed. I. INTRODUCTION Viruses have developped various specific strategies over the evolution in order to infect higher organisms. -
Two-Stage Dynamics of in Vivo Bacteriophage Genome Ejection
View metadata, citation and similar papers at core.ac.uk brought to you by CORE PHYSICAL REVIEW X 8, 021029 (2018) provided by Caltech Authors Two-Stage Dynamics of In Vivo Bacteriophage Genome Ejection † ‡ Yi-Ju Chen,1,* David Wu,2, William Gelbart,3 Charles M. Knobler,3 Rob Phillips,2,4, and Willem K. Kegel5,§ 1Department of Physics, California Institute of Technology, Pasadena, California 91125, USA 2Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, California 91125, USA 3Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA 4Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA 5Van ’t Hoff Laboratory for Physical and Colloid Chemistry, Debye Institute, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands (Received 1 July 2017; revised manuscript received 27 January 2018; published 1 May 2018) Biopolymer translocation is a key step in viral infection processes. The transfer of information-encoding genomes allows viruses to reprogram the cell fate of their hosts. Constituting 96% of all known bacterial viruses [A. Fokine and M. G. Rossmann, Molecular architecture of tailed double-stranded DNA phages, Bacteriophage 4, e28281 (2014)], the tailed bacteriophages deliver their DNA into host cells via an “ejection” process, leaving their protein shells outside of the bacteria; a similar scenario occurs for mammalian viruses like herpes, where the DNA genome is ejected into the nucleus of host cells, while the viral capsid remains bound outside to a nuclear-pore complex. In light of previous experimental measurements of in vivo bacteriophage λ ejection, we analyze here the physical processes that give rise to the observed dynamics. -
Biosoft Frontiers: Physics of Soft And
BioSoft Frontiers: Physics of Soft and Biological Matter Research Workshop of the Israel Science Foundation September 18-21, 2016 Weizmann Institute and Tel Aviv University Sponsors Israel Science Foundation Weizmann Institute of Science Tel Aviv University Chorafas Institute for Scientific Exchange, Weizmann Institute Clore Center for Biological Physics, Weizmann Institute Schmidt Minerva Center, Weizmann Institute Department of Materials and Interfaces, Weizmann Institute Faculty of Exact Sciences, Tel Aviv University School of Physics & Astronomy, Tel Aviv University School of Chemistry, Tel Aviv University Sackler Institute of Solid State Physics, Tel Aviv University Sackler Institute of Chemical Physics, Tel Aviv University 1 Scientific Program 18/9/16 Weizmann Institute (Lopatie Center) 12:00-13:45 Arrival and Lunch 13:45-14:00 Opening 14:00-15:25 Session 1. Chair: Jacques Prost (Institut Curie, Paris) 14:00-14:30 Fred MacKintosh (VU University, Amsterdam) Phase transitions and non-equilibrium behavior in living systems 14:30-14:50 Ayelet Lesman (Tel Aviv University) The influence of contractile forces on biological processes 14:50-15:05 Xingpeng Xu (Weizmann Institute) Nonlinear elastic responses of biopolymer gels under compression 15:05-15:35 Tsvi Tlusty (IAS, Princeton) Proteins as learning amorphous matter: dimension and spectrum of the genotype-to-phenotype map 15:35-16:20 Coffee 16:20-17:25 Session 2. Chair: Nihat Berker (Sabanci University, Istanbul) 16:20-16:50 Christoph Schmidt (Universitaet Goettingen) Active soft matter builds life 16:50-17:05 Kinjal Dasbiswas (University of Chicago) Mechanobiological induction of long-range contractility by diffusing biomolecules and size scaling in cell assemblies 17:05-17:25 Yoram Burak (Hebrew University) Encoding of an animal's trajectory by grid cells in the entorhinal cortex 18:00 Dinner (Lopatie Center) 2 19/9/16 Weizmann Institute (Lopatie Center) 09:00-09:30 Arrival and coffee 09:30-10:35 Session 3. -
Mathematical Virology Reidun Twarock
INFERENCE / Vol. 5, No. 3 Mathematical Virology Reidun Twarock ymmetry is ubiquitous in nature. It occurs in icosahedron from, 4, 8, and 20 equilateral triangles, respec- snowflakes, crystals, and molecules; and it is cen- tively. tral to our understanding of subatomic particles. Both the icosahedron and its dual, the dodecahedron, SAlthough the importance of symmetry in chemistry and possess icosahedral symmetry, and together they com- physics is widely appreciated, its significance in biology prise the largest rotational symmetry group in three is often underestimated. Viruses are notable examples of dimensions.3 Given a set of identical building blocks biological systems in which symmetry plays a pivotal role. under a repeating pattern of assembly, it is an icosahe- Mathematical techniques directed at understanding their drally symmetric shape that optimizes container volume. structure and symmetry have a transformative potential Since viruses are under selective pressure to package their both within virology and biology as a whole. genetic material efficiently, it is no surprise that evolution has forced their convergence to icosahedrally symmetric iral genomes are packaged in protein containers shapes. known as viral capsids. These containers function like Trojan horses, facilitating the release of the nlike other types of rotational symmetries in viralV genome into host cells and providing protection from three dimensions, icosahedral symmetry is non- host defense mechanisms between rounds of infection. In crystallographic: it is not possible to tessellate a their simplest form, viral capsids are less than 20 nano- Uthree-dimensional physical space using a single icosahe- meters (nm) in diameter and encapsulate short genomic drally symmetric shape without creating gaps or overlaps. -
How a Virus Circumvents Energy Barriers to Form Symmetric Shells Sanaz Panahandeh, Siyu Li, Laurent Marichal, Rafael Leite Rubim, Guillaume Tresset, Roya Zandi
How a Virus Circumvents Energy Barriers to Form Symmetric Shells Sanaz Panahandeh, Siyu Li, Laurent Marichal, Rafael Leite Rubim, Guillaume Tresset, Roya Zandi To cite this version: Sanaz Panahandeh, Siyu Li, Laurent Marichal, Rafael Leite Rubim, Guillaume Tresset, et al.. How a Virus Circumvents Energy Barriers to Form Symmetric Shells. ACS Nano, American Chemical Society, 2020, 14 (3), pp.3170-3180. 10.1021/acsnano.9b08354. hal-03035711 HAL Id: hal-03035711 https://hal.archives-ouvertes.fr/hal-03035711 Submitted on 4 Jan 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. How a virus circumvents energy barriers to form symmetric shells Sanaz Panahandeh,y Siyu Li,y Laurent Marichal,z Rafael Leite Rubim,z Guillaume Tresset,z and Roya Zandi∗,y yDepartment of Physics and Astronomy, University of California, Riverside, California 92521, USA zLaboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France E-mail: [email protected] Abstract Previous self-assembly experiments on a model icosahedral plant virus have shown that, under physiological conditions, capsid proteins initially binds to the genome through an en masse mechanism and form nucleoprotein complexes in a disordered state, which raises the questions as to how virions are assembled into a highly or- dered structure in the host cell. -
Physics of Viral Dynamics
REVIEWS Physics of viral dynamics Robijn F. Bruinsma1, Gijs J. L. Wuite2 and Wouter H. Roos 3 ✉ Abstract | Viral capsids are often regarded as inert structural units, but in actuality they display fascinating dynamics during different stages of their life cycle. With the advent of single-particle approaches and high-resolution techniques, it is now possible to scrutinize viral dynamics during and after their assembly and during the subsequent development pathway into infectious viruses. In this Review, the focus is on the dynamical properties of viruses, the different physical virology techniques that are being used to study them, and the physical concepts that have been developed to describe viral dynamics. Capsids Humans and other animals, as well as plants, are plagued and new methods of analysis and numerical modelling. Protein shells that surround the by infections caused by viruses. These are parasites that We first review some of the dynamic methods that viral genome. cannot reproduce by themselves and that are incapable are being applied to study the assembly of empty viral of metabolic activity. Instead, after viruses infect cells, capsids, then focus on the role of genome molecules Triangulation numbers Classification system, they alter cellular molecular machinery so that it pro- (RNA/DNA) during assembly, followed by a discussion developed by Caspar and duces new viruses, which are then released into the envi- of studies of the steady-state dynamics of assembled Klug, for icosahedral viruses. ronment. This sequence of events, the viral life cycle, is viruses. BOx 2 summarizes several experimental tech- T-numbers are integers and schematically discussed in BOx 1. -
DNA Could Trap Viruses Irfan* Department of Microbiology, King Saud University, Saudi Arabia
& Bioch ial em OPEN ACCESS Freely available online b ic ro a c l i T M e f c h o n l o a Journal of n l o r g u y o J ISSN: 1948-5948 Microbial & Biochemical Technology Short Communication DNA could trap viruses Irfan* Department of Microbiology, King Saud University, Saudi Arabia INTRODUCTION also be used as a type of "virus trap." If they we have a tendency tore to be coated with virus-binding molecules at the inside, they have To date, there aren't any powerful antidotes towards maximum to be prepared to bind viruses tightly and consequently be capable virus infections. Scientists have now evolved a brand new approach: of take them out of circulation. For this, however, the hole our they engulf and neutralize viruses with nano-pills tailor-made from bodies might even should very own sufficiently large openings thru genetic cloth the use of the DNA origami method. The approach that viruses gets into the shells. has already been examined towards hepatitis and adeno-related viruses in mobileular cultures. It might also show a hit towards "None of the gadgets that we had engineered victimization corona viruses. deoxyribonucleic acid artwork generation at that factor might were prepared to engulf a whole virus -- they had been simply too small," There are antibiotics towards risky bacteria, but few antidotes to deal with acute infectious agent infections. Some infections can says Hendrik Dietz in retrospect. "Building solid hole our bodies of be averted via way of means of vaccination however growing new this length changed into a huge challenge. -
Abstracts of Special Session Presentations Biology of Plant Pathogens
Abstracts of Special Session Presentations Biology of Plant Pathogens Aquatic Plant Pathology Development of an indigenous pathogen for management of the submersed freshwater macrophyte Hydrilla verticillata. J. F. SHEARER. Fungal pathogens: Their role in the ecology of floating and submerged U.S. Army Corps of Engineers, Research and Development Center, freshwater plants. R. CHARUDATTAN. Plant Pathology Dept., University Vicksburg, MS. Phytopathology 95:S120. Publication no. P-2005-0003-SSA. of Florida, Gainesville, FL. Phytopathology 95:S120. Publication no. P-2005- Hydrilla verticillata 0001-SSA. (L.f.) Royle (hydrilla) is considered one of the three most important aquatic weeds in the world. Plant infestations can impede navi- Freshwater plants encompass a diverse group of morphologically and gation, clog drainage or irrigation canals, affect water intake systems, interfere taxonomically dissimilar plants adapted to life in a highly unstable habitat. with recreational activities, and disrupt wildlife habitats. The plant is an These plants can be emergent and free-floating, emergent and rooted, fully excellent competitor in aquatic habitats because it can photosynthesize at low submerged and free-floating, or fully submerged and rooted. A variety of light levels, has wide environmental tolerances, and produces several types of fungi in the Oomycota, Chytridiomycota, Anamorphic fungi, Ascomycota, extended survival propagules. The indigenous fungal pathogen, Mycolepto- and Basidiomycota cause diseases on these plants. While pathogenic fungi can discus terrestris (Gerd.) Ostazeski, (Mt) has shown significant potential for regulate plant population density by limiting plant growth and seedling use as a bioherbicide for management of hydrilla. Liquid fermentation recruitment, opportunistic parasites accelerate senescence of older growth and methods have been developed and patented that yield stable, effective recycle nutrients from dead tissues. -
From the President's Desk
APRIL 2005 From the President’s desk: The sequence of the human genome underscores the necessity for genetic analysis to define gene function and validates the importance of genomic and genetic approaches in model organisms for gene discovery. The GSA promotes genetic research in model organisms and its application to human genetics via our journal Genetics, supporting public education and congressional lobbying through the Joint Steering Committee for Public Policy (www.jscpp.org) and in its sponsorship of scientific meetings. The GSA support of scientific meetings includes providing the crucial infrastructure, organization, administration, and financial foundation, as well as recognition for students and postdocs through the awards we sponsor. The society’s sponsorship of model organisms meetings in C. elegans, Drosophila, Fungi, Yeast and Zebrafish has enabled those research communities to hold conferences that are particularly accessible to students and postdocs who are our future. The support of the GSA has been key in enabling these very successful meetings while permitting each of the model organism communities the independence to organize the meeting according to their needs. In recognition of the importance of genomics in our field, this year the GSA will support a new meeting of biocurators and database developers with the goal of bringing together developers of these bioinformatics tools for a variety of organisms. Your membership in the GSA entitles you to a reduced registration fee for all of these meetings. The GSA will organize its own meeting “Genetic Analysis: Model Organisms to Human Biology,” Jan. 5-7, 2006 in San Diego to draw together the entire constituency of our society and to promote interactions with our colleagues directly studying human disease. -
Symposium to Honor Eminent FSU Scientist Florida State University News FLORIDA STATE UNIVERSITY NEWS the OFFICIAL NEWS SOURCE of FLORIDA STATE UNIVERSITY
1/9/2017 Symposium to honor eminent FSU scientist Florida State University News FLORIDA STATE UNIVERSITY NEWS THE OFFICIAL NEWS SOURCE OF FLORIDA STATE UNIVERSITY Symposium to honor eminent FSU scientist BY: KATHLEEN HAUGHNEY (MAILTO:[email protected]) | PUBLISHED: JANUARY 5, 2017 (HTTP://NEWS.FSU.EDU/NEWS/SCIENCE‑TECHNOLOGY/2017/01/05/SYMPOSIUM‑ HONOR‑EMINENT‑FSU‑SCIENTIST/) | 1:34 PM | SHARE: A symposium to honor a retired Florida State professor who made major contributions to the world of structural biology is attracting an unprecedented number of members of the National Academy of Sciences to Tallahassee. The Caspar Structural Biology Symposium, to be held Jan. 7‑8 at Florida State University, honors Donald Caspar, professor emeritus of biological science at Florida State, who will also turn 90 during the symposium. “Don Caspar is a legend in the structural biology field,” said Piotr Fajer, director of the Institute of Molecular Biophysics at Florida State. “All of these people coming here is a tribute to him.” The event features 15 members of the National Academy of Sciences who will discuss the latest developments in the field and technologies such as Donald Caspar, professor emeritus of biological science at Florida State x‑ray crystallography and electron microscopy. “I don’t think there’s been a conference that attracted this many academy members to Tallahassee before,” Fajer said. FSU Professor of Biophysics Kenneth Taylor, who uses electron microscopy to study the tiniest muscle filaments in the body, will also be among the speakers. Andrew Brown, author of a biography on J.D. Bernal, a pioneer in x‑ray crystallography in structural biology, will wrap up the symposium with a talk on Sunday.