The Cytoskeleton Lattice-Based Kinetic Simulator
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Mechanical Design of Translocating Motor Proteins
Cell Biochem Biophys (2009) 54:11–22 DOI 10.1007/s12013-009-9049-4 REVIEW PAPER Mechanical Design of Translocating Motor Proteins Wonmuk Hwang Æ Matthew J. Lang Published online: 19 May 2009 Ó Humana Press Inc. 2009 Abstract Translocating motors generate force and move Introduction along a biofilament track to achieve diverse functions including gene transcription, translation, intracellular cargo Motor proteins form distinct classes in the protein universe transport, protein degradation, and muscle contraction. as they can convert chemical energy directly into mechan- Advances in single molecule manipulation experiments, ical work. Among them, translocating motors move along structural biology, and computational analysis are making biopolymer tracks, such as nucleic acids, polypeptides, or it possible to consider common mechanical design princi- quaternary biofilament structures like F-actin or microtu- ples of these diverse families of motors. Here, we propose a bule (Kolomeisky and Fisher proposed the term ‘‘translo- mechanical parts list that include track, energy conversion case’’ for these motors [41]. However, we prefer to use machinery, and moving parts. Energy is supplied not just ‘‘translocating motor,’’ since translocase refers to mem- by burning of a fuel molecule, but there are other sources brane-bound motors such as SecA, whose function is to or sinks of free energy, by binding and release of a fuel or translocate a protein across the membrane [24]). Movement products, or similarly between the motor and the track. is an essential part of their function. For example, RNA Dynamic conformational changes of the motor domain can polymerase (RNAP) walks along the DNA molecule and be regarded as controlling the flow of free energy to and transcribes the genetic code into RNA [25]. -
Theory of Cytoskeletal Reorganization During Crosslinker-Mediated Mitotic Spindle Assembly
bioRxiv preprint doi: https://doi.org/10.1101/419135; this version posted March 1, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Theory of cytoskeletal reorganization during crosslinker-mediated mitotic spindle assembly A. R. Lamson, C. J. Edelmaier, M. A. Glaser, and M. D. Betterton Abstract Cells grow, move, and respond to outside stimuli by large-scale cytoskeletal reorganization. A prototypical example of cytoskeletal remodeling is mitotic spindle assembly, during which micro- tubules nucleate, undergo dynamic instability, bundle, and organize into a bipolar spindle. Key mech- anisms of this process include regulated filament polymerization, crosslinking, and motor-protein activity. Remarkably, using passive crosslinkers, fission yeast can assemble a bipolar spindle in the absence of motor proteins. We develop a torque-balance model that describes this reorganization due to dynamic microtubule bundles, spindle-pole bodies, the nuclear envelope, and passive crosslink- ers to predict spindle-assembly dynamics. We compare these results to those obtained with kinetic Monte Carlo-Brownian dynamics simulations, which include crosslinker-binding kinetics and other stochastic effects. Our results show that rapid crosslinker reorganization to microtubule overlaps facilitates crosslinker-driven spindle assembly, a testable prediction for future experiments. Combin- ing these two modeling techniques, we illustrate a general method for studying cytoskeletal network reorganization. 1 bioRxiv preprint doi: https://doi.org/10.1101/419135; this version posted March 1, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. -
Construction and Loss of Bacterial Flagellar Filaments
biomolecules Review Construction and Loss of Bacterial Flagellar Filaments Xiang-Yu Zhuang and Chien-Jung Lo * Department of Physics and Graduate Institute of Biophysics, National Central University, Taoyuan City 32001, Taiwan; [email protected] * Correspondence: [email protected] Received: 31 July 2020; Accepted: 4 November 2020; Published: 9 November 2020 Abstract: The bacterial flagellar filament is an extracellular tubular protein structure that acts as a propeller for bacterial swimming motility. It is connected to the membrane-anchored rotary bacterial flagellar motor through a short hook. The bacterial flagellar filament consists of approximately 20,000 flagellins and can be several micrometers long. In this article, we reviewed the experimental works and models of flagellar filament construction and the recent findings of flagellar filament ejection during the cell cycle. The length-dependent decay of flagellar filament growth data supports the injection-diffusion model. The decay of flagellar growth rate is due to reduced transportation of long-distance diffusion and jamming. However, the filament is not a permeant structure. Several bacterial species actively abandon their flagella under starvation. Flagellum is disassembled when the rod is broken, resulting in an ejection of the filament with a partial rod and hook. The inner membrane component is then diffused on the membrane before further breakdown. These new findings open a new field of bacterial macro-molecule assembly, disassembly, and signal transduction. Keywords: self-assembly; injection-diffusion model; flagellar ejection 1. Introduction Since Antonie van Leeuwenhoek observed animalcules by using his single-lens microscope in the 18th century, we have entered a new era of microbiology. -
Review of Molecular Motors
REVIEWS CYTOSKELETAL MOTORS Moving into the cell: single-molecule studies of molecular motors in complex environments Claudia Veigel*‡ and Christoph F. Schmidt§ Abstract | Much has been learned in the past decades about molecular force generation. Single-molecule techniques, such as atomic force microscopy, single-molecule fluorescence microscopy and optical tweezers, have been key in resolving the mechanisms behind the power strokes, ‘processive’ steps and forces of cytoskeletal motors. However, it remains unclear how single force generators are integrated into composite mechanical machines in cells to generate complex functions such as mitosis, locomotion, intracellular transport or mechanical sensory transduction. Using dynamic single-molecule techniques to track, manipulate and probe cytoskeletal motor proteins will be crucial in providing new insights. Molecular motors are machines that convert free energy, data suggest that during the force-generating confor- mostly obtained from ATP hydrolysis, into mechanical mational change, known as the power stroke, the lever work. The cytoskeletal motor proteins of the myosin and arm of myosins8,11 rotates around its base at the catalytic kinesin families, which interact with actin filaments and domain11–17, which can cause the displacement of bound microtubules, respectively, are the best understood. Less cargo by several nanometres18 (FIG. 1B). In kinesins, the is known about the dynein family of cytoskeletal motors, switching of the neck linker (~13 amino acids connecting which interact with microtubules. Cytoskeletal motors the catalytic core to the cargo-binding stalk domain) from power diverse forms of motility, ranging from the move- an ‘undocked’ state to a state in which it is ‘docked’ to the ment of entire cells (as occurs in muscular contraction catalytic domain, is the equivalent of the myosin power or cell locomotion) to intracellular structural dynamics stroke10. -
A Standardized Kinesin Nomenclature • Lawrence Et Al
JCB: COMMENT A standardized kinesin nomenclature Carolyn J. Lawrence,1 R. Kelly Dawe,1,2 Karen R. Christie,3,4 Don W. Cleveland,3,5 Scott C. Dawson,3,6 Sharyn A. Endow,3,7 Lawrence S.B. Goldstein,3,8 Holly V. Goodson,3,9 Nobutaka Hirokawa,3,10 Jonathon Howard,3,11 Russell L. Malmberg,1,3 J. Richard McIntosh,3,12 Harukata Miki,3,10 Timothy J. Mitchison,3,13 Yasushi Okada,3,10 Anireddy S.N. Reddy,3,14 William M. Saxton,3,15 Manfred Schliwa,3,16 Jonathan M. Scholey,3,17 Ronald D. Vale,3,18 Claire E. Walczak,3,19 and Linda Wordeman3,20 1Department of Plant Biology, The University of Georgia, Athens, GA 30602 2Department of Genetics, The University of Georgia, Athens, GA 30602 3These authors contributed equally to this work and are listed alphabetically 4Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305 5Ludwig Institute for Cancer Research, 3080 CMM-East, 9500 Gilman Drive, La Jolla, CA 92093 6Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720 7Department of Cell Biology, Duke University Medical Center, Durham, NC 27710 8Department of Cellular and Molecular Medicine, Howard Hughes Medical Institute, School of Medicine, University of California, San Diego, La Jolla, CA 92093 9Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46628 10Department of Cell Biology and Anatomy, University of Tokyo, Graduate School of Medicine, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan 11Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany 12Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309 13Institute for Chemistry and Cell Biology, Harvard Medical School, Boston, MA 02115 Downloaded from 14Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523 15Department of Biology, Indiana University, Bloomington, IN 47405 16Adolf-Butenandt-Institut, Zellbiologie, University of Munich, Schillerstr. -
Tension on the Linker Gates the ATP-Dependent Release of Dynein from Microtubules
ARTICLE Received 4 Apr 2014 | Accepted 3 Jul 2014 | Published 11 Aug 2014 DOI: 10.1038/ncomms5587 Tension on the linker gates the ATP-dependent release of dynein from microtubules Frank B. Cleary1, Mark A. Dewitt1, Thomas Bilyard2, Zaw Min Htet2, Vladislav Belyy1, Danna D. Chan2, Amy Y. Chang2 & Ahmet Yildiz2 Cytoplasmic dynein is a dimeric motor that transports intracellular cargoes towards the minus end of microtubules (MTs). In contrast to other processive motors, stepping of the dynein motor domains (heads) is not precisely coordinated. Therefore, the mechanism of dynein processivity remains unclear. Here, by engineering the mechanical and catalytic properties of the motor, we show that dynein processivity minimally requires a single active head and a second inert MT-binding domain. Processivity arises from a high ratio of MT-bound to unbound time, and not from interhead communication. In addition, nucleotide-dependent microtubule release is gated by tension on the linker domain. Intramolecular tension sensing is observed in dynein’s stepping motion at high interhead separations. On the basis of these results, we propose a quantitative model for the stepping characteristics of dynein and its response to chemical and mechanical perturbation. 1 Biophysics Graduate Group, University of California, Berkeley, California 94720, USA. 2 Department of Physics, University of California, Berkeley, California 94720, USA. Correspondence and requests for materials should be addressed to A.Y. (email: [email protected]). NATURE COMMUNICATIONS | 5:4587 | DOI: 10.1038/ncomms5587 | www.nature.com/naturecommunications 1 & 2014 Macmillan Publishers Limited. All rights reserved. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5587 ytoplasmic dynein is responsible for nearly all microtubule dynein’s MT-binding domain (MTBD) is located at the end of a (MT) minus-end-directed transport in eukaryotes1.In coiled-coil stalk10. -
List of Life Members As on 20Th January 2021
LIST OF LIFE MEMBERS AS ON 20TH JANUARY 2021 10. Dr. SAURABH CHANDRA SAXENA(2154) ALIGARH S/O NAGESH CHANDRA SAXENA POST HARDNAGANJ 1. Dr. SAAD TAYYAB DIST ALIGARH 202 125 UP INTERDISCIPLINARY BIOTECHNOLOGY [email protected] UNIT, ALIGARH MUSLIM UNIVERSITY ALIGARH 202 002 11. Dr. SHAGUFTA MOIN (1261) [email protected] DEPT. OF BIOCHEMISTRY J. N. MEDICAL COLLEGE 2. Dr. HAMMAD AHMAD SHADAB G. G.(1454) ALIGARH MUSLIM UNIVERSITY 31 SECTOR OF GENETICS ALIGARH 202 002 DEPT. OF ZOOLOGY ALIGARH MUSLIM UNIVERSITY 12. SHAIK NISAR ALI (3769) ALIGARH 202 002 DEPT. OF BIOCHEMISTRY FACULTY OF LIFE SCIENCE 3. Dr. INDU SAXENA (1838) ALIGARH MUSLIM UNIVERSITY, ALIGARH 202 002 HIG 30, ADA COLONY [email protected] AVANTEKA PHASE I RAMGHAT ROAD, ALIGARH 202 001 13. DR. MAHAMMAD REHAN AJMAL KHAN (4157) 4/570, Z-5, NOOR MANZIL COMPOUND 4. Dr. (MRS) KHUSHTAR ANWAR SALMAN(3332) DIDHPUR, CIVIL LINES DEPT. OF BIOCHEMISTRY ALIGARH UP 202 002 JAWAHARLAL NEHRU MEDICAL COLLEGE [email protected] ALIGARH MUSLIM UNIVERSITY ALIGARH 202 002 14. DR. HINA YOUNUS (4281) [email protected] INTERDISCIPLINARY BIOTECHNOLOGY UNIT ALIGARH MUSLIM UNIVERSITY 5. Dr. MOHAMMAD TABISH (2226) ALIGARH U.P. 202 002 DEPT. OF BIOCHEMISTRY [email protected] FACULTY OF LIFE SCIENCES ALIGARH MUSLIM UNIVERSITY 15. DR. IMTIYAZ YOUSUF (4355) ALIGARH 202 002 DEPT OF CHEMISTRY, [email protected] ALIGARH MUSLIM UNIVERSITY, ALIGARH, UP 202002 6. Dr. MOHAMMAD AFZAL (1101) [email protected] DEPT. OF ZOOLOGY [email protected] ALIGARH MUSLIM UNIVERSITY ALIGARH 202 002 ALLAHABAD 7. Dr. RIAZ AHMAD(1754) SECTION OF GENETICS 16. -
Department of Biotechnology Annual Report
DEPARTMENT OF BIOTECHNOLOGY INDIAN INSTITUTE OF TECHNOLOGY GUWAHATI ANNUAL REPORT APRIL 2011 to MARCH 2012 Page 1 of 38 1. INTRODUCTION Contributing to the fascinating and emerging areas of Science, Indian Institute of Technology Guwahati established Department of Biotechnology in the year 2002. The Department is one of its kind in the north-eastern region of Indian and is dedicated for promoting goal-oriented interdisciplinary research by interfacing modern biology with applied engineering sciences, addressing problems affecting human health/welfare, and training students to be the next generation engineers and researchers. As of now, the department has twenty-five faculty members from diverse streams and specializations, eight well-trained scientific staff members, and two administrative staff members. The detailed activities of the Department of the Biotechnology are given in below. 2. ACADEMIC ACTIVITIES: The department offers B. Tech., M. Tech., and PhD programmes. 3. STUDENT INTAKE: 46 in B. Tech., 30 in M. Tech, and 31 in Ph. D. 4. FACULTY STRENGTH: 25 (as on March 31, 2012). 5. MAJOR EQUIPMENTS AND FACILITIES Atomic Force Microscope - Contact Mode, Autotensiometer, Bioreactor, Trinocular Phase Contrast Microscope with Fluorescence attachment, Trinocular Stereo Zoom Microscope with Fibre Optic Light, DuoFlow, FACS Calibur Flowcytometer Analyser, Compact Spectrofluorometer, FPLC System, Digital Imaging System, Gradient PCR Thermal Cycler, HPLC System, Ion Chromatography system, Gas Chromatography system, Bioreactors, Freeze Dryer, Manual Rotary Microtome, Multimode Microplate Reader, Real-Time PCR System, Ultracentrifuge 6. RESEARCH AND DEVELOPMENT ACTIVITIES The research in the Department of Biotechnology covers as diverse areas as biochemical engineering, plant biotechnology, environmental biotechnology, nanobiotechnology, protein and peptide chemistry, molecular biology, structural and computational biology, bioinformatics, parasite biology, tissue engineering, stem cell biology and gene therapy, enzymology, and proteomics. -
Single-Molecule Analysis of a Novel Kinesin Motor Protein
Single-Molecule Analysis of a Novel Kinesin Motor Protein Jeremy Meinke Advisor: Dr. Weihong Qiu Oregon State University, Department of Physics June 7, 2017 Abstract Kinesins are intracellular motor proteins that transform chemical energy into mechanical energy through ATP hydrolysis to move along microtubules. Kinesin roles can vary among transportation, regulation, and spindle alignment within most cells. Many kinesin have been found to move towards the plus end of microtubules at a steady velocity. For this experiment, we investigate BimC - a kinesin-5 as- sociated with mitotic spindle regulation - under high salt conditions. Using single molecule imaging with Total Internal Reflection Fluorescence Microscopy, we found BimC to be directed towards the minus end of microtubules at a high velocity of 597±214 nm/s (mean±S.D, n=124). BimC then joins the few other kinesin found so far to be minus-end-directed. However, preliminary results at low salt condi- tions suggest that BimC switches towards the plus end. BimC could very well be an early example of a kinesin motor protein that is directionally-dependent upon ionic strength. These results suggest multiple branches of further investigation into directionally-dependent kinesin proteins and what purposes they might have. Contents 1 Introduction 1 1.1 Kinesin Proteins . 1 1.2 Total Internal Reflection Fluorescence Microscopy . 3 1.3 Protein Motion Analysis . 3 2 Methods 5 2.1 Design, Expression, and Purification of BimC . 5 2.2 Single Molecule Imaging . 7 2.3 Analysis of Data/Results . 7 3 Results 9 3.1 Single Molecule Imaging of BimC . 9 3.2 Directionality of BimC in High Salt Conditions . -
3053.Full.Pdf
The Journal of Neuroscience, April 1995, 75(4): 3053-3064 The Activation of Protein Kinase A Pathway Selectively Inhibits Anterograde Axonal Transport of Vesicles but Not Mitochondria Transport or Retrograde Transport ~II viva Yasushi Okada, Reiko Sato-Yoshitake, and Nobutaka Hirokawa Department of Anatomy and Cell Biology, Faculty of Medicine, University of Tokyo, Hongo, Tokyo, 113, Japan To shed light on how axonal transport is regulated, we ex- is an especially well developed intracellular organelle transport amined the possible roles of protein kinase A (PKA) in viva system. Many studies have been focused on the mechanismof suggested by our previous work (Sato-Yoshitake et al., this transport, but little is known about its regulation. As a pu- 1992). Pharmacological probes or the purified catalytic tative mechanismfor the regulation, we have proposeda model subunit of PKA were applied to the permeabilized-reacti- from our recent studies (Hirokawa et al., 1990, 1991) that the vated model of crayfish walking leg giant axon, and the anterogrademotor kinesin is decommissionedat the axon ter- effect was monitored by the quantitative video-enhanced minal, and that the retrogrademotor cytoplasmic dynein is trans- light microscopy and the quantitative electron microscopy. ported, presumably in an inactive form, by the anterogradeor- Dibutyryl cyclic AMP caused concentration-dependent ganelle transport to the axon terminal, where it should be transient reduction in the number of anterogradely trans- activated to support the retrograde organelle transport. ported small vesicles, while the retrogradely transported Our present study was undertakento examine this regulation organelles and anterogradely transported mitochondria mechanism.One plausiblemechanism is through protein kinases showed no decrease. -
Motor-Driven Dynamics in Actin-Myosin Networks Loïc Le Goff, François Amblard, Eric Furst
Motor-Driven Dynamics in Actin-Myosin Networks Loïc Le Goff, François Amblard, Eric Furst To cite this version: Loïc Le Goff, François Amblard, Eric Furst. Motor-Driven Dynamics in Actin-Myosin Networks. Physical Review Letters, American Physical Society, 2001, 88 (1), pp.018101. 10.1103/phys- revlett.88.018101. hal-02415553 HAL Id: hal-02415553 https://hal.archives-ouvertes.fr/hal-02415553 Submitted on 19 Dec 2019 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. VOLUME 88, NUMBER 1PHYSICALREVIEWLETTERS7JANUARY 2002 Motor-Driven Dynamics in Actin-Myosin Networks Loïc Le Goff, François Amblard,* and Eric M. Furst† Institut Curie, Physico-Chimie Curie, UMR CNRS/IC 168, 26 rue d’Ulm, 75248 Paris Cedex 05, France (Received 29 May 2001; published 14 December 2001) The effect of myosin motor protein activity on the filamentous actin (F-actin) rheological response is studied using diffusing wave spectroscopy. Under conditions of saturating motor activity, we find an enhancement of longitudinal filament fluctuations corresponding to a scaling of the viscoelastic shear 7͞8 modulus Gd͑v͒ϳv . As the adenosine tri-phosphate reservoir sustaining motor activity is depleted, we find an abrupt transient to a passive, “rigor state” and a return to dissipation dominated by transverse filament modes. -
Theoretical Aspects of Motor Protein Induced Filament Depolymerisation
Institut f¨ur Theoretische Physik Fakult¨at Mathematik und Naturwissenschaft Technische Universit¨at Dresden Theoretical aspects of motor protein induced filament depolymerisation Dissertation Zur Erlangung des akademischen Grades Doktor der Naturwissenschaften (Dr. rer. nat.) angefertigt am Max Planck Institut f¨ur Physik komplexer Systeme Dresden vorgelegt von Gernot A. Klein Dresden, 2005 Contents 1 Introduction 1 2 The cytoskeleton and motor proteins 5 2.1 Cytoskeletalfilaments . ... 5 2.1.1 Structure and organisation of actin and intermediate filaments . 6 2.1.2 Assembly and structure of microtubules . ..... 8 2.2 Cytoskeletal motor proteins . ..... 10 2.2.1 Myosinanddynein............................. 11 2.2.2 Kinesin ................................... 12 2.3 Microtubuledynamicsandstructures. ....... 14 2.3.1 Force generation by polymerising filaments . ...... 14 2.3.2 Dynamic instability of growing microtubules . ....... 16 2.3.3 Reorganisation of microtubules during mitosis . ......... 17 2.4 Microtubule-depolymerising motor proteins . .......... 18 2.4.1 Properties of kinesin-13 motors . 19 2.4.2 Mechanism of microtubule depolymerisation . ....... 20 2.4.3 Cellularfunctions. .. .. .. .. .. .. .. .. 22 2.5 Theoretical description of motor proteins . ......... 23 2.5.1 Phenomenological approach . 23 2.5.2 Isothermalratchetmodels . 25 2.5.3 Stochastic models on discrete lattices . ....... 26 3 General description of motor induced filament depolymerisation 29 3.1 Filament depolymerisation . ..... 29 i ii Contents 3.1.1 Dynamics of motor densities . 30 3.1.2 Motor induced filament depolymerisation . ..... 31 3.1.3 Processivesubunitremoval . 32 3.2 Steady-statesolutions . 32 3.2.1 Density profiles of motor proteins . 33 3.2.2 Stabilityofsolutions . 34 3.3 Dynamic accumulation of motor proteins . ....... 36 3.3.1 Mechanisms of motor accumulation at filament ends .