scholarly journals Simulations and Electrostatic Analysis Suggest an Active Role for DNA Conformational Changes During Genome Packaging by Bacteriophages

2018 ◽  
Author(s):  
Kim A. Sharp ◽  
Xiang-Jun Lu ◽  
Gino Cingolani ◽  
Stephen C. Harvey
Keyword(s):  
Conformational Changes ◽  
Electrostatic Potential ◽  
Atp Hydrolysis ◽  
Active Role ◽  
Human Pathogens ◽  
Dna Translocation ◽  
Genome Packaging ◽  
Dna Translocases ◽  
Dna Conformational Changes ◽  
Cyclic Changes

AbstractMotors that move DNA, or that move along DNA, play essential roles in DNA replication, transcription, recombination, and chromosome segregation. The mechanisms by which these DNA translocases operate remain largely unknown. Some double-stranded DNA (dsDNA) viruses use an ATP-dependent motor to drive DNA into preformed capsids. These include several human pathogens, as well as dsDNA bacteriophages – viruses that infect bacteria. We previously proposed that DNA is not a passive substrate of bacteriophage packaging motors but is, instead, an active component of the machinery. Computational studies on dsDNA in the channel of viral portal proteins reported here reveal DNA conformational changes consistent with that hypothesis. dsDNA becomes longer (“stretched”) in regions of high negative electrostatic potential, and shorter (“scrunched”) in regions of high positive potential. These results suggest a mechanism that couples the energy released by ATP hydrolysis to DNA translocation: The chemical cycle of ATP binding, hydrolysis and product release drives a cycle of protein conformational changes. This produces changes in the electrostatic potential in the channel through the portal, and these drive cyclic changes in the length of dsDNA. The DNA motions are captured by a coordinated protein-DNA grip-and-release cycle to produce DNA translocation. In short, the ATPase, portal and dsDNA work synergistically to promote genome packaging.

scholarly journals Structure and mechanism of the ATPase that powers viral genome packaging

2015 ◽  
Vol 112 (29) ◽  
pp. E3792-E3799 ◽  
Author(s):  
Brendan J. Hilbert ◽  
Janelle A. Hayes ◽  
Nicholas P. Stone ◽  
Caroline M. Duffy ◽  
Banumathi Sankaran ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Structural Model ◽  
Atp Hydrolysis ◽  
Mechanistic Model ◽  
Published Data ◽  
Dna Translocation ◽  
Genome Packaging ◽  
Large Rotation ◽  
Arginine Finger ◽  
Motor Structure

Many viruses package their genomes into procapsids using an ATPase machine that is among the most powerful known biological motors. However, how this motor couples ATP hydrolysis to DNA translocation is still unknown. Here, we introduce a model system with unique properties for studying motor structure and mechanism. We describe crystal structures of the packaging motor ATPase domain that exhibit nucleotide-dependent conformational changes involving a large rotation of an entire subdomain. We also identify the arginine finger residue that catalyzes ATP hydrolysis in a neighboring motor subunit, illustrating that previous models for motor structure need revision. Our findings allow us to derive a structural model for the motor ring, which we validate using small-angle X-ray scattering and comparisons with previously published data. We illustrate the model’s predictive power by identifying the motor’s DNA-binding and assembly motifs. Finally, we integrate our results to propose a mechanistic model for DNA translocation by this molecular machine.

scholarly journals DNA Conformational Changes Play a Force-Generating Role during Bacteriophage Genome Packaging

2019 ◽  
Vol 116 (3) ◽  
pp. 500a ◽  
Author(s):  
Kim A. Sharp ◽  
Xiang-Jun Lu ◽  
Gino Cingolani ◽  
Stephen C. Harvey
Keyword(s):  
Conformational Changes ◽  
Genome Packaging ◽  
Bacteriophage Genome ◽  
Dna Conformational Changes

scholarly journals DNA Conformational Changes Play a Force-Generating Role during Bacteriophage Genome Packaging

2019 ◽  
Vol 116 (11) ◽  
pp. 2172-2180 ◽  
Author(s):  
Kim A. Sharp ◽  
Xiang-Jun Lu ◽  
Gino Cingolani ◽  
Stephen C. Harvey
Keyword(s):  
Conformational Changes ◽  
Genome Packaging ◽  
Bacteriophage Genome ◽  
Dna Conformational Changes

Role of spectrin in membrane fusion and in shape change of human erythrocyte ghost

1978 ◽  
Vol 36 (2) ◽  
pp. 328-329
Author(s):  
Hideo Hayashi ◽  
Yoshikazu Hirai ◽  
John T. Penniston
Keyword(s):  
Conformational Changes ◽  
Human Erythrocyte ◽  
Shape Change ◽  
Membrane Surface ◽  
Slight Modification ◽  
Active Role ◽  
Main Role ◽  
Bank Blood ◽  
Human Erythrocyte Ghost

Spectrin is a membrane associated protein most of which properties have been tentatively elucidated. A main role of the protein has been assumed to give a supporting structure to inside of the membrane. As reported previously, however, the isolated spectrin molecule underwent self assemble to form such as fibrous, meshwork, dispersed or aggregated arrangements depending upon the buffer suspended and was suggested to play an active role in the membrane conformational changes. In this study, the role of spectrin and actin was examined in terms of the molecular arrangements on the erythrocyte membrane surface with correlation to the functional states of the ghosts.Human erythrocyte ghosts were prepared from either freshly drawn or stocked bank blood by the method of Dodge et al with a slight modification as described before. Anti-spectrin antibody was raised against rabbit by injection of purified spectrin and partially purified.

scholarly journals A structural framework for unidirectional transport by a bacterial ABC exporter

2020 ◽  
Vol 117 (32) ◽  
pp. 19228-19236
Author(s):  
Chengcheng Fan ◽  
Jens T. Kaiser ◽  
Douglas C. Rees
Keyword(s):  
Conformational Changes ◽  
Iron Homeostasis ◽  
Atp Hydrolysis ◽  
Transmembrane Helix ◽  
Reverse Direction ◽  
Conformational States ◽  
X Ray Crystallography ◽  
Binding Domains ◽  
Structural Framework ◽  
Glutathione Derivatives

The ATP-binding cassette (ABC) transporter of mitochondria (Atm1) mediates iron homeostasis in eukaryotes, while the prokaryotic homolog fromNovosphingobium aromaticivorans(NaAtm1) can export glutathione derivatives and confer protection against heavy-metal toxicity. To establish the structural framework underlying theNaAtm1 transport mechanism, we determined eight structures by X-ray crystallography and single-particle cryo-electron microscopy in distinct conformational states, stabilized by individual disulfide crosslinks and nucleotides. AsNaAtm1 progresses through the transport cycle, conformational changes in transmembrane helix 6 (TM6) alter the glutathione-binding site and the associated substrate-binding cavity. Significantly, kinking of TM6 in the post-ATP hydrolysis state stabilized by MgADPVO4eliminates this cavity, precluding uptake of glutathione derivatives. The presence of this cavity during the transition from the inward-facing to outward-facing conformational states, and its absence in the reverse direction, thereby provide an elegant and conceptually simple mechanism for enforcing the export directionality of transport byNaAtm1. One of the disulfide crosslinkedNaAtm1 variants characterized in this work retains significant glutathione transport activity, suggesting that ATP hydrolysis and substrate transport by Atm1 may involve a limited set of conformational states with minimal separation of the nucleotide-binding domains in the inward-facing conformation.

scholarly journals Myosinome: A Database of Myosins from Select Eukaryotic Genomes to Facilitate Analysis of Sequence-Structure-Function Relationships

2012 ◽  
Vol 6 ◽  
pp. BBI.S9902 ◽  
Author(s):  
Divya P. Syamaladevi ◽  
Margaret S Sunitha ◽  
S. Kalaimathy ◽  
Chandrashekar C. Reddy ◽  
Mohammed Iftekhar ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Atp Hydrolysis ◽  
Homo Sapiens ◽  
Relevant Literature ◽  
Myosin Ii ◽  
Coiled Coil ◽  
Structural Features ◽  
Model Organisms ◽  
Congenital Diseases ◽  
C Elegans

Myosins are one of the largest protein superfamilies with 24 classes. They have conserved structural features and catalytic domains yet show huge variation at different domains resulting in a variety of functions. Myosins are molecules driving various kinds of cellular processes and motility until the level of organisms. These are ATPases that utilize the chemical energy released by ATP hydrolysis to bring about conformational changes leading to a motor function. Myosins are important as they are involved in almost all cellular activities ranging from cell division to transcriptional regulation. They are crucial due to their involvement in many congenital diseases symptomatized by muscular malfunctions, cardiac diseases, deafness, neural and immunological dysfunction, and so on, many of which lead to death at an early age. We present Myosinome, a database of selected myosin classes (myosin II, V, and VI) from five model organisms. This knowledge base provides the sequences, phylogenetic clustering, domain architectures of myosins and molecular models, structural analyses, and relevant literature of their coiled-coil domains. In the current version of Myosinome, information about 71 myosin sequences belonging to three myosin classes (myosin II, V, and VI) in five model organisms ( Homo Sapiens, Mus musculus, D. melanogaster, C. elegans and S. cereviseae) identified using bioinformatics surveys are presented, and several of them are yet to be functionally characterized. As these proteins are involved in congenital diseases, such a database would be useful in short-listing candidates for gene therapy and drug development. The database can be accessed from http://caps.ncbs.res.in/myosinome .

scholarly journals A FRET-Based Sensor Reveals Large ATP Hydrolysis–Induced Conformational Changes and Three Distinct States of the Molecular Motor Myosin

Cell ◽  
2000 ◽  
Vol 102 (5) ◽  
pp. 683-694 ◽  
Author(s):  
William M Shih ◽  
Zygmunt Gryczynski ◽  
Joseph R Lakowicz ◽  
James A Spudich
Keyword(s):  
Conformational Changes ◽  
Atp Hydrolysis ◽  
Molecular Motor

What controls the unusual melting profiles of small AuNPs/DNA complexes

2019 ◽  
Vol 21 (21) ◽  
pp. 11019-11032 ◽  
Author(s):  
Elia Grueso ◽  
Rosa M. Giráldez-Pérez ◽  
Pilar Perez-Tejeda ◽  
Emilio Roldán ◽  
R. Prado-Gotor
Keyword(s):  
Gold Nanoparticles ◽  
Conformational Changes ◽  
Dna Complexes ◽  
Low Salt ◽  
Dna Conformational Changes

The effect of the addition of low salt concentrations on ds-DNA and ss-DNA conformational changes induced by small N-(2-mercaptopropionyl)glycine gold nanoparticles (AuNPs) is studied in detail by using different techniques. The results are correlated with the unusual melting profiles of the AuNPs/DNA complexes.

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