当前位置： SCI文献检索 > BIOCHEMISTRY期刊下所有文献 > All-atom molecular dynamics simulations of actin-myosin interactions: a comparative study of cardiac α myosin, β myosin, and fast skeletal muscle myosin.

All-atom molecular dynamics simulations of actin-myosin interactions: a comparative study of cardiac α myosin, β myosin, and fast skeletal muscle myosin.

Abstract：

:Myosins are a superfamily of actin-binding motor proteins with significant variations in kinetic properties (such as actin binding affinity) between different isoforms. It remains unknown how such kinetic variations arise from the structural and dynamic tuning of the actin-myosin interface at the amino acid residue level. To address this key issue, we have employed molecular modeling and simulations to investigate, with atomistic details, the isoform dependence of actin-myosin interactions in the rigor state. By combining electron microscopy-based docking with homology modeling, we have constructed three all-atom models for human cardiac α and β and rabbit fast skeletal muscle myosin in complex with three actin subunits in the rigor state. Starting from these models, we have performed extensive all-atom molecular dynamics (MD) simulations (total of 100 ns per system) and then used the MD trajectories to calculate actin-myosin binding free energies with contributions from both electrostatic and nonpolar forces. Our binding calculations are in good agreement with the experimental finding of isoform-dependent differences in actin binding affinity between these myosin isoforms. Such differences are traced to changes in actin-myosin electrostatic interactions (i.e., hydrogen bonds and salt bridges) that are highly dynamic and involve several flexible actin-binding loops. By partitioning the actin-myosin binding free energy to individual myosin residues, we have also identified key myosin residues involved in the actin-myosin interactions, some of which were previously validated experimentally or implicated in cardiomyopathy mutations, and the rest make promising targets for future mutational experiments.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Li M,Zheng W

doi

10.1021/bi4006896

subject

Has Abstract

pub_date

2013-11-26 00:00:00

pages

8393-405

issue

47

eissn

0006-2960

issn

1520-4995

journal_volume

52

pub_type

杂志文章

相关文献

BIOCHEMISTRY文献大全
  • Mapping global angular transitions of proteins in assemblies using multiple extrinsic reporter groups.

    abstract：:The fluorescence polarization intensities from fluorescent probes and the electron paramagnetic resonance spectra from spin probes, specifically modifying elements of a biological assembly such as myosin sulfhydryl 1 (SH1) in muscle fibers, are interpreted in terms of probe order parameters using a model-independent m...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00116a029

    authors： Burghardt TP,Ajtai K

    更新日期：1992-01-14 00:00:00

  • Binding of metal cyanide complexes to bovine liver rhodanese in the crystalline state.

    abstract：:Bovine liver rhodanese, which catalyzes the transfer of sulfur atoms between a variety of sulfur donor and sulfur acceptor substrates, is inhibited by metal cyanide complexes [Volini, M., Van Sweringen, B., & Chen, F.-Sh. (1978) Arch. Biochem. Biophys. 191, 205-215]. Crystallographic studies are described which reveal...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00281a026

    authors： Lijk LJ,Kalk KH,Brandenburg NP,Hol WG

    更新日期：1983-06-07 00:00:00

  • Glycosylinositol phospholipid anchors of the scrapie and cellular prion proteins contain sialic acid.

    abstract：:The only identified component of the scrapie prion is PrPSc, a glycosylinositol phospholipid (GPI)-linked protein that is derived from the cellular isoform (PrPC) by an as yet unknown posttranslational event. Analysis of the PrPSc GPI has revealed six different glycoforms, three of which are unprecedented. Two of the ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00136a600

    authors： Stahl N,Baldwin MA,Hecker R,Pan KM,Burlingame AL,Prusiner SB

    更新日期：1992-06-02 00:00:00

  • The nickel site of Bacillus pasteurii UreE, a urease metallo-chaperone, as revealed by metal-binding studies and X-ray absorption spectroscopy.

    abstract：:UreE is a homodimeric metallo-chaperone that assists the insertion of Ni(2+) ions in the active site of urease. The crystal structures of UreE from Bacillus pasteurii and Klebsiella aerogenes have been determined, but the details of the nickel-binding site were not elucidated due to solid-state effects that caused dis...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi0601003

    authors： Stola M,Musiani F,Mangani S,Turano P,Safarov N,Zambelli B,Ciurli S

    更新日期：2006-05-23 00:00:00

  • Determination of Fe-CO geometry in the subunits of carbonmonoxy hemoglobin M Boston using femtosecond infrared spectroscopy.

    abstract：:We have undertaken ultrafast infrared (IR) spectroscopic studies in order to elucidate the geometry of bound CO in the alpha and beta subunits of hemoglobin (Hb) M Boston 13CO. Hb M Boston is a mutant human Hb in which the distal histidine in the alpha subunits is replaced by a tyrosine. The IR absorptions of bound 13...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00073a013

    authors： Lian T,Locke B,Kitagawa T,Nagai M,Hochstrasser RM

    更新日期：1993-06-08 00:00:00

  • Detection of a water molecule in the active-site of bacteriorhodopsin: hydrogen bonding changes during the primary photoreaction.

    abstract：:FTIR-difference spectroscopy in combination with site-directed mutagenesis has been used to investigate the role of water during the photocycle of bacteriorhodopsin. At least one water molecule is detected which undergoes an increase in H-bonding during the primary bR-->K phototransition. Bands due to water appear in ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00209a005

    authors： Fischer WB,Sonar S,Marti T,Khorana HG,Rothschild KJ

    更新日期：1994-11-01 00:00:00

  • A solution NMR investigation into the early events of amelogenin nanosphere self-assembly initiated with sodium chloride or calcium chloride.

    abstract：:Using solution-state NMR spectroscopy, new insights into the early events governing amelogenin supramolecular self-assembly have been identified using sodium chloride and calcium chloride to trigger the association. Two-dimensional 1H-15N HSQC spectra were recorded for 15N- and 13C-labeled murine amelogenin as a funct...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi8018288

    authors： Buchko GW,Tarasevich BJ,Bekhazi J,Snead ML,Shaw WJ

    更新日期：2008-12-16 00:00:00

  • Progesterone-binding components of chick oviduct: analysis of receptor structure by limited proteolysis.

    abstract：:An endogenous calcium-activated sulfhydryl protease in chick oviduct cytosol has been utilized to study the structure of the chick oviduct progesterone receptor subunits, progestophilins A (79 000 g/mol) and B (117 000 g/mol). The protease is not a normal component of the native progesterone receptor aggregate (6 and ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00543a015

    authors： Vedeckis WV,Schrader WT,O'Malley BW

    更新日期：1980-01-22 00:00:00

  • Carbohydrate chains of human thyrotropin are differentially susceptible to endoglycosidase removal on combined and free polypeptide subunits.

    abstract：:The accessibility of the asparagine-linked carbohydrate chains of human thyrotropin (hTSH) and free alpha and beta subunits was investigated by their susceptibility to endoglycosidases H and F as well as to peptide:N-glycosidase F. Iodinated hTSH or subunits were incubated with a commercial enzyme preparation containi...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00392a040

    authors： Ronin C,Papandreou MJ,Canonne C,Weintraub BD

    更新日期：1987-09-08 00:00:00

  • Analysis of the structural core of the human estrogen receptor ligand binding domain by selective proteolysis/mass spectrometric analysis.

    abstract：:The structure of the ca. 250 amino acid hormone binding domain of the human estrogen receptor (hER-LBD), expressed in E. coli and purified as a complex with estradiol, has been probed by selective proteolysis, with analysis of the protein fragments both by classical methods (SDS-PAGE and Edman N-terminal sequencing) a...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00039a016

    authors： Seielstad DA,Carlson KE,Kushner PJ,Greene GL,Katzenellenbogen JA

    更新日期：1995-10-03 00:00:00

  • Proximity between nucleotide/dinucleotide and metal ion binding sites in DNA-dependent RNA polymerase from Escherichia coli.

    abstract：:In order to understand translocation in transcription, it is important to develop a continuous functional assay for RNA polymerase (RNAP) activity in vitro. Fluorescent derivatives of ATP, UTP, UpA, and CpA with aminonaphthalene-5-sulfonic acid (AmNS) attached to the nucleotide triphosphates via a gamma-phosphoramidat...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00143a013

    authors： Tyagi SC,Wu FY

    更新日期：1992-07-21 00:00:00

  • Cytochrome bo from Escherichia coli: binding of azide to CuB.

    abstract：:Azide binds to fast cytochrome bo with a stoichiometry of 1:1, the dissociation constant for this reaction being approximately 2 x 10(-5) M. The changes induced in the electronic absorption are very slight and are consistent with heme o remaining hexacoordinate high-spin, an observation confirmed by room temperature M...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi961221d

    authors： Little RH,Cheesman MR,Thomson AJ,Greenwood C,Watmough NJ

    更新日期：1996-10-29 00:00:00

  • A conformational rearrangement in gramicidin A: from a double-stranded left-handed to a single-stranded right-handed helix.

    abstract：:A conformational transition is described for the polypeptide, gramicidin A, in which a dimer that forms a left-handed intertwined antiparallel helix is converted to a single-stranded amino terminus to amino terminus right-handed helix. The starting structure is determined here by solution NMR methods while reference i...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00152a019

    authors： Zhang Z,Pascal SM,Cross TA

    更新日期：1992-09-22 00:00:00

  • DNA polymerase λ inactivation by oxidized abasic sites.

    abstract：:Base excision repair (BER) plays a vital role in maintaining genomic integrity in mammalian cells. DNA polymerase λ (Pol λ) is believed to play a backup role to DNA polymerase β (Pol β) in base excision repair. Two oxidized abasic lesions that are produced by a variety of DNA-damaging agents, including several antitum...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi301592x

    authors： Stevens AJ,Guan L,Bebenek K,Kunkel TA,Greenberg MM

    更新日期：2013-02-05 00:00:00

  • Influence of sequence-dependent cytosine protonation and methylation on DNA triplex stability.

    abstract：:To investigate cytosine protonation and its influence on the sequence-dependent thermal stability of DNA triplexes in detail, we have employed homo- and heteronuclear NMR experiments on specifically (15)N-labeled oligodeoxynucleotides that were designed to fold into intramolecular triple helices of the pyrimidine moti...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi992630n

    authors： Leitner D,Schröder W,Weisz K

    更新日期：2000-05-16 00:00:00

  • Differentiation of secreted and membrane-type matrix metalloproteinase activities based on substitutions and interruptions of triple-helical sequences.

    abstract：:The turnover of the collagen triple-helical structure (collagenolysis) is a tightly regulated process in normal physiology and has been ascribed to a small number of proteases. Several members of the matrix metalloproteinase (MMPs) family possess collagenolytic activity, and the mechanisms by which these enzymes proce...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi062199j

    authors： Minond D,Lauer-Fields JL,Cudic M,Overall CM,Pei D,Brew K,Moss ML,Fields GB

    更新日期：2007-03-27 00:00:00

  • Bacterial Renalase: Structure and Kinetics of an Enzyme with 2- and 6-Dihydro-β-NAD(P) Oxidase Activity from Pseudomonas phaseolicola.

    abstract：:Despite a lack of convincing in vitro evidence and a number of sound refutations, it is widely accepted that renalase is an enzyme unique to animals that catalyzes the oxidative degradation of catecholamines in blood in order to lower vascular tone. Very recently, we identified isomers of β-NAD(P)H as substrates for r...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.5b00451

    authors： Hoag MR,Roman J,Beaupre BA,Silvaggi NR,Moran GR

    更新日期：2015-06-23 00:00:00

  • Distribution and properties of the genes encoding the biosynthesis of the bacterial cofactor, pyrroloquinoline quinone.

    abstract：:Pyrroloquinoline quinone (PQQ) is a small, redox active molecule that serves as a cofactor for several bacterial dehydrogenases, introducing pathways for carbon utilization that confer a growth advantage. Early studies had implicated a ribosomally translated peptide as the substrate for PQQ production. This study pres...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi201763d

    authors： Shen YQ,Bonnot F,Imsand EM,RoseFigura JM,Sjölander K,Klinman JP

    更新日期：2012-03-20 00:00:00

  • Additive transfer free energies of the peptide backbone unit that are independent of the model compound and the choice of concentration scale.

    abstract：:With knowledge of individual transfer free energies of chemical groups that become newly exposed on protein denaturation and assuming the group transfer free energy contributions are additive, it should be possible to predict the stability of a protein in the presence of denaturant. Unfortunately, several unresolved i...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi035908r

    authors： Auton M,Bolen DW

    更新日期：2004-02-10 00:00:00

  • Real-time monitoring of the interactions of two-stranded de novo designed coiled-coils: effect of chain length on the kinetic and thermodynamic constants of binding.

    abstract：:We have de novo designed a heterodimeric coiled-coil formed by two peptides as a capture/delivery system that can be used in applications such as affinity tag purification, immobilization in biosensors, etc. The two strands are designated as K coil (KVSALKE heptad sequence) and E coil (EVSALEK heptad sequence), where ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi0268450

    authors： De Crescenzo G,Litowski JR,Hodges RS,O'Connor-McCourt MD

    更新日期：2003-02-18 00:00:00

  • The C-terminal domain of the utrophin tandem calponin-homology domain appears to be thermodynamically and kinetically more stable than the full-length protein.

    abstract：:Domains are in general less stable than the corresponding full-length proteins. Human utrophin tandem calponin-homology (CH) domain seems to be an exception. Reversible, equilibrium denaturant melts indicate that the isolated C-terminal domain (CH2) is thermodynamically more stable than the tandem CH domain. Thermal m...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi500120e

    authors： Bandi S,Singh SM,Mallela KM

    更新日期：2014-04-15 00:00:00

  • Structural Elucidation of Peptide Binding to KLHL-12, a Substrate Specific Adapter Protein in a Cul3-Ring E3 Ligase Complex.

    abstract：:KLHL-12 is a substrate specific adapter protein for a Cul3-Ring ligase complex. It is a member of the Kelch β-propeller domain subclass of Cullin-Ring substrate recognition domains. This E3 ubiquitin ligase complex has many activities, including acting as a negative regulator of the Wnt signaling pathway by mediating ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.9b01073

    authors： Zhao B,Payne WG,Sai J,Lu Z,Olejniczak ET,Fesik SW

    更新日期：2020-03-03 00:00:00

  • Studies with recombinant Saccharomyces cerevisiae CaaX prenyl protease Rce1p.

    abstract：:Eukaryotic proteins with carboxyl-terminal CaaX motifs undergo three post-translational processing reactions-protein prenylation, endoproteolysis, and carboxymethylation. Two genes in yeast encoding CaaX endoproteases, AFC1 and RCE1, have been identified. Rce1p is solely responsible for proteolysis of yeast Ras protei...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi9923611

    authors： Dolence JM,Steward LE,Dolence EK,Wong DH,Poulter CD

    更新日期：2000-04-11 00:00:00

  • Influence of histidine tag attachment on picosecond protein dynamics.

    abstract：:Polyhistidine affinity tags are routinely employed as a convenient means of purifying recombinantly expressed proteins. A tacit assumption is commonly made that His tags have little influence on protein structure and function. Attachment of a His tag to the N-terminus of the robust globular protein myoglobin leads to ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi2003923

    authors： Thielges MC,Chung JK,Axup JY,Fayer MD

    更新日期：2011-06-28 00:00:00

  • Molecular exchange at the lipid-rhodopsin interface: spin-label electron spin resonance studies of rhodopsin-dimyristoylphosphatidylcholine recombinants.

    abstract：:The photoreceptor protein rhodopsin has been reconstituted with a single phospholipid species, dimyristoylphosphatidylcholine, at a range of different lipid/protein ratios, and the exchange rate at the lipid-protein interface has been determined from the electron spin resonance spectra of spin-labeled phosphatidylchol...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00385a045

    authors： Ryba NJ,Horváth LI,Watts A,Marsh D

    更新日期：1987-06-02 00:00:00

  • Stimulation of lignocellulosic biomass hydrolysis by proteins of glycoside hydrolase family 61: structure and function of a large, enigmatic family.

    abstract：:Currently, the relatively high cost of enzymes such as glycoside hydrolases that catalyze cellulose hydrolysis represents a barrier to commercialization of a biorefinery capable of producing renewable transportable fuels such as ethanol from abundant lignocellulosic biomass. Among the many families of glycoside hydrol...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi100009p

    authors： Harris PV,Welner D,McFarland KC,Re E,Navarro Poulsen JC,Brown K,Salbo R,Ding H,Vlasenko E,Merino S,Xu F,Cherry J,Larsen S,Lo Leggio L

    更新日期：2010-04-20 00:00:00

  • Organization and interaction of cholesterol and phosphatidylcholine in model bilayer membranes.

    abstract：:The molecular organization of sterols in liposomes of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) at 37 degrees C is examined by utilizing the fluorescent analogue of cholesterol cholesta-5,7,9-trien-3 beta-ol (cholestatrienol). (1) Cholestatrienol is shown to be indistinguishable from native cholesterol i...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00456a027

    authors： Hyslop PA,Morel B,Sauerheber RD

    更新日期：1990-01-30 00:00:00

  • Loss of DNA minor groove interactions by exonuclease-deficient Klenow polymerase inhibits O6-methylguanine and abasic site translesion synthesis.

    abstract：:The importance of DNA polymerase-DNA minor groove interactions on translesion synthesis (TLS) was examined in vitro using variants of exonuclease-deficient Klenow polymerase and site-specifically modified DNA oligonucleotides. Polymerase variant R668A lacks primer strand interactions, while variant Q849A lacks templat...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi047591g

    authors： Gestl EE,Eckert KA

    更新日期：2005-05-10 00:00:00

  • Structure and Dynamics of N-Glycosylated Human Ribonuclease 1.

    abstract：:Glycosylation is a common modification that can endow proteins with altered physical and biological properties. Ribonuclease 1 (RNase 1), which is the human homologue of the archetypal enzyme RNase A, undergoes N-linked glycosylation at asparagine residues 34, 76, and 88. We have produced the three individual glycofor...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.0c00191

    authors： Kilgore HR,Latham AP,Ressler VT,Zhang B,Raines RT

    更新日期：2020-09-01 00:00:00

  • Cryoenzymic studies on actomyosin ATPase. Evidence that the degree of saturation of actin with myosin subfragment 1 affects the kinetics of the binding of ATP.

    abstract：:The initial steps of actomyosin subfragment 1 (acto-S1) ATPase (dissociation and binding of ATP) were studied at -15 degrees C with 40% ethylene glycol as antifreeze. The dissociation kinetics were followed by light scattering in a stopped-flow apparatus, and the binding of ATP was followed by the ATP chase method in ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00459a026

    authors： Tesi C,Travers F,Barman T

    更新日期：1990-02-20 00:00:00