General Methods for Analysis of Sequential “n-step” Kinetic Mechanisms: Application to Single Turnover Kinetics of Helicase-Catalyzed DNA Unwinding

scientific article published on October 1, 2003

General Methods for Analysis of Sequential “n-step” Kinetic Mechanisms: Application to Single Turnover Kinetics of Helicase-Catalyzed DNA Unwinding is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1016/S0006-3495(03)74648-7
P953full work available at URLhttp://www.cell.com/article/S0006349503746487/pdf
https://europepmc.org/articles/PMC1303449
https://europepmc.org/articles/PMC1303449?pdf=render
https://api.elsevier.com/content/article/PII:S0006349503746487?httpAccept=text/plain
https://api.elsevier.com/content/article/PII:S0006349503746487?httpAccept=text/xml
P932PMC publication ID1303449
P698PubMed publication ID14507688
P5875ResearchGate publication ID9081535

P50authorTimothy M. LohmanQ7807375
P2093author name stringChristopher J. Fischer
Aaron L. Lucius
Nasib K. Maluf
P2860cites workToroidal structure of lambda-exonucleaseQ27743192
Processive translocation and DNA unwinding by individual RecBCD enzyme moleculesQ30980458
A general model for nucleic acid helicases and their "coupling" within macromolecular machinesQ32025143
DNA helicases: 'inching forward'.Q33840733
Single-molecule studies of the effect of template tension on T7 DNA polymerase activity.Q33893261
Bead movement by single kinesin molecules studied with optical tweezersQ33957127
Structure and function of hexameric helicases.Q34019405
The kinetics and processivity of nucleic acid polymerasesQ34056708
Unwinding and rewinding of DNA by the RecBC enzymeQ34252088
A helicase assay based on the displacement of fluorescent, nucleic acid-binding ligandsQ34593225
Spectrophotometric assay for enzyme-mediated unwinding of double-stranded DNA.Q35464341
DNA helicasesQ37886473
Direct measurement of single-stranded DNA translocation by PcrA helicase using the fluorescent base analogue 2-aminopurineQ38293169
Translocation step size and mechanism of the RecBC DNA helicaseQ38311846
Kinetic mechanism of the single-stranded DNA recognition by Escherichia coli replicative helicase DnaB protein. Application of the matrix projection operator technique to analyze stopped-flow kineticsQ38315832
An oligomeric form of E. coli UvrD is required for optimal helicase activityQ38318982
Mechanisms of helicase-catalyzed DNA unwindingQ41114786
The design plan of kinesin motorsQ41689406
E. coli Rep oligomers are required to initiate DNA unwinding in vitroQ43655291
Complexes of Rep protein with ATP and DNA as a basis for helicase actionQ43815327
Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicaseQ44175920
DNA unwinding step-size of E. coli RecBCD helicase determined from single turnover chemical quenched-flow kinetic studiesQ44225424
A Dimer of Escherichia coli UvrD is the active form of the helicase in vitroQ44277846
Movement of microtubules by single kinesin moleculesQ46085669
Kinetic measurement of the step size of DNA unwinding by Escherichia coli UvrD helicaseQ47315601
Analysis of numerical methods for computer simulation of kinetic processes: development of KINSIM--a flexible, portable system.Q52706984
Single-turnover kinetics of helicase-catalyzed DNA unwinding monitored continuously by fluorescence energy transfer.Q54623590
Characterization of the helicase activity of the Escherichia coli RecBCD enzyme using a novel helicase assay.Q54731400
The DExH protein NPH-II is a processive and directional motor for unwinding RNAQ57259026
Single kinesin molecules studied with a molecular force clampQ59066796
χ-Sequence recognition and DNA translocation by single RecBCD helicase/nuclease moleculesQ59098644
Statistical kinetics of processive enzymesQ71574318
Bacteriophage T4 Dda Helicase Translocates in a Unidirectional Fashion on Single-stranded DNAQ72054987
Monte Carlo applications to thermal and chemical denaturation experiments of nucleic acids and proteinsQ74048422
Kinetic models of translocation, head-on collision, and DNA cleavage by type I restriction endonucleasesQ77594570
P433issue4
P407language of work or nameEnglishQ1860
P921main subjectbiophysicsQ7100
chemical modelQ25109595
P1104number of pages16
P304page(s)2224-2239
P577publication date2003-10-01
P1433published inBiophysical JournalQ2032955
P1476titleGeneral methods for analysis of sequential "n-step" kinetic mechanisms: application to single turnover kinetics of helicase-catalyzed DNA unwinding
General Methods for Analysis of Sequential “n-step” Kinetic Mechanisms: Application to Single Turnover Kinetics of Helicase-Catalyzed DNA Unwinding
P478volume85

Reverse relations

cites work (P2860)
Q47113485A Multi-stage Representation of Cell Proliferation as a Markov Process
Q43535639A helicase staircase
Q42030386A nonuniform stepping mechanism for E. coli UvrD monomer translocation along single-stranded DNA
Q60158574A simplified formula of Laplace inversion based on wavelet theory
Q50891337A steady-state theory for processive cellulases.
Q48831196A stepwise 2'-hydroxyl activation mechanism for the bacterial transcription termination factor Rho helicase
Q37663603ATPγS competes with ATP for binding at Domain 1 but not Domain 2 during ClpA catalyzed polypeptide translocation
Q42065424Analysis of kinetic intermediates in single-particle dwell-time distributions
Q36526232Asymmetric regulation of bipolar single-stranded DNA translocation by the two motors within Escherichia coli RecBCD helicase
Q33900524Autoinhibition of Escherichia coli Rep monomer helicase activity by its 2B subdomain
Q54437963Bacillus stearothermophilus PcrA monomer is a single-stranded DNA translocase but not a processive helicase in vitro.
Q41883688Chemical modifications of DNA for study of helicase mechanisms
Q41220996Comparative Analysis of the Structure and Function of AAA+ Motors ClpA, ClpB, and Hsp104: Common Threads and Disparate Functions
Q36731305Coupling of DNA unwinding to nucleotide hydrolysis in a ring-shaped helicase
Q42063417DNA synthesis provides the driving force to accelerate DNA unwinding by a helicase
Q34652749DNA unwinding and protein displacement by superfamily 1 and superfamily 2 helicases
Q54455405DNA unwinding by Escherichia coli DNA helicase I (TraI) provides evidence for a processive monomeric molecular motor.
Q36024282Dda helicase tightly couples translocation on single-stranded DNA to unwinding of duplex DNA: Dda is an optimally active helicase
Q35187537Development of a "modular" scheme to describe the kinetics of transcript elongation by RNA polymerase
Q64260618Dynamics of the Eukaryotic Replicative Helicase at Lagging-Strand Protein Barriers Support the Steric Exclusion Model
Q37570875E. coli ClpA catalyzed polypeptide translocation is allosterically controlled by the protease ClpP.
Q36452037Enhancement of human DNA polymerase η activity and fidelity is dependent upon a bipartite interaction with the Werner syndrome protein
Q37725328Ensemble methods for monitoring enzyme translocation along single stranded nucleic acids
Q36406795Escherichia coli ClpB is a non-processive polypeptide translocase
Q41921786Escherichia coli RecBC helicase has two translocase activities controlled by a single ATPase motor
Q27487760Establishing a Mechanistic Basis for the Large Kinetic Steps of the NS3 Helicase
Q37208512Experimental and computational analysis of DNA unwinding and polymerization kinetics
Q37051642Fluorescence methods to study DNA translocation and unwinding kinetics by nucleic acid motors
Q37694802Fluorescence tools to measure helicase activity in real time.
Q35199422G-quadruplexes significantly stimulate Pif1 helicase-catalyzed duplex DNA unwinding
Q36209445Helicase processivity and not the unwinding velocity exhibits universal increase with force
Q34003758Hepatitis C virus non-structural protein 3 (HCV NS3): a multifunctional antiviral target
Q83228197Homology sensing via non-linear amplification of sequence-dependent pausing by RecQ helicase
Q54206546How Does a Helicase Unwind DNA? Insights from RecBCD Helicase.
Q38288937Influence of DNA end structure on the mechanism of initiation of DNA unwinding by the Escherichia coli RecBCD and RecBC helicases
Q37777437Insight into helicase mechanism and function revealed through single-molecule approaches
Q64388590Intermediates revealed in the kinetic mechanism for DNA unwinding by a monomeric helicase
Q33876054Kinetic mechanism for DNA unwinding by multiple molecules of Dda helicase aligned on DNA.
Q36721673Kinetic mechanism of DNA translocation by the RSC molecular motor
Q27936457Kinetic model for the ATP-dependent translocation of Saccharomyces cerevisiae RSC along double-stranded DNA.
Q38345204Kinetics of DNA unwinding by the RecD2 helicase from Deinococcus radiodurans
Q37178673Kinetics of motor protein translocation on single-stranded DNA.
Q47583592Large domain movements upon UvrD dimerization and helicase activation
Q39434646Linear models of activation cascades: analytical solutions and coarse-graining of delayed signal transduction
Q36775572Mechanism of DNA loading by the DNA repair helicase XPD.
Q38332393Multiple full-length NS3 molecules are required for optimal unwinding of oligonucleotide DNA in vitro
Q34770065Non-hexameric DNA helicases and translocases: mechanisms and regulation
Q43037770Nucleic acid unwinding by hepatitis C virus and bacteriophage t7 helicases is sensitive to base pair stability
Q42986507Periodic cycles of RNA unwinding and pausing by hepatitis C virus NS3 helicase
Q57752886Pif1 helicase unfolding of G-quadruplex DNA is highly dependent on sequence and reaction conditions
Q41677133Probing the stochastic property of endoreduplication in cell size determination of Arabidopsis thaliana leaf epidermal tissue.
Q42252139Processive DNA Unwinding by RecBCD Helicase in the Absence of Canonical Motor Translocation
Q41556498Processivity of cellobiohydrolases is limited by the substrate.
Q37533474Pulsed IR heating studies of single-molecule DNA duplex dissociation kinetics and thermodynamics
Q24650931RecBCD enzyme and the repair of double-stranded DNA breaks
Q39769965Recombination hotspots attenuate the coupled ATPase and translocase activities of an AddAB-type helicase-nuclease
Q57752804Regulation of UvrD Helicase Activity by MutL
Q34313069Simultaneous binding to the tracking strand, displaced strand and the duplex of a DNA fork enhances unwinding by Dda helicase
Q36490245Step-by-step progress toward understanding the hepatitis C virus RNA helicase
Q38318511Structural and biological identification of residues on the surface of NS3 helicase required for optimal replication of the hepatitis C virus
Q61451641Synergy between RecBCD subunits is essential for efficient DNA unwinding
Q36160717The Bacteroides sp. 3_1_23 Pif1 protein is a multifunctional helicase.
Q33904389The DNA-unwinding mechanism of the ring helicase of bacteriophage T7.
Q27933808The RNA helicase Mtr4p modulates polyadenylation in the TRAMP complex
Q42777752The RNA-mediated, asymmetric ring regulatory mechanism of the transcription termination Rho helicase decrypted by time-resolved nucleotide analog interference probing (trNAIP).
Q45651468The functional interaction of the hepatitis C virus helicase molecules is responsible for unwinding processivity
Q36619949Tight intramolecular regulation of the human Upf1 helicase by its N- and C-terminal domains
Q36783587Translocation of Saccharomyces cerevisiae Pif1 helicase monomers on single-stranded DNA.
Q42017301Unmasking the active helicase conformation of nonstructural protein 3 from hepatitis C virus
Q27932247Yeast Pif1 helicase exhibits a one-base-pair stepping mechanism for unwinding duplex DNA

Search more.