Backbone Dynamics of Ribonuclease HI: Correlations with Structure and Function in an Active Enzyme

Mandel, Arthur; Akke, Mikael; Palmer, Arthur G.

doi:10.1006/jmbi.1994.0073

Cited by 957 publications

(1,347 citation statements)

References 0 publications

Supporting

Mentioning

1,297

Contrasting

Unclassified

Order By: Relevance

“…The spin-relaxation data were described using five models: (1) S 2 only; (2) S 2 and τ e ; (3) S 2 and R ex ; (4) model 2 plus R ex ; and (5) S 2 f , S 2 , and τ e , the extended two-time scale model (Cole and Loria, 2003;Lipari and Szabo, 1982b). Herein, S 2 is the generalized order parameter, τ e is the internal correlation time, S 2 f , is the fast motion order parameter with a typical correlation time of <10 ps; and R ex is the additional line broadening owing to assumed two-site conformational exchange, which depends on the equilibrium site population, the rate of exchange between conformers, and chemical shift differences (Mandel et al, 1995). Motion parameters were fitted to the spin-relaxation data using the program FASTModel-free with Model-Free 4.2 (Cole and Loria, 2003;Palmer et al, 1991).…”

Section: Model-free Analysismentioning

confidence: 99%

“…Motion parameters were fitted to the spin-relaxation data using the program FASTModel-free with Model-Free 4.2 (Cole and Loria, 2003;Palmer et al, 1991). Model selection was based on the statistical testing protocol described previously by Mandel group (Mandel et al, 1995). The rotational diffusion tensor was estimated from R 2 /R 1 ratios and the program 'R2R1_diffusion' using the solution coordinates, and the program 'pdbinertia' (Fairbrother et al, 1998;Mandel et al, 1995;Palmer et al, 1991).…”

Section: Model-free Analysismentioning

confidence: 99%

“…Model selection was based on the statistical testing protocol described previously by Mandel group (Mandel et al, 1995). The rotational diffusion tensor was estimated from R 2 /R 1 ratios and the program 'R2R1_diffusion' using the solution coordinates, and the program 'pdbinertia' (Fairbrother et al, 1998;Mandel et al, 1995;Palmer et al, 1991). The criteria for the inclusion of residues in the diffusion tensor estimate relied on the method of Tjandra et al (1995).…”

Section: Model-free Analysismentioning

confidence: 99%

“…NMR-derived dynamics parameters of HP-RR r Model free analysis was performed as described to obtain global and site-specific dynamics information (Cole and Loria, 2003;Mandel et al, 1995). Using an axially symmetric diffusion tensor, the rotational correlation time, τ m, of HP-RR r was found to be 12.67 ± 0.28 ns and the determined D par /D per ratio was 1.30.…”

Section: Solution Nmr Experiments Of Hp-rr Rmentioning

confidence: 99%

See 3 more Smart Citations

Backbone Dynamics of an Atypical Orphan Response Regulator Protein, Helicobacter pylori 1043

Jeong

Lee

et al. 2013

Molecules and Cells

View full text Add to dashboard Cite

An atypical orphan response regulator protein, HP1043 (HP-RR) in Helicobacter pylori, is proven to be essential for cell growth and does not require the well known phosphorelay scheme. HP-RR was identified as a symmetric dimer with two functional domains, an N-terminal regulatory domain (HP-RR r ) and a C-terminal effector domain (HP-RR e ). HP-RR is a new class of response regulator, as a phosphorylation-independent regulator. Previously, we have presented a detailed three-dimensional structure of HP-RR using NMR spectroscopy and X-ray crystallography. In this study, in order to understand the functional importance of flexibilities in HP-RR r and HP-RR e , T 1 , T 2 , heteronuclear NOE experiments have been performed and backbone dynamics of HP-RR r and HP-RR e were investigated. HP-RR r is a symmetric dimer and the interface region, α4-β5-α5 of dimer, showed high rigidity (high S 2 values). Site of rearrangements associated with phosphorylation of HP-RR r (Ser 75 : R ex = 3.382, Ile 95 : R ex = 5.228) showed slow chemical exchanges. HP-RR e is composed of three α-helices flanked on two sides by anti-parallel β-sheets. Low order parameters as well as conformational exchanges in the centers of loop regions known as the DNA binding site and transcription site of HP-RR e suggested that flexibility of HP-RR e is essential for interaction with DNA. In conclusion, backbone dynamics information for HP-RR implies that structural flexibilities in HP-RR r are necessary for the phosphorylation site and the dynamic nature of HP-RR e is essential for the regulation of interaction between protein and DNA.

show abstract

Section: Model-free Analysismentioning

confidence: 99%

Section: Model-free Analysismentioning

confidence: 99%

Section: Model-free Analysismentioning

confidence: 99%

Section: Solution Nmr Experiments Of Hp-rr Rmentioning

confidence: 99%

See 2 more Smart Citations

Backbone Dynamics of an Atypical Orphan Response Regulator Protein, Helicobacter pylori 1043

Jeong

Lee

et al. 2013

Molecules and Cells

View full text Add to dashboard Cite

show abstract

“…Relaxation data were analysed using in-house software; this incorporates the model-free formalism of Lipari and Szabo, [8] using spectral density functions appropriate for axially symmetric rotational diffusion [18] and non-colinearity of the NÀH bond vector and the principal component of the 15 N chemical shift tensor, [19a] with model selection and Monte Carlo error estimation as described by Mandel et al [20] The relaxation data were fitted using six models: S 2 only (model 1), S 2 and R ex (model 2), S 2 and t e (model 3), S 2 , R ex , and t e (model 4), the extended model of Clore et al [21] with S 2 f , S 2 s and t s (model 5), and the extended model with S 2 f , S 2 s , t s and R ex (model 6). S 2 is the generalized order parameter, R ex is the chemical exchange contribution to T 2 , and t e is the effective correlation time for internal motion on a fast timescale.…”

mentioning

confidence: 99%

The Dynamics of Lysozyme from Bacteriophage Lambda in Solution Probed by NMR and MD Simulations

et al. 2013

View full text Add to dashboard Cite

Abstract15N NMR relaxation studies, analyses of NMR data to include chemical shifts, residual dipolar couplings (RDC), NOEs and HN–Hα coupling constants, and molecular dynamics (MD) simulations have been used to characterise the behaviour of lysozyme from bacteriophage lambda (λ lysozyme) in solution. The lower and upper lip regions in λ lysozyme (residues 51–60 and 128–141, respectively) show reduced 1H–15N order parameters indicating mobility on a picosecond timescale. In addition, residues in the lower and upper lips also show exchange contributions to T2 indicative of slower timescale motions. The chemical shift, RDC, coupling constant and NOE data for λ lysozyme indicate that two fluctuating β‐strands (β3 and β4) are populated in the lower lip region while the N terminus of helix α6 (residues 136–139) forms dynamic helical turns in the upper lip region. This behaviour is confirmed by MD simulations that show hydrogen bonds, indicative of the β‐sheet and helical secondary structure in the lip regions, with populations of 40–60 %. Thus in solution λ lysozyme adopts a conformational ensemble that will contain both the open and closed forms observed in the crystal structures of the protein.

show abstract

A 500-ps molecular dynamics simulation trajectory of cardiotoxin II from Taiwan cobra venom in solution: Correlation with NMR and X-ray crystallography data

et al. 1999

View full text Add to dashboard Cite

Backbone Dynamics of Ribonuclease HI: Correlations with Structure and Function in an Active Enzyme

Cited by 957 publications

References 0 publications

Backbone Dynamics of an Atypical Orphan Response Regulator Protein, Helicobacter pylori 1043

Backbone Dynamics of an Atypical Orphan Response Regulator Protein, Helicobacter pylori 1043

The Dynamics of Lysozyme from Bacteriophage Lambda in Solution Probed by NMR and MD Simulations

A 500-ps molecular dynamics simulation trajectory of cardiotoxin II from Taiwan cobra venom in solution: Correlation with NMR and X-ray crystallography data

Contact Info

Product

Resources

About