The YTH domain of YTHDC1 belongs to a class of protein "readers", recognizing the N6-methyladenosine (m?A) chemical modification in mRNA. Static ensemble-averaged structures revealed details of N6-methyl recognition via a conserved aromatic cage. Here, we performed molecular dynamics (MD) simulations along with nuclear magnetic resonance (NMR) and isothermal titration calorimetry (ITC) to examine how dynamics and solvent interactions contribute to the m?A recognition and negative selectivity...
[NMR paper] Transient helicity in intrinsically disordered Axin-1 studied by NMR spectroscopy and molecular dynamics simulations.
Transient helicity in intrinsically disordered Axin-1 studied by NMR spectroscopy and molecular dynamics simulations.
Related Articles Transient helicity in intrinsically disordered Axin-1 studied by NMR spectroscopy and molecular dynamics simulations.
PLoS One. 2017;12(3):e0174337
Authors: Bomblies R, Luitz MP, Scanu S, Madl T, Zacharias M
Abstract
Many natural proteins are, as a whole or in part, intrinsically disordered. Frequently, such intrinsically disordered regions (IDRs) undergo a transition to a defined and often...
nmrlearner
Journal club
0
03-30-2017 06:42 PM
[NMR paper] Protein-Carbohydrate Interactions Studied by NMR. from Molecular Recognition to Drug Design.
Protein-Carbohydrate Interactions Studied by NMR. from Molecular Recognition to Drug Design.
Related Articles Protein-Carbohydrate Interactions Studied by NMR. from Molecular Recognition to Drug Design.
Curr Protein Pept Sci. 2012 Dec 10;
Authors: Fernandez-Alonso MD, Diaz D, Berbis MA, Marcelo F, Jimenez-Barbero J
Abstract
Diseases that result from infection are, in general, a consequence of specific interactions between a pathogenic organism and the cells. The study of host-pathogen interactions has provided insights for the design of...
nmrlearner
Journal club
0
02-03-2013 10:22 AM
Structure of the lipodepsipeptide syringomycin E in phospholipids and sodium dodecylsulphate micelle studied by circular dichroism, NMR spectroscopy and molecular dynamics.
Structure of the lipodepsipeptide syringomycin E in phospholipids and sodium dodecylsulphate micelle studied by circular dichroism, NMR spectroscopy and molecular dynamics.
Structure of the lipodepsipeptide syringomycin E in phospholipids and sodium dodecylsulphate micelle studied by circular dichroism, NMR spectroscopy and molecular dynamics.
Biochim Biophys Acta. 2011 Sep;1808(9):2102-10
Authors: Anselmi M, Eliseo T, Zanetti-Polzi L, Fullone MR, Fogliano V, Di Nola A, Paci M, Grgurina I
Abstract
Syringomycin E (SRE) is a member of a...
nmrlearner
Journal club
0
09-13-2011 08:27 PM
[NMR paper] The hydration of amides in helices; a comprehensive picture from molecular dynamics,
The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR.
Related Articles The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR.
Protein Sci. 2003 Mar;12(3):520-31
Authors: Walsh ST, Cheng RP, Wright WW, Alonso DO, Daggett V, Vanderkooi JM, DeGrado WF
We examined the hydration of amides of alpha(3)D, a simple, designed three-helix bundle protein. Molecular dynamics calculations show that the amide carbonyls on the surface of the protein tilt away from the...
nmrlearner
Journal club
0
11-24-2010 09:01 PM
[NMR paper] NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex.
NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex.
Related Articles NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex.
J Mol Biol. 2000 Oct 6;302(5):1101-17
Authors: Tsui V, Radhakrishnan I, Wright PE, Case DA
The hydration of a high-affinity protein-DNA complex involving the three amino terminal zinc finger domains of transcription factor IIIA (TFIIIA) and a 15-base-pair DNA duplex was investigated by NMR spectroscopy and molecular dynamics (MD) simulations. Intermolecular nuclear...
nmrlearner
Journal club
0
11-19-2010 08:29 PM
[NMR paper] Backbone dynamics of the A-domain of HMG1 as studied by 15N NMR spectroscopy.
Backbone dynamics of the A-domain of HMG1 as studied by 15N NMR spectroscopy.
Related Articles Backbone dynamics of the A-domain of HMG1 as studied by 15N NMR spectroscopy.
Biochemistry. 1995 Dec 26;34(51):16608-17
Authors: Broadhurst RW, Hardman CH, Thomas JO, Laue ED
The HMG-box sequence motif (approximately 80 residues) occurs in a number of abundant eukaryotic chromosomal proteins such as HMG1, which binds DNA without sequence specificity, but with "structure specificity", as well as in several sequence-specific transcription factors. HMG1...
nmrlearner
Journal club
0
08-22-2010 03:50 AM
[NMR paper] Hydration-coupled dynamics in proteins studied by neutron scattering and NMR: the cas
Hydration-coupled dynamics in proteins studied by neutron scattering and NMR: the case of the typical EF-hand calcium-binding parvalbumin.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-cellhub.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Hydration-coupled dynamics in proteins studied by neutron scattering and NMR: the case of the typical EF-hand calcium-binding parvalbumin.
Biophys J. 1999 May;76(5):2390-411
Authors: ...
nmrlearner
Journal club
0
08-21-2010 04:03 PM
The Role of Basic Amino Acids in the Molecular Recognition of Hydroxyapatite by Stath
The Role of Basic Amino Acids in the Molecular Recognition of Hydroxyapatite by Statherin using Solid State NMR.
Related Articles The Role of Basic Amino Acids in the Molecular Recognition of Hydroxyapatite by Statherin using Solid State NMR.
Surf Sci. 2010 Aug 15;604(15-16):L39-L42
Authors: Ndao M, Ash JT, Stayton PS, Drobny GP
Organisms use proteins such as statherin to control the growth of hydroxyapatite (HAP), which is the principal component of teeth and bone. Though much emphasis has been placed on the acidic character of these...
Recognition of N6-Methyladenosine by the YTHDC1 YTH Domain Studied by Molecular Dynamics and NMR Spectroscopy: The Role of Hydration
Linear Mode
