MD Simulations of Papillomavirus DNA-E2 Protein Complexes Hints at a Protein Structural Code for DNA Deformation
TLDR
Results show that the protein indirect DNA readout is not only addressable to the DNA molecule flexibility but it is finely tuned by the mechanical and dynamical properties of the protein scaffold involved in the interaction.About:
This article is published in Biophysical Journal.The article was published on 2008-08-01 and is currently open access. It has received 13 citations till now. The article focuses on the topics: DNA-binding domain & Molecular models of DNA.read more
Citations
More filters
Journal ArticleDOI
Disordered interactome of human papillomavirus.
TL;DR: This review analyzes the plentitude and demeanor of intrinsic disorder in proteins from HPVs and their cellular targets to support the economic usage of the viral genetic material.
Journal ArticleDOI
Deciphering the structural properties that confer stability to a DNA nanocage
Mattia Falconi,Francesco Oteri,Giovanni Chillemi,Felicie F. Andersen,David Tordrup,Cristiano L. P. Oliveira,Jan Skov Pedersen,Birgitta R. Knudsen,Alessandro Desideri +8 more
TL;DR: Global properties, principal component analysis, and DNA geometrical parameters, calculated along the entire trajectory, indicate that the cage is stable and that the B-DNA conformation, also if slightly distorted, is maintained for all the simulation time.
Journal ArticleDOI
Mechanism of DNA recognition by the restriction enzyme EcoRV.
TL;DR: A three-step recognition mechanism is suggested for EcoRV, where the protein and DNA interact more closely, allowing cleavage, and the cognate TA sequence, which is easier to bend, allowing specific, high-occupancy hydrogen bonds to form in the complex.
Journal ArticleDOI
Protein flexibility directs DNA recognition by the papillomavirus E2 proteins
Craig Brown,Karen Campos-León,Madeleine Strickland,Christopher Williams,Victoria Fairweather,R. Leo Brady,Matthew P. Crump,Kevin Gaston +7 more
TL;DR: It is shown that protein dynamics are important in DNA recognition using the well-characterized human papillomavirus type 6 E2 protein as a model system and mutation results in increased flexibility within the hydrophobic core and loop regions that orient the DNA binding helices.
Journal ArticleDOI
Indirect DNA Readout on the Protein Side: Coupling between Histidine Protonation, Global Structural Cooperativity, Dynamics, and DNA Binding of the Human Papillomavirus Type 16 E2C Domain
Tommaso Eliseo,Ignacio E. Sánchez,Alejandro D. Nadra,Alejandro D. Nadra,Mariano Dellarole,Maurizio Paci,Daniel O. Cicero +6 more
TL;DR: The patterns of residue substitution in genital papillomavirus type 16 E2C beta-barrel support the importance of the protonation states of His288 and His318 and suggest that protein-dependent indirect readout and histidine pH titration may regulate DNA binding in the cell.
References
More filters
Journal ArticleDOI
UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F. Pettersen,Thomas D. Goddard,Conrad C. Huang,Gregory S. Couch,Daniel M. Greenblatt,Elaine C. Meng,Thomas E. Ferrin +6 more
TL;DR: Two unusual extensions are presented: Multiscale, which adds the ability to visualize large‐scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales.
Journal ArticleDOI
Comparison of simple potential functions for simulating liquid water
TL;DR: In this article, the authors compared the Bernal Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P potential functions for liquid water in the NPT ensemble at 25°C and 1 atm.
Journal ArticleDOI
Molecular dynamics with coupling to an external bath.
TL;DR: In this paper, a method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling, which can be easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints.
Journal ArticleDOI
Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems
TL;DR: An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms.