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Protein Dynamics and Contact Topology Reveal Protein–DNA ...

Protein Dynamics and Contact Topology Reveal Protein–DNA ...

Protein Dynamics and Contact Topology Reveal Protein–DNA ...

However, protein dynamics-based attributes could not be found for DNA-binding residues. Interestingly, DNA orientation can be identified by an ' ...

Protein Dynamics and Contact Topology Reveal Protein-DNA ...

Protein Dynamics and Contact Topology Reveal Protein-DNA Binding Orientation. J Chem Theory Comput. 2016 Nov 8;12(11):5269-5277. doi: 10.1021/acs.jctc.

Protein Dynamics and Contact Topology Reveal Protein–DNA ...

We show that protein–DNA docking orientation is a function of protein intrinsic dynamics, but the binding site itself does not display unique patterns.

Protein Dynamics and Contact Topology Reveal Protein-DNA ...

Request PDF | Protein Dynamics and Contact Topology Reveal Protein-DNA Binding Orientation | Structure-encoded conformational dynamics are crucial for ...

Protein Dynamics and Contact Topology Reveal Protein–DNA ...

Here, we show that protein-DNA docking orientation is a function of protein intrinsic dynamics, but the binding site itself does not display unique patterns in ...

Protein dynamics and contact topology reveal protein-DNA binding ...

Protein dynamics and contact topology reveal protein-DNA binding orientation. Authors: Aravind Chandrasekaran · Justin Chan · Carmay Lim · Lee-Wei Yang. Issue ...

Protein Dynamics and Contact Topology Reveal ... - ACS Figshare

Save and organize your research references with the Papers cloud library. Access your library anytime, anywhere with the Papers web, desktop, or mobile apps ...

Protein Dynamics and Contact Topology Reveal Protein–DNA ...

Protein Dynamics and Contact Topology Reveal Protein–DNA Binding Orientation. J. Chem. Theory Comput. Pub Date : 2016-10-21. DOI : 10.1021/acs.jctc.6b00688.

Protein/DNA interactions in complex DNA topologies - NCBI

... dynamics of a closed DNA topology is important. Cryo-electron microscopy ... Interplay of protein and DNA structure revealed in simulations of the lac operon.

Protein Sliding along DNA: Dynamics and Structural Characterization

The presented model that captures various experimental features of facilitated diffusion has the potency to address other questions regarding the nature of DNA ...

Exploring the effect of network topology, mRNA and protein ... - Nature

We explore factors affecting stability by coupling the dynamics of mRNAs and proteins in a growing cell. We find that mRNA degradation rate does not affect ...

Probing Conformational Dynamics by Protein Contact Networks

Protein structure networks and their topological analysis are good tools for the analysis of protein folding [17,18], dynamics [19,20], and identification ...

Long-range correlation in protein dynamics - PLOS

... contact topology defines the slow-mode dynamics of the native proteins. ... proteins show both dense packing and fractal topology. Lastly ...

Protein-Folding Analysis Using Features Obtained by Persistent ...

In this study, we applied persistent homology, an emerging method to analyze topological features in a data set, to reveal protein-folding dynamics.

DNA topology confers sequence specificity to nonspecific ... - PNAS

... protein in wild-type loops attached to the Lac repressor. The computations show how a protein with no discernible DNA sequence-recognizing ...

The protein folding rate and the geometry and topology of the native ...

Proteins fold in 3-dimensional conformations which are important for their function. Characterizing the global conformation of proteins ...

Determining the topology of stable protein–DNA complexes

Difference topology is an experimental technique that can be used to unveil the topological structure adopted by two or more DNA segments in ...

Long-range correlation in protein dynamics - Semantic Scholar

In this paper, we elucidate the structural origin of the long-range correlation and describe how native contact topology defines the slow-mode ...

The Topology and Dynamics of Protein Complexes: Insights from Intra

Proteins rarely act alone but interact with other proteins, DNA, RNA and small molecules to perform their biological processes in living organisms [131] . Among ...

Biological insights from topology independent comparison of protein ...

The sequence alignment between the two proteins as inferred from the structural alignment is show below. The superimposed residues that are in contact with the ...