Dataset Information

An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass.

ABSTRACT: Proteins are highly dynamic entities attaining a myriad of different conformations. Protein side chains change their states during dynamics, causing clashes that are propagated at distal sites. A convenient formalism to analyze protein dynamics is based on network theory using Protein Structure Networks (PSNs). Despite their broad applicability, few efforts have been devoted to benchmarking PSN methods and to provide the community with best practices. In many applications, it is convenient to use the centers of mass of the side chains as nodes. It becomes thus critical to evaluate the minimal distance cutoff between the centers of mass which will provide stable network properties. Moreover, when the PSN is derived from a structural ensemble collected by molecular dynamics (MD), the impact of the MD force field has to be evaluated. We selected a dataset of proteins with different fold and size and assessed the two fundamental properties of the PSN, i.e. hubs and connected components. We identified an optimal cutoff of 5?Å that is robust to changes in the force field and the proteins. Our study builds solid foundations for the harmonization and standardization of the PSN approach.

SUBMITTER: Salamanca Viloria J

PROVIDER: S-EPMC5460117 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass.

Salamanca Viloria Juan J Allega Maria Francesca MF Lambrughi Matteo M Papaleo Elena E

Scientific reports 20170606 1

Proteins are highly dynamic entities attaining a myriad of different conformations. Protein side chains change their states during dynamics, causing clashes that are propagated at distal sites. A convenient formalism to analyze protein dynamics is based on network theory using Protein Structure Networks (PSNs). Despite their broad applicability, few efforts have been devoted to benchmarking PSN methods and to provide the community with best practices. In many applications, it is convenient to us ...[more]

PMID: 28588190

Similar Datasets

Project description:Robots have proven very useful in automating industrial processes. Their rigid components and powerful actuators, however, render them unsafe or unfit to work in normal human environments such as schools or hospitals. Robots made of compliant, softer materials may offer a valid alternative. Yet, the dynamics of these compliant robots are much more complicated compared to normal rigid robots of which all components can be accurately controlled. It is often claimed that, by using the concept of morphological computation, the dynamical complexity can become a strength. On the one hand, the use of flexible materials can lead to higher power efficiency and more fluent and robust motions. On the other hand, using embodiment in a closed-loop controller, part of the control task itself can be outsourced to the body dynamics. This can significantly simplify the additional resources required for locomotion control. To this goal, a first step consists in an exploration of the trade-offs between morphology, efficiency of locomotion, and the ability of a mechanical body to serve as a computational resource. In this work, we use a detailed dynamical model of a Mass-Spring-Damper (MSD) network to study these trade-offs. We first investigate the influence of the network size and compliance on locomotion quality and energy efficiency by optimizing an external open-loop controller using evolutionary algorithms. We find that larger networks can lead to more stable gaits and that the system's optimal compliance to maximize the traveled distance is directly linked to the desired frequency of locomotion. In the last set of experiments, the suitability of MSD bodies for being used in a closed loop is also investigated. Since maximally efficient actuator signals are clearly related to the natural body dynamics, in a sense, the body is tailored for the task of contributing to its own control. Using the same simulation platform, we therefore study how the network states can be successfully used to create a feedback signal and how its accuracy is linked to the body size.

Dataset Information

An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass.

Publications

An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets