Designed Elastic Networks: Models of Complex Protein Machinery.

Int J Mol Sci

Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.

Published: October 2018

Recently, the design of mechanical networks with protein-inspired responses has become increasingly popular. Here, we review contributions which were motivated by studies of protein dynamics employing coarse-grained elastic network models. First, the concept of evolutionary optimization that we developed to design network structures which execute prescribed tasks is explained. We then review what presumably marks the origin of the idea to design complex functional networks which encode protein-inspired behavior, namely the design of an elastic network structure which emulates the cycles of ATP-powered conformational motion in protein machines. Two recent applications are reviewed. First, the construction of a model molecular motor, whose operation incorporates both the tight coupling power stroke as well as the loose coupling Brownian ratchet mechanism, is discussed. Second, the evolutionary design of network structures which encode optimal long-range communication between remote sites and represent mechanical models of allosteric proteins is presented. We discuss the prospects of designed protein-mimicking elastic networks as model systems to elucidate the design principles and functional signatures underlying the operation of complex protein machinery.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6214024PMC
http://dx.doi.org/10.3390/ijms19103152DOI Listing

Publication Analysis

Top Keywords

elastic networks
8
complex protein
8
protein machinery
8
elastic network
8
design network
8
network structures
8
design
6
designed elastic
4
networks
4
networks models
4

Similar Publications

Response of Differently Structured Dental Polymer-Based Composites to Increasingly Aggressive Aging Conditions.

Nanomaterials (Basel)

January 2025

Department of Conservative Dentistry, University Hospital, Ludwig-Maximilians-University, Goethestr. 70, D-80336 Munich, Germany.

Objective: It is hypothesized that the way nano- and micro-hybrid polymer-based composites are structured and cured impacts the way they respond to aging.

Material And Methods: A polymer-ceramic interpenetrating network composite (Vita Enamic/VE), an industrially polymerized (Brillinat CriosST/BC), and an in situ light-cured composite with discrete inorganic fillers (Admira Fusion5/AF5) were selected. Specimens (308) were either cut from CAD/CAM blocks (VE/BC) or condensed and cured in white polyoxymethylene molds (AF5) and subjected to four different aging conditions ( = 22): (a) 24 h storage in distilled water at 37 °C; (b) 24 h storage in distilled water at 37 °C followed by thermal cycling for 10,000 cycles 5/55 °C (TC); (c) TC followed by storage in a 75% ethanol-water solution; and (d) TC followed by a 3-week demineralization/remineralization cycling.

View Article and Find Full Text PDF

ModeHunter is a modular Python software package for the simulation of 3D biophysical motion across spatial resolution scales using modal analysis of elastic networks. It has been curated from our in-house Python scripts over the last 15 years, with a focus on detecting similarities of elastic motion between atomic structures, coarse-grained graphs, and volumetric data obtained from biophysical or biomedical imaging origins, such as electron microscopy or tomography. With ModeHunter, normal modes of biophysical motion can be analyzed with various static visualization techniques or brought to life by dynamics animation in terms of single or multimode trajectories or decoy ensembles.

View Article and Find Full Text PDF

Scaling up integrated care for chronic diseases in belgium: A process evaluation.

Health Policy

December 2024

Department of Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Belgium; Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium.

Introduction: Few integrated care studies elaborate how interventions are brought to wider scale. The SCUBY project developed interventions for scale-up of an Integrated Care Package (ICP) for two common diseases - type 2 diabetes and hypertension-, comprising evidence-based roadmaps and policy dialogues. This paper's aim is to report on the process evaluation of the ICP scale-up in Belgium.

View Article and Find Full Text PDF

Organic-inorganic hybrid materials are explored for application as solid electrolytes for lithium-ion batteries. The material consists of a porous silica network, of which the pores are infiltrated by poly(ethylene oxide) and lithium perchlorate. The synthesis involves two steps: First, the inorganic backbone is created by the acid-catalyzed sol-gel synthesis of tetraethyl orthosilicate to ensure continuity of the backbone in three dimensions.

View Article and Find Full Text PDF

The pathogenesis of metabolic dysfunction-associated steatotic liver disease-associated hepatocellular carcinoma (MASLD-HCC) is complex and exhibits sex-specific differences. Effective methods for monitoring MASLD progression to HCC are lacking. Transcriptomic data from liver tissue samples sourced from multiple public databases were integrated.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!