Dataset Information

Modeling Conformationally Flexible Proteins With X-ray Scattering and Molecular Simulations.

ABSTRACT: Proteins and protein complexes with high conformational flexibility participate in a wide range of biological processes. These processes include genome maintenance, gene expression, signal transduction, cell cycle regulation, and many others. Gaining a structural understanding of conformationally flexible proteins and protein complexes is arguably the greatest problem facing structural biologists today. Over the last decade, some progress has been made toward understanding the conformational flexibility of such systems using hybrid approaches. One particularly fruitful strategy has been the combination of small-angle X-ray scattering (SAXS) and molecular simulations. In this article, we provide a brief overview of SAXS and molecular simulations and then discuss two general approaches for combining SAXS data and molecular simulations: minimal ensemble approaches and full ensemble approaches. In minimal ensemble approaches, one selects a minimal ensemble of structures from the simulations that best fit the SAXS data. In full ensemble approaches, one validates a full ensemble of structures from the simulations using SAXS data. We argue that full ensemble models are more realistic than minimal ensemble searches models and that full ensemble approaches should be used wherever possible.

SUBMITTER: Powers KT

PROVIDER: S-EPMC6495069 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Modeling Conformationally Flexible Proteins With X-ray Scattering and Molecular Simulations.

Powers Kyle T KT Gildenberg Melissa S MS Washington M Todd MT

Computational and structural biotechnology journal 20190422

Proteins and protein complexes with high conformational flexibility participate in a wide range of biological processes. These processes include genome maintenance, gene expression, signal transduction, cell cycle regulation, and many others. Gaining a structural understanding of conformationally flexible proteins and protein complexes is arguably the greatest problem facing structural biologists today. Over the last decade, some progress has been made toward understanding the conformational fle ...[more]

PMID: 31073392

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Project description:Structurally engineered molecules which can behave as stimuli-controlled mechanical nanomachines such as molecular shuttles, rotors, ratchets, and springs are important in several research areas, including molecular robotics, actuation, sensing, cargo transportation, etc. Helicenes, by virtue of their unique screw-type structures, were proposed as functional models for molecular springs; however, experimental realization has remained an elusive and unmet task until now, because of the lack of appropriate helicene molecules consisting of backbone-decorated dynamic architectures. Aiming to explore this unearthed direction, we present herein a novel class of modular flexible heterohelicenes with a stimuli (acid/base and light)-responsive core and peripheral modules. By applying pH (at core-embedded free imidazole sites) and light (at backbone-tethered dithienylethene units) stimuli, we demonstrate that these flexible heterohelicenes exhibit spring-like movement, with the reversible contraction/extension of the helical pitch. The uniquely functionalized structure of these molecules played a critical role in bestowing such capability, as revealed by crystallographic, spectroscopic and computational data. Careful assessment disclosed that the protonation/deprotonation-induced reversible generation and delocalization of positive charge throughout the π-conjugated helical rim switch the operative interactions between the π clouds of the terminal overlapping arene rings of the helicenes between repulsive and attractive, leading to extension/contraction of the helical pitch. On the other hand, in the case of the light stimulus, it was analyzed that the light-induced ring-closure of the photoactive dithienylethene units created a geometric distortion causing the helicenic wings to bend outward from the helicene rim, which resulted in extension of the helical pitch. The photo-assisted (or thermal) reverse ring-opening reaction converted the system to its original conformation, thus enabling the helicene molecule to display spring-like reversible extension/contraction motion. The new insights on the reversible dynamic features of this class of heterohelicenes under the influence of external stress would guide crucial design principles of helicene-based molecular springs for potential applications.

Dataset Information

Modeling Conformationally Flexible Proteins With X-ray Scattering and Molecular Simulations.

Publications

Modeling Conformationally Flexible Proteins With X-ray Scattering and Molecular Simulations.

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