The Experts below are selected from a list of 15021 Experts worldwide ranked by ideXlab platform
Benjamin Schuler - One of the best experts on this subject based on the ideXlab platform.
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perspective chain dynamics of unfolded and intrinsically disordered proteins from nanosecond fluorescence correlation spectroscopy combined with single molecule fret
Journal of Chemical Physics, 2018Co-Authors: Benjamin SchulerAbstract:The dynamics of unfolded proteins are important both for the process of protein folding and for the behavior of intrinsically disordered proteins. However, methods for investigating the global chain dynamics of these structurally diverse systems have been limited. A versatile experimental approach is single-molecule spectroscopy in combination with Forster resonance energy transfer and nanosecond fluorescence correlation spectroscopy. The concepts of Polymer Physics offer a powerful framework both for interpreting the results and for understanding and classifying the properties of unfolded and intrinsically disordered proteins. This information on long-range chain dynamics can be complemented with spectroscopic techniques that probe different length scales and time scales, and integration of these results greatly benefits from recent advances in molecular simulations. This increasing convergence between the experiment, theory, and simulation is thus starting to enable an increasingly detailed view of the dynamics of disordered proteins.The dynamics of unfolded proteins are important both for the process of protein folding and for the behavior of intrinsically disordered proteins. However, methods for investigating the global chain dynamics of these structurally diverse systems have been limited. A versatile experimental approach is single-molecule spectroscopy in combination with Forster resonance energy transfer and nanosecond fluorescence correlation spectroscopy. The concepts of Polymer Physics offer a powerful framework both for interpreting the results and for understanding and classifying the properties of unfolded and intrinsically disordered proteins. This information on long-range chain dynamics can be complemented with spectroscopic techniques that probe different length scales and time scales, and integration of these results greatly benefits from recent advances in molecular simulations. This increasing convergence between the experiment, theory, and simulation is thus starting to enable an increasingly detailed view of the ...
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single molecule fret spectroscopy and the Polymer Physics of unfolded and intrinsically disordered proteins
Annual Review of Biophysics, 2016Co-Authors: Benjamin Schuler, Andrea Soranno, Hagen Hofmann, Daniel NettelsAbstract:The properties of unfolded proteins have long been of interest because of their importance to the protein folding process. Recently, the surprising prevalence of unstructured regions or entirely disordered proteins under physiological conditions has led to the realization that such intrinsically disordered proteins can be functional even in the absence of a folded structure. However, owing to their broad conformational distributions, many of the properties of unstructured proteins are difficult to describe with the established concepts of structural biology. We have thus seen a reemergence of Polymer Physics as a versatile framework for understanding their structure and dynamics. An important driving force for these developments has been single-molecule spectroscopy, as it allows structural heterogeneity, intramolecular distance distributions, and dynamics to be quantified over a wide range of timescales and solution conditions. Polymer concepts provide an important basis for relating the physical properties of unstructured proteins to folding and function.
Rohit V Pappu - One of the best experts on this subject based on the ideXlab platform.
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Polymer Physics of intracellular phase transitions
Nature Physics, 2015Co-Authors: Clifford P Brangwynne, Peter Tompa, Rohit V PappuAbstract:Intracellular organelles are either membrane-bound vesicles or membrane-less compartments that are made up of proteins and RNA. These organelles play key biological roles, by compartmentalizing the cell to enable spatiotemporal control of biological reactions. Recent studies suggest that membrane-less intracellular compartments are multicomponent viscous liquid droplets that form via phase separation. Proteins that have an intrinsic tendency for being conformationally heterogeneous seem to be the main drivers of liquid–liquid phase separation in the cell. These findings highlight the relevance of classical concepts from the Physics of Polymeric phase transitions for understanding the assembly of intracellular membrane-less compartments. However, applying these concepts is challenging, given the heteroPolymeric nature of protein sequences, the complex intracellular environment, and non-equilibrium features intrinsic to cells. This provides new opportunities for adapting established theories and for the emergence of new Physics. The internal structure of cells is organized into compartments, many of which lack a confining membrane and instead resemble viscous liquid droplets. Evidence is mounting that these compartments form via spontaneous phase transitions. The internal structure of cells is organized into compartments, many of which lack a confining membrane and instead resemble viscous liquid droplets. Evidence is mounting that these compartments form via spontaneous phase transitions.
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relating sequence encoded information to form and function of intrinsically disordered proteins
Current Opinion in Structural Biology, 2015Co-Authors: Kiersten M Ruff, Rohit V PappuAbstract:Intrinsically disordered proteins (IDPs) showcase the importance of conformational plasticity and heterogeneity in protein function. We summarize recent advances that connect information encoded in IDP sequences to their conformational properties and functions. We focus on insights obtained through a combination of atomistic simulations and biophysical measurements that are synthesized into a coherent framework using Polymer Physics theories.
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A Polymer Physics perspective on driving forces and mechanisms for protein aggregation.
Archives of Biochemistry and Biophysics, 2008Co-Authors: Rohit V Pappu, Xiaoling Wang, Andreas Vitalis, Scott L. CrickAbstract:Protein aggregation is a commonly occurring problem in biology. Cells have evolved stress-response mechanisms to cope with problems posed by protein aggregation. Yet, these quality control mechanisms are overwhelmed by chronic aggregation-related stress and the resultant consequences of aggregation become toxic to cells. As a result, a variety of systemic and neurodegenerative diseases are associated with various aspects of protein aggregation and rational approaches to either inhibit aggregation or manipulate the pathways to aggregation might lead to an alleviation of disease phenotypes. To develop such approaches, one needs a rigorous and quantitative understanding of protein aggregation. Much work has been done in this area. However, several unanswered questions linger, and these pertain primarily to the actual mechanism of aggregation as well as to the types of intermolecular associations and intramolecular fluctuations realized at low protein concentrations. It has been suggested that the concepts underlying protein aggregation are similar to those used to describe the aggregation of synthetic Polymers. Following this suggestion, the relevant concepts of Polymer aggregation are introduced. The focus is on explaining the driving forces for Polymer aggregation and how these driving forces vary with chain length and solution conditions. It is widely accepted that protein aggregation is a nucleation-dependent process. This view is based mainly on the presence of long times for the accumulation of aggregates and the elimination of these lag times with “seeds”. In this sense, protein aggregation is viewed as being analogous to the aggregation of colloidal particles. The theories for Polymer aggregation reviewed in this work suggest an alternative mechanism for the origin of long lag times in protein aggregation. The proposed mechanism derives from the recognition that Polymers have unique dynamics that distinguish them from other aggregation-prone systems such as colloidal particles.
Glenn H Fredrickson - One of the best experts on this subject based on the ideXlab platform.
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coherent states field theory in supramolecular Polymer Physics
Journal of Chemical Physics, 2018Co-Authors: Glenn H Fredrickson, Kris T DelaneyAbstract:In 1970, Edwards and Freed presented an elegant representation of interacting branched Polymers that resembles the coherent states (CS) formulation of second-quantized field theory. This CS Polymer field theory has been largely overlooked during the intervening period in favor of more conventional “auxiliary field” (AF) interacting Polymer representations that form the basis of modern self-consistent field theory (SCFT) and field-theoretic simulation approaches. Here we argue that the CS representation provides a simpler and computationally more efficient framework than the AF approach for broad classes of reversibly bonding Polymers encountered in supramolecular Polymer science. The CS formalism is reviewed, initially for a simple homoPolymer solution, and then extended to supramolecular Polymers capable of forming reversible linkages and networks. In the context of the Edwards model of a non-reacting homoPolymer solution and one and two-component models of telechelic reacting Polymers, we discuss the structure of CS mean-field theory, including the equivalence to SCFT, and show how weak-amplitude expansions (random phase approximations) can be readily developed without explicit enumeration of all reaction products in a mixture. We further illustrate how to analyze CS field theories beyond SCFT at the level of Gaussian field fluctuations and provide a perspective on direct numerical simulations using a recently developed complex Langevin technique.In 1970, Edwards and Freed presented an elegant representation of interacting branched Polymers that resembles the coherent states (CS) formulation of second-quantized field theory. This CS Polymer field theory has been largely overlooked during the intervening period in favor of more conventional “auxiliary field” (AF) interacting Polymer representations that form the basis of modern self-consistent field theory (SCFT) and field-theoretic simulation approaches. Here we argue that the CS representation provides a simpler and computationally more efficient framework than the AF approach for broad classes of reversibly bonding Polymers encountered in supramolecular Polymer science. The CS formalism is reviewed, initially for a simple homoPolymer solution, and then extended to supramolecular Polymers capable of forming reversible linkages and networks. In the context of the Edwards model of a non-reacting homoPolymer solution and one and two-component models of telechelic reacting Polymers, we discuss the st...
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thermoreversible associating Polymer networks i interplay of thermodynamics chemical kinetics and Polymer Physics
Journal of Chemical Physics, 2009Co-Authors: Robert S Hoy, Glenn H FredricksonAbstract:Hybrid molecular dynamics/Monte Carlo simulations are used to study melts of unentangled, thermoreversibly associating supramolecular Polymers. In this first of a series of papers, we describe and validate a model that is effective in separating the effects of thermodynamics and chemical kinetics on the dynamics and mechanics of these systems, and is extensible to arbitrarily nonequilibrium situations and nonlinear mechanical properties. We examine the model’s quiescent (and heterogeneous) dynamics, nonequilibrium chemical dynamics, and mechanical properties. Many of our results may be understood in terms of the crossover from diffusion-limited to kinetically limited sticky bond recombination, which both influences and is influenced by Polymer Physics, i.e., the connectivity of the parent chains.
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thermoreversible associating Polymer networks i interplay of thermodynamics chemical kinetics and Polymer Physics
arXiv: Soft Condensed Matter, 2009Co-Authors: Robert S Hoy, Glenn H FredricksonAbstract:Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular Polymers. In this first of a series of papers, we describe and validate a model that is effective in separating the effects of thermodynamics and chemical kinetics on the dynamics and mechanics of these systems, and is extensible to arbitrarily nonequilibrium situations and nonlinear mechanical properties. We examine the model's quiescent (and heterogeneous) dynamics, nonequilibrium chemical dynamics, and mechanical properties. Many of our results may be understood in terms of the crossover from diffusion-limited to kinetically-limited sticky bond recombination, which both influences and is influenced by Polymer Physics, i. e. the connectivity of the parent chains.
Raffaele Mezzenga - One of the best experts on this subject based on the ideXlab platform.
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proteins fibrils from a Polymer Physics perspective
Macromolecules, 2012Co-Authors: Jozef Adamcik, Raffaele MezzengaAbstract:Protein fibrils resulting from assembly of proteins or peptides into long, insoluble, highly ordered fibrillar structures are emerging as one of the fastest growing scientific areas, since interest in these systems spans disciplines as broad and diverse as medicine, biology, soft condensed matter, nanotechnology, and materials science. Since the discovery of the implication of protein amyloid fibrils in neurodegenerative diseases, to their more recent applications in high-performance materials, the understanding of these intriguing macromolecular assemblies has been steadily widening and deepening. Thus, the precise characterization of structural, physical, and mechanical properties of protein fibrils is the first critical step toward our understanding of these systems not only in the context of biology and medicine but also in nanotechnology and advanced biomaterials applications. In this Perspective we wish to discuss how Polymer and colloidal science concepts can be efficiently used to unravel very use...
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single step direct measurement of amyloid fibrils stiffness by peak force quantitative nanomechanical atomic force microscopy
Applied Physics Letters, 2011Co-Authors: Jozef Adamcik, Alexandre Berquand, Raffaele MezzengaAbstract:We present an original application of a new atomic force microscopy mode called peak force tapping for the investigation of the mechanical properties of β-lactoglobulin amyloid fibrils. The values of Young’s modulus obtained by this technique are in perfect agreement with the indirect evaluation of fibrils stiffness obtained by combining Polymer Physics and topological statistical analysis on fibrils’ structural conformations. This technique shows great promise in the estimation of the elastic properties of nanostructured objects relevant in biology, soft matter, and nanotechnology.
Xiaozheng Duan - One of the best experts on this subject based on the ideXlab platform.
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chain conformation of hyperbranched Polymers with uniform branching subchains in dilute solution near the θ point
Macromolecules, 2020Co-Authors: Mo Zhu, Jinxian Yang, Xiaozheng DuanAbstract:Conformation statistics of macromolecules in dilute solution is one of the fundamental issues in Polymer Physics. Herein, we experimentally explore the average conformation of model randomly hyperb...