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Register a new userMultiple scales and phases in discrete chains with application to folded proteins
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Chiral heteropolymers such as larger globular proteins can simultaneously support multiple length scales. The interplay between different scales brings about conformational diversity, and governs the structure of the energy landscape. Multiple scales produces also complex dynamics, which in the case of proteins sustains live matter. However, thus far no clear understanding exist, how to distinguish the various scales that determine the structure and dynamics of a complex protein. Here we propose a systematic method to identify the scales in chiral heteropolymers such as a protein. For this we introduce a novel order parameter, that not only reveals the scales but also probes the phase structure. In particular, we argue that a chiral heteropolymer can simultaneously display traits of several different phases, contingent on the length scale at which it is scrutinized. Our approach builds on a variant of Kadanoffs block-spin transformation that we employ to coarse grain piecewise linear chains such as the C$alpha$ backbone of a protein. We derive analytically and then verify numerically a number of properties that the order parameter can display. We demonstrate how, in the case of crystallographic protein structures in Protein Data Bank, the order parameter reveals the presence of different length scales, and we propose that a relation must exist between the scales, phases, and the complexity of folding pathways.
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The folding of a protein towards its native state is a rather complicated process. However there are empirical evidences that the folding time correlates with the contact order, a simple measure of the spatial organisation of the native state of the protein. Contact order is related to the average length of the main chain loops formed by amino acids which are in contact. Here we argue that folding kinetics can be influenced also by the entanglement that loops may undergo within the overall three dimensional protein structure. In order to explore such possibility, we introduce a novel descriptor, which we call maximum intrachain contact entanglement. Specifically, we measure the maximum Gaussian entanglement between any looped portion of a protein and any other non-overlapping subchain of the same protein, which is easily computed by discretized line integrals on the coordinates of the $C_{alpha}$ atoms. By analyzing experimental data sets of two-state and multistate folders, we show that also the new index is a good predictor of the folding rate. Moreover, being only partially correlated with previous methods, it can be integrated with them to yield more accurate predictions.
Recent experiments and simulations have revealed glassy features in the cytoplasm, living tissues as well as dense assemblies of self propelled colloids. This leads to a fundamental question: how do these non-equilibrium (active) amorphous materials differ from conventional passive glasses, created either by lowering temperature or by increasing density? To address this we investigate the aging behaviour after a quench to an almost arrested state of a model active glass former, a Kob-Andersen glass in two dimensions. Each constituent particle is driven by a constant propulsion force whose direction diffuses over time. Using extensive molecular dynamics simulations we reveal rich aging behaviour of this dense active matter system: short persistence times of the active forcing lead to effective thermal aging; in the opposite limit we find a two-step aging process with active athermal aging at short times followed by activity-driven aging at late times. We develop a dedicated simulation method that gives access to this long-time scaling regime for highly persistent active forces.
The beautiful structures of single and multi-domain proteins are clearly ordered in some fashion but cannot be readily classified using group theory methods that are successfully used to describe periodic crystals. For this reason, protein structures are considered to be aperiodic, and may have evolved this way for functional purposes, especially in instances that require a combination of softness and rigidity within the same molecule. By analyzing the solved protein structures, we show that orientational symmetry is broken in the aperiodic arrangement of the secondary structural elements (SSEs), which we deduce by calculating the nematic order parameter, $P_{2}$. We find that the folded structures are nematic droplets with a broad distribution of $P_{2}$. We argue that non-zero values of $P_{2}$, leads to an arrangement of the SSEs that can resist mechanical forces, which is a requirement for allosteric proteins. Such proteins, which resist mechanical forces in some regions while being flexible in others, transmit signals from one region of the protein to another (action at a distance) in response to binding of ligands (oxygen, ATP or other small molecules).
Many-body systems with multiple emergent time scales arise in various contexts, including classical critical systems, correlated quantum materials, and ultra-cold atoms. We investigate such non-trivial quantum dynamics in a new setting: a spin-1 bilinear-biquadratic chain. It has a solvable entangled groundstate, but a gapless excitation spectrum that is poorly understood. By using large-scale DMRG simulations, we find that the lowest excitations have a dynamical exponent $z$ that varies from 2 to 3.2 as we vary a coupling in the Hamiltonian. We find an additional gapless mode with a continuously varying exponent $2leq z <2.7$, which establishes the presence of multiple dynamics. In order to explain these striking properties, we construct a continuum wavefunction for the groundstate, which correctly describes the correlations and entanglement properties. We also give a continuum parent Hamiltonian, but show that additional ingredients are needed to capture the excitations of the chain. By using an exact mapping to the non-equilibrium dynamics of a classical spin chain, we find that the large dynamical exponent is due to subdiffusive spin motion. Finally, we discuss the connections to other spin chains and to a family of quantum critical models in 2d.
Water plays a fundamental role in protein stability. However, the effect of the properties of water on the behaviour of proteins is only partially understood. Several theories have been proposed to give insight into the mechanisms of cold and pressure denaturation, or the limits of temperature and pressure above which no protein has a stable, functional state, or how unfolding and aggregation are related. Here we review our results based on a theoretical approach that can rationalise the water contribution to protein solutions free energy. We show, using Monte Carlo simulations, how we can rationalise experimental data with our recent results. We discuss how our findings can help develop new strategies for the design of novel synthetic biopolymers or possible approaches for mitigating neurodegenerative pathologies.
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