Search results for "folding"
showing 10 items of 330 documents
Abelian antipowers in infinite words
2019
Abstract An abelian antipower of order k (or simply an abelian k-antipower) is a concatenation of k consecutive words of the same length having pairwise distinct Parikh vectors. This definition generalizes to the abelian setting the notion of a k-antipower, as introduced in Fici et al. (2018) [7] , that is a concatenation of k pairwise distinct words of the same length. We aim to study whether a word contains abelian k-antipowers for arbitrarily large k. S. Holub proved that all paperfolding words contain abelian powers of every order (Holub, 2013 [8] ). We show that they also contain abelian antipowers of every order.
From the barbecue to the sauna: A comparative account of the folding of media reception into the everyday life
2021
How and why do people still get print newspapers in an era dominated by mobile and social media communication? In this article, we answer this question about the permanence of traditional media in a digital media ecosystem by analyzing 488 semi-structured interviews conducted in Argentina, Finland, Israel, Japan, and the United States. We focus on three mechanisms of media reception: access, sociality, and ritualization. Our findings show that these mechanisms are decisively shaped by patterns of everyday life that are not captured by the scholarly foci on either content- or technology-influences on media use. Thus, we argue that a non-media centric approach improves descriptive fit and ad…
Interaction of explicit solvent with hydrophobic/philic/charged residues of a protein: Residue character vs. conformational context
1998
Molecular dynamics simulations of model solutes in explicit molecular water have recently elicited novel aspects of the strong nonpair additivity of the potential of mean force (PMF) and related solvent-induced forces (SIFs) and hydration. Here we present the results of the same type of work on SIFs acting on bovine pancreatic trypsin inhibitor (BPTI) at single residue/sidechain resolution. In this system, nonpair additivity and the consequent dependence of SIFs on the protein conformational context are sufficiently strong to overturn SIFs on some individual residues, relative to expectations based on their individual characters. This finding calls for a revisitation and offers a richer and…
Non-Equilibrium Markov State Modeling of the Globule-Stretch Transition
2016
We describe a systematic approach to construct coarse-grained Markov state models from molecular dynamics data of systems driven into a nonequilibrium steady state. We apply this method to study the globule-stretch transition of a single tethered model polymer in shear flow. The folding and unfolding rates of the coarse-grained model agree with the original detailed model. We demonstrate that the folding and unfolding proceeds through the same narrow region of configuration space but along different cycles.
Unfolding dynamics of small peptides biased by constant mechanical forces
2018
We show how multi-ensemble Markov state models can be combined with constant-force equilibrium simulations. Besides obtaining the unfolding/folding rates, Markov state models allow gaining detailed insights into the folding dynamics and pathways through identifying folding intermediates and misfolded structures. For two specific peptides, we demonstrate that the end-to-end distance is an insufficient reaction coordinate. This problem is alleviated through constructing models with multiple collective variables, for which we employ the time-lagged independent component analysis requiring only minimal prior knowledge. Our results show that combining Markov state models with constant-force simu…
Assessment of the probabilities for evolutionary structural changes in protein folds.
2007
Abstract Motivation: The evolution of protein sequences can be described by a stepwise process, where each step involves changes of a few amino acids. In a similar manner, the evolution of protein folds can be at least partially described by an analogous process, where each step involves comparatively simple changes affecting few secondary structure elements. A number of such evolution steps, justified by biologically confirmed examples, have previously been proposed by other researchers. However, unlike the situation with sequences, as far as we know there have been no attempts to estimate the comparative probabilities for different kinds of such structural changes. Results: We have tried …
A Hooke's law-based approach to protein folding rate
2014
Kinetics is a key aspect of the renowned protein folding problem. Here, we propose a comprehensive approach to folding kinetics where a polypeptide chain is assumed to behave as an elastic material described by the Hooke[U+05F3]s law. A novel parameter called elastic-folding constant results from our model and is suggested to distinguish between protein with two-state and multi-state folding pathways. A contact-free descriptor, named folding degree, is introduced as a suitable structural feature to study protein-folding kinetics. This approach generalizes the observed correlations between varieties of structural descriptors with the folding rate constant. Additionally several comparisons am…
Global stability of protein folding from an empirical free energy function
2013
The principles governing protein folding stand as one of the biggest challenges of Biophysics. Modeling the global stability of proteins and predicting their tertiary structure are hard tasks, due in part to the variety and large number of forces involved and the difficulties to describe them with sufficient accuracy. We have developed a fast, physics-based empirical potential, intended to be used in global structure prediction methods. This model considers four main contributions: Two entropic factors, the hydrophobic effect and configurational entropy, and two terms resulting from a decomposition of close-packing interactions, namely the balance of the dispersive interactions of folded an…
Folding Patterns in a Family of Oligoamide Foldamers
2015
A series of small, unsymmetrical pyridine-2,6-dicarboxylamide oligoamide foldamers with varying lengths and substituents at the end groups were synthetized to study their conformational properties and folding patterns. The @-type folding pattern resembled the oxyanion-hole motifs of enzymes, but several alternative folding patterns could also be characterized. Computational studies revealed several alternative conformers of nearly equal stability. These folding patterns differed from each other in their intramolecular hydrogen-bonding patterns and aryl-aryl interactions. In the solid state, the foldamers adopted either the globular @-type fold or the more extended S-type conformers, which w…
Conformational properties and folding analysis of a series of seven oligoamide foldamers
2016
33 crystal structures (11 unsolvated and 22 solvates) of a series of seven oligoamide foldamers were analysed. The crystal structures revealed that despite the structural and environmental differences the series of foldamers prefer only two general conformations, a protohelical @-conformation and a sigmoidal S-conformation. Both conformations also have preferred crystal packing motifs and solvate forming tendencies. Hydrogen bonding was found to be the most decisive factor in conformational preference, but steric properties, the type of the peripheral substituents, as well as solvent and aromatic interactions were also found to have an effect on the conformational details and crystal form. …