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Identifying subtle conformational fluctuations underlying the dynamics of bio macromolecules is crucial for resolving their free energy landscape. We show that a collective variable, originally proposed for crystalline solids, is able to filter out essential macromolecular motions more efficiently than other approaches. While homogenous or `affine' deformations of the biopolymer are trivial, biopolymer conformations are complicated by the occurrence of in-homogenous or `non-affine' displacements of atoms relative to their positions in the native structure. We show that these displacements encode functionally relevant conformations of macromolecule and, in combination with a formalism based upon time-structured independent component analysis, quantitatively resolve the free energy landscape of a number of macromolecules of hierarchical complexity. The kinetics of conformational transitions among the basins can now be mapped within the framework of a Markov state model. The non-affine modes, obtained by projecting out homogenous fluctuations from the local displacements, are found to be responsible for local structural changes required for transitioning between pairs of macro states.
This article was published in the following journal.
Name: Journal of chemical theory and computation
Motivated by qualitative experimental observations in collective behavior of self-propelled camphor particles at air-water interfaces, we study a generic aggregate forming system in two dimensions (2D...
One of the important physicochemical features of the proteins specifically multi-subunit types is their stability at high temperatures. The kinetics of the dissociation and denaturation of proteins po...
The intriguing process of protein folding comprises discrete steps that stabilize the protein molecules in different conformations. The metastable state of protein is represented by specific conformat...
Molecular dynamics plays an important role for the biological function of proteins. For protein ligand interactions, changes of conformational entropy of protein and hydration layer are relevant for t...
Because of their small size and their beneficial biochemical and economic properties (size, affinity, specificity, stability, production cost), nanobodies are now increasingly used for routine and mor...
The purpose of this study is to determine the temporal relationship between motor fluctuations and non-motor fluctuations in persons with Parkinson's disease. Observational study case-onl...
This study will advance computer tailoring by adapting machine learning collective intelligence algorithms that have been used outside healthcare by companies like Amazon and Google to enh...
To quantify the association between multiple intentional weight losses (i.e., weight fluctuations) and the development of hypertension and diabetes mellitus among 50,790 female nurses part...
The purpose of this study is to evaluate local disease control after 2 years in patients with non-metastatic, non-operated non-small-cell lung cancer treated by radiotherapy. Eligible pat...
Schemas describe mental structures storing recurrent and organized pattern of information. Schemas may have a strong influence on the process of storing and retrieving new information into...
A family of intracellular calcium-sensing proteins found predominately in NEURONS and PHOTORECEPTOR CELLS. They contain EF HAND MOTIFS and undergo conformational changes upon calcium-binding. Neuronal calcium-sensor proteins interact with other regulatory proteins to mediate physiological responses to a change in intracellular calcium concentration.
Fungal genes that mostly encode TRANSCRIPTION FACTORS. In some FUNGI they also encode PHEROMONES and PHEROMONE RECEPTORS. The transcription factors control expression of specific proteins that give a cell its mating identity. Opposite mating type identities are required for mating.
Protein domains that are enriched in PROLINE. The cyclical nature of proline causes the peptide bonds it forms to have a limited degree of conformational mobility. Therefore the presence of multiple prolines in close proximity to each other can convey a distinct conformational arrangement to a peptide chain.
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
Family of cell adhesion molecules consisting of a lectin-like domain, an epidermal growth factor-like domain, and a variable number of domains that encode proteins homologous to complement-binding proteins. Selectins mediate the binding of leukocytes to the vascular endothelium. (From Dorland, 28th ed)