Journal of Biomolecular Structure & Dynamics 

About: Journal of Biomolecular Structure & Dynamics is an academic journal published by Taylor & Francis. The journal publishes majorly in the area(s): Medicine & Chemistry. It has an ISSN identifier of 0739-1102. Over the lifetime, 8006 publications have been published receiving 115375 citations.

A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat.

Abstract: We have examined some subtle parameter modifications to the Cornell et al. force field, which has proven quite successful in reproducing nucleic acid properties, but whose C2'-endo sugar pucker phase and helical repeat for B DNA appear to be somewhat underestimated. Encouragingly, the addition of a single V2 term involving the atoms C(sp3)-O-(sp3)-C(sp3)-N(sp2), which can be nicely rationalized because of the anomeric effect (lone pairs on oxygen are preferentially oriented relative to the electron withdrawing N), brings the sugar pucker phase of C2'-endo sugars to near perfect agreement with ab initio calculations (W near 162 degrees). Secondly, the use of high level ab initio calculations on entire nucleosides (in contrast to smaller model systems necessitated in 1994-95 by computer limitations) lets one improve the chi torsional potential for nucleic acids. Finally, the O(sp3)-C(sp3)- C(sp3)-O(sp3) V2 torsional potential has been empirically adjusted to reproduce the ab initio calculated relative energy of C2'-endo and C3'-endo nucleosides. These modifications are tested in molecular dynamics simulations of mononucleosides (to assess sugar pucker percentages) and double helices of DNA and RNA (to assess helical and sequence specific structural properties). In both areas, the modified force field leads to improved agreement with experimental data.

The Definition of Generalized Helicoidal Parameters and of Axis Curvature for Irregular Nucleic Acids

Abstract: An algorithm is presented which solves the problem of obtaining a rigorous helicoidal description of an irregular nucleic acid segment. Central to this approach is the definition of a function describing simultaneously the curvature of the nucleic acid segment in question and the corresponding stepwise variation of helicoidal parameters along the segment. Minimisation of this function leads to an optimal distribution of the conformational irregularity of the segment between these two components. Further, it is shown that this approach can be applied equally easily to single or double stranded nucleic acids. The results of this analysis yield both the absolute helicoidal parameters of individual bases/base pairs and the relative helicoidal parameters between successive bases/base pairs as well as the overall locus of the helical axis. The possibilities of this mathematical approach are demonstrated with the help of a computer program termed "Curves" which is applied to the study of a number of different nucleic acid structures.

Defining the structure of irregular nucleic acids: conventions and principles.

Abstract: The algorithm "Curves", that we have recently presented in this journal (J. Biolmol. Str. Dynam. 6, 63-91 (1988], is updated to take into account the conventions developed at the Cambridge meeting on DNA curvature (September 1988) and extended to the calculation of local parameters. In addition, the principles which govern the choices made in establishing the Curves algorithm are compared with the approaches adopted by other authors.

A Protein-Chameleon: Conformational Plasticity of α-Synuclein, a Disordered Protein Involved in Neurodegenerative Disorders

Abstract: Under the physiological conditions in vitro, α-synuclein, a conservative presynaptic protein, the aggregation and fibrillation of which is assumed to be involved into the pathogenesis of Parkinson's disease and several other neurodegenerative disorders, known as synucleinopathies, is characterized by the lack of rigid well-defined structure; i.e., it belongs to the class of intrinsically unstructured proteins. Intriguingly, α-synuclein is characterized by a remarkable conformational plasticity, adopting a series of different conformations depending on the environment. For example, this protein may either stay substantially unfolded, or adopt an amyloidogenic partially folded conformation, or fold into α-helical or β-structural species, both monomeric and oligomeric. Furthermore, it might form several morphologically different types of aggregates, including oligomers (spheres or doughnuts), amorphous aggregates, and or amyloid-like fibrils. The peculiarities of this astonishing conformational beha...

Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life

Abstract: Intrinsically disordered proteins and intrinsically disordered protein regions are highly abundant in nature. However, the quantitative and qualitative measures of protein intrinsic disorder in species with known genomes are still not available. Furthermore, although the correlation between high fraction of disordered residues and advanced species has been reported, the details of this correlation and the connection between the disorder content and proteome complexity have not been reported as of yet. To fill this gap, we analysed entire proteomes of 3484 species from three domains of life (archaea, bacteria and eukaryotes) and from viruses. Our analysis revealed that the evolution process is characterized by distinctive patterns of changes in the protein intrinsic disorder content. We are showing here that viruses are characterized by the widest spread of the proteome disorder content (the percentage of disordered residues ranges from 7.3% in human coronavirus NL63 to 77.3% in Avian carcinoma virus). For several organisms, a clear correlation is seen between their disorder contents and habitats. In multicellular eukaryotes, there is a weak correlation between the complexity of an organism (evaluated as a number of different cell types) and its overall disorder content. For both the prokaryotes and eukaryotes, the disorder content is generally independent of the proteome size. However, disorder shows a sharp increase associated with the transition from prokaryotic to eukaryotic cells. This suggests that the increased disorder content in eukaryotic proteomes might be used by nature to deal with the increased cell complexity due to the appearance of the various cellular compartments.