Browsing by Subject "Hydrogen bond"

Now showing 1 - 4 of 4

Open Access
Atomic scale study of superlow friction between hydrogenated diamond surfaces
(American Physical Society, 2004) Dag, S.; Çıracı, Salim
Strong attractive interaction between two clean diamond (001) slabs turns repulsive upon the hydrogenation of surfaces. This repulsive interaction serves as if a boundary lubricant and prevents the sliding surfaces from being closer to each other even under high normal forces. As a result, calculated lateral force variation generated during sliding has small magnitude under high constant loading forces. Superlow friction observed earlier between diamondlike carbon-coated surfaces can be understood by the steady repulsive interaction between sliding surfaces, as well as strong and stiff carbon-carbon and carbon-hydrogen bonds which do not favor energy dissipation. In ambient conditions, the steady repulsive interaction is, however, destroyed by oxygen atoms which chemically modify those stiff surface bonds.
Open Access
DFT explorations of quadrupole coupling constants for planar 5-fluorouracil pairs
(Elsevier, 2016-08) Mirzaei, M.; Gülseren, O.; Hadipour, N.
Atomic scale properties of quadrupole coupling constants (CQ) have been evaluated for singular and paired 5-fluorouracil (FU) models. Structural possibilities and properties for various types of hydrogen bonded (HB) homo pairs of FU have been investigated based on density functional theory (DFT) calculations. The models have been optimized to obtain the minimum energy level structures and only the planar molecular pairs have been considered. Various types of HB interactions have also managed the molecular shapes for the FU pairs. Different types of energies and also electron transferring properties have been investigated by the evaluated optimized properties. The atomic scale results indicated different strengths of HB interactions for FU pairs according to the changes of CQ properties for atoms in the singular and paired systems depending on the strength of interactions.
Open Access
Glycosaminoglycan-Mimetic Signals Direct the Osteo/Chondrogenic Differentiation of Mesenchymal Stem Cells in a Three-Dimensional Peptide Nanofiber Extracellular Matrix Mimetic Environment
(American Chemical Society, 2016-02) Arslan, E.; Güler, Mustafa O.; Tekinay, A. B.
Recent efforts in bioactive scaffold development focus strongly on the elucidation of complex cellular responses through the use of synthetic systems. Designing synthetic extracellular matrix (ECM) materials must be based on understanding of cellular behaviors upon interaction with natural and artificial scaffolds. Hence, due to their ability to mimic both the biochemical and mechanical properties of the native tissue environment, supramolecular assemblies of bioactive peptide nanostructures are especially promising for development of bioactive ECM-mimetic scaffolds. In this study, we used glycosaminoglycan (GAG) mimetic peptide nanofiber gel as a three-dimensional (3D) platform to investigate how cell lineage commitment is altered by external factors. We observed that amount of fetal bovine serum (FBS) presented in the cell media had synergistic effects on the ability of GAG-mimetic nanofiber gel to mediate the differentiation of mesenchymal stem cells into osteogenic and chondrogenic lineages. In particular, lower FBS concentration in the culture medium was observed to enhance osteogenic differentiation while higher amount FBS promotes chondrogenic differentiation in tandem with the effects of the GAG-mimetic 3D peptide nanofiber network, even in the absence of externally administered growth factors. We therefore demonstrate that mesenchymal stem cell differentiation can be specifically controlled by the combined influence of growth medium components and a 3D peptide nanofiber environment.
Open Access
Protein folding, misfolding and aggregation: the importance of two-electron stabilizing interactions
(Public Library of Science, 2017) Cieplak, A. S.
Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates’ morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer’s and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the Cα atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer’s amyloid β and tau, Parkinson’s α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrPC, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrPSc fibrils. The model does account for: (i) structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii) effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and chirality of solid-liquid interface on the rate and morphology of aggregation; (iii) fibril-surface catalysis of secondary nucleation; and (iv) self-propagation of infectious strains of mammalian prions. © 2017 Andrzej Stanisław Cieplak. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.