Comparative Analysis Of Structural Properties Research Articles

Comparative dynamics and structural analysis of extremophilic serine proteases from diverse environments.

While life is found in a wide range of environments, many of the chemical functions required for homeostasis and reproduction are conserved. A large subset of these functions are fulfilled by proteins, which themselves have common requirements for both structural stability and chemical function. Organisms living in extreme environments, such as psychrophiles in the arctic ocean or thermophiles around hydrothermal vents, must thus develop adaptations to maintain protein structure and function under widely varying conditions. Here, we consider one ubiquitous enzyme class - the serine proteases - which are found in all known cells. Using genomic data from prokaryotes living under different environmental conditions, we model proteases from the S9, S11, S12, and S13 serine protease families. We predict three-dimensional structures of each enzyme using comparative modeling with in silico maturation to correct for known post-translational modifications, also correcting protonation states for each enzyme's native environment. Using atomistic molecular dynamics (MD) simulations, we obtain locally equilibrated explicit solvent structures for each enzyme, as well as longer trajectories for selected cases drawn from different thermal environments. We perform a comparative analysis of structural properties including surface exposures and secondary structure content across environmental conditions, showing both conserved and variable properties by environment. We also employ protein structure networks to examine structural cohesion, and active site networks to examine differences in active site structure and dynamics. Our analyses suggest patterns of adaptation within the serine proteases, in response to the challenges of life in distinct environmental conditions.

A comparative analysis of structural properties on single and poly-crystalline potassium sulfate crystals at shock wave loaded conditions

In recent years, the investigation of the effect of shock waves on crystalline materials has emerged as a prolific research area in materials science branch. The impact of shock waves on K2SO4 was investigated such that the molecular and structural stabilities under pre and post-shock wave loaded conditions at Mach number 2.2 with 50 and 100 shocks were established. Molecular stability of the test samples has been identified making use of FTIR spectrometer and the structural stability of the samples has been investigated by a Powder X-ray diffractometer (PXRD) which reveals that shock waves induce lattice orientational changes and micro distortions but, the original crystal system is not affected. The above-mentioned crystallographic studies show the impressive physical properties of K2SO4 which also has a stable crystal structure under shock wave loaded conditions. A comparison of single and poly-crystalline structural responses has been made with respect to the number of shock pulses. The fascinating findings of the shock wave impacts on K2SO4 samples are clearly discussed in this article.

Transition metal complexes with thiosemicarbazide-based ligands. Part 61. Comparative analysis of structural properties of the pyridoxal thiosemicarbazone ligands. Crystal structure of PLTSC·HCl·2H2O and its complex [Fe(PLTSC)Cl2(H2O)]Cl

A novel pyridoxal thiosemicarbazone (PLTSC) compound, exhibiting ligating properties, of the formula PLTSC·HCl·2H2O (1) was synthesized and characterized by X-ray analysis. The PLTSC ligand 1 displays significantly different conformation in comparison to the five previously reported compounds of this type. The structural properties of six PLTSC ligands in different conformations were compared in order to establish the structural differences and understand the factors that facilitate particular conformations. The analysis indicated great structural flexibility of the PLTSC ligands. The PLTSC ligand 1 is essentially a planar molecule with the r.m.s deviation of all non-H atoms equal to 0.06 A. Consequently, the molecules of 1 form a layered three-dimensional structure which is stabilized by a variety of hydrogen bonds: O–H⋯O, O–H⋯N, O–H⋯Cl, O–H⋯S, N–H⋯O, N–H⋯N, N–H⋯Cl, N–H⋯S. In addition, the crystal structure of the Fe(III) complex with the ligand 1 of the formula [Fe(PLTSC)Cl2(H2O)]Cl was resolved by single-crystal X-ray analysis and structural properties of this octahedral complex were discussed and compared to those of uncoordinated PLTSC ligand.

Crystal Structure of Human Lectin-like, Oxidized Low-Density Lipoprotein Receptor 1 Ligand Binding Domain and Its Ligand Recognition Mode to OxLDL

Lectin-like, oxidized low-density lipoprotein (LDL) receptor 1, LOX-1, is the major receptor for oxidized LDL (OxLDL) in endothelial cells. We have determined the crystal structure of the ligand binding domain of LOX-1, with a short stalk region connecting the domain to the membrane-spanning region, as a homodimer linked by an interchain disulfide bond. In vivo assays with LOX-1 mutants revealed that the "basic spine," consisting of linearly aligned arginine residues spanning over the dimer surface, is responsible for ligand binding. Single amino acid substitution in the dimer interface caused a severe reduction in LOX-1 binding activity, suggesting that the correct dimer arrangement is crucial for binding to OxLDL. Based on the LDL model structure, possible binding modes of LOX-1 to OxLDL are proposed.

Comparative analysis of structural properties of Portunid Crab Hemocyanin

In order to explore the hemocyanin adaptative potential and evolutive dynamics, we have analyzed the structural properties of this oxygen-carrier protein, in some species of portunid Crabs, (Brachyura, Portunida). We have compared the intra- and interspecific subunits patterns, in native and denaturant conditions, to estimate the phenetic relationships and the different stabilities of the protein.

Cobra venom factor: structural homology with the third component of human complement.

The functional analogy between cobra venom factor (CVF), the complement-activating protein in cobra venom, and C3b, the activated form of the third complement component, prompted us to conduct a comparative analysis of structural properties of the two proteins derived from two phylogenetically distant species. We subjected CVF and human C3 and its physiologic cleavage products, C3b and C3c, to a variety of biochemical analyses. We report here structural similarities of these proteins, which include similarities in amino acid composition, far and near UV circular dichroism spectra, secondary structure, band patterns and pI values from isoelectric focusing, immunochemical cross-reactivity, ultrastructural morphology, and amino-terminal amino acid sequences. Analysis of these data reveals that, structurally, CVF resembles C3c more than C3b. We conclude that CVF is not the product of a convergent evolution, but is, in all likelihood, derived from a common C3 ancestor protein.

Computer-Aided Comparative Analysis of Structural Properties of Large-Scale Organization Systems

Recently a package of computer programs, called DIANA-6, has been worked out at the Systems Research Institute of Polish Academy of Sciences. It is intended for the computer-aided diagnostic analysis of complex management systems. A significant part of the diagnostic analysis consists in thé comparative analysis of structural properties. The paper presents a methodology, on which, such an analysis is based. Some algorithms being elements of the most important computer-aided comparison procedures are described and discussed.