ABSTRACT
The influence of binding of the orthosteric ligands on the conformational dynamics of the beta-2-adrenoreceptor was identified using the molecular dynamics method. It was found that there was alittle fraction of the active states of the receptor in its apo (ligand free) ensemble. Analysis of the MD trajectories indicated that such spontaneous activation of the receptor is accompanied by the motion of its VI helix. Thus receptor's constitutive activity is the direct result of its conformational dynamics. On other hand binding of the full agonist resulted in the significant shift of the initial equilibrium towards its active state. Finally binding of the inverse agonist stabilized receptor in its inactive state. Its likely that the binding of the inverse agonists might be the universal way of the constitutive activity inhibition. Our results indicate that ligand binding rather redistribute prexisting conformational degrees of freedom (in accordance to the Monod-Wyman-Changeux-Model) than cause induced fit in it. Therefore ensemble of the biological-relevant receptor conformations have been encoded in its spatial structure and individual conformations from that ensemble might be used by the cell according to the physiological behavior.
Subject(s)
Adrenergic beta-2 Receptor Agonists/pharmacology , Molecular Docking Simulation , Molecular Dynamics Simulation , Receptors, Adrenergic, beta-2/chemistry , Adrenergic beta-2 Receptor Agonists/chemistry , Amino Acid Sequence , Animals , Humans , Ligands , Molecular Sequence Data , Protein Binding , Receptors, Adrenergic, beta-2/metabolismABSTRACT
A study is reported of the functional-relevant dynamics of three typical water-soluble proteins: Calmodulin, Src-tyrosine kinase as well as repressor of Trp operon. Application of the state-of-art methods of structural bioinformatics allowed to identify dynamics seen in the X-ray structures of the investigated proteins associated with their specific biological functions. In addition, Normal Mode analysis technique revealed the most probable directions of the functionally-relevant motions for all that proteins were also predicted. Importantly, overall type of the motions observed on the lowest-frequency modes was very similar to the motions seen from the analysis of the X-ray data of the examined macromolecules. Thereby it was shown that the large-scale as well as local conformational motions of the proteins might be predetermined already at the level of their tertiary structures. In particular, the determining factor might be the specific fold of the alpha-helixes. Thus functionally-relevant in vivo dynamics of the investigated proteins might be evolutionally formed by means of natural selection at the level of the spatial topology.
Subject(s)
Bacterial Proteins/chemistry , Calmodulin/chemistry , Protein Conformation , Repressor Proteins/chemistry , Water/chemistry , src-Family Kinases/chemistry , Bacterial Proteins/genetics , Calmodulin/genetics , Computational Biology , Crystallography, X-Ray , Humans , Principal Component Analysis , Repressor Proteins/genetics , Selection, Genetic , Solubility , src-Family Kinases/geneticsABSTRACT
The structural dynamics of three different ligand-activated G-protein coupled receptors (GPCRs) and the photoreactive receptor rhodopsin from mammals were comparatively studied. As a result, diagrams demonstrating the main structural differences between the studied membrane receptors were obtained. These diagrams represent the projection of the crystal structures of rhodopsin photointermediates and ligand-activated receptors onto the plane defined by the principal components. Thus, we were able to associate the activation process of the receptors with large-scale movements of their individual transmembrane (TM) domains. In addition, the dynamics of extracellular loops of ligand-activated receptors responsible for recognition and initial binding of ligands was studied. Based on these results, two parameters of functionally significant structural dynamics of membrane receptors can be thoroughly analyzed simultaneously - movements of individual TM helices and of extracellular loops.
Subject(s)
Movement , Principal Component Analysis , Receptors, G-Protein-Coupled/chemistry , Receptors, G-Protein-Coupled/metabolism , Crystallography, X-Ray , Ligands , Models, Molecular , Protein ConformationABSTRACT
In this work structural behavior of apo form of the adenosine A2A receptor in the implicit membrane-mimicking environment was investigated by means of molecular dynamics (MD) technique. For better interpretation of the obtained data they were analyzed using principal components analysis. The principal components analysis technique was applied to both MD snapshots as well as X-ray structures of the adenosine receptor. As the result the charts were obtained which reflected an interconnection interdependence between dynamic behavior of the receptor observed on the MD trajectories as well as experimental dataset of investigated protein. The calculated MD trajectories allow to observe represent pronounced structural dynamics of the A2A receptor especially in the intracellular part loop connecting TM 5 and 6 of that protein. This observation generally corresponds to the dynamic behavior of the investigated protein seen on the experimental dataset. Therefore the pattern of the intramolecular motions might be following directly from the spatial architecture (fold) of the receptor under study.
Subject(s)
Molecular Dynamics Simulation , Receptor, Adenosine A2A/chemistry , Rhodopsin/chemistry , Carbon Tetrachloride/chemistry , Humans , Principal Component Analysis , Protein Structure, Secondary , Protein Structure, Tertiary , Structural Homology, Protein , Thermodynamics , Water/chemistryABSTRACT
We report a classification of the crystallographic structures of bovine and squid rhodopsins corresponding to different stages of their photocycles. Using the resource Protein (Structure) Comparison, Knowledge, Similarity, and Information server (ProCKSI, http://www.procksi.net/), selected spatial structures were compared on the basis of classification schemes (dendrograms). To compare the spatial structures of transmembrane proteins, optimal consensus was developed from methods implemented in ProCKSI. Structures were also clustered using principal component analysis, resulting in good agreement with the classification based on the ProCKSI consensus method. Analysis of the results revealed the basic movements of individual transmembrane domains of these proteins that we were able to relate to different stages of the photoactivation of rhodopsin. A combination of methods identified in this study can be used as an up-to-date analytical tool to study the conformational dynamics of membrane receptors.
Subject(s)
Computational Biology , Rhodopsin/chemistry , Rhodopsin/classification , Algorithms , Animals , Cattle , Decapodiformes/metabolism , Internet , Principal Component Analysis , Protein Structure, Tertiary , Rhodopsin/metabolismABSTRACT
A number of effects of weak combined (static and alternating) magnetic fields with an alternating component of tens and hundreds nT at a collinear static field of 42 microT, which is equivalent to the geomagnetic field, have been found: the activation of fission and regeneration of planarians Dugesia tigrina, the inhibition of the growth of the Ehrlich ascites carcinoma in mice, the stimulation of the production of the tumor necrosis factor by macrophages, a decrease in the protection of chromatin against the action of DNase 1, and the enhancement of protein hydrolysis in systems in vivo and in vitro. The frequency and amplitude ranges for the alternating component of weak combined magnetic fields have been determined at which it affects various biological systems. Thus, the optimal amplitude at a frequency of 4.4 Hz is 100 nT (effective value); at a frequency of 16.5 Hz, the range of effective amplitudes is broader, 150-300 nT; and at a frequency of 1 (0.5) Hz, it is 300 nT. The sum of close frequencies (e.g., 16 and 17 Hz) produces a similar biological effect as the product of the modulating (0.5 Hz) and carrying frequencies (16.5 Hz), which is explained by the ratio A = A0sin omega1t + A0sin omega2t = A0sin(omega1 + omega2)t/2cos(omega1 - omega2)t/2. The efficiency of magnetic signals with pulsations (the sum of close frequencies) is more pronounced than that of sinusoidal frequencies. These data may indicate the presence of several receptors of weak magnetic fields in biological systems and, as a consequence, a higher efficiency of the effect at the simultaneous adjustment to these frequencies by the field. Even with consideration of these facts, the mechanism of the biological action of weak combined magnetic fields remains still poorly understood.
Subject(s)
Carcinoma, Ehrlich Tumor/pathology , Electromagnetic Fields , Planarians/radiation effects , Proteins/radiation effects , Amyloid beta-Peptides/metabolism , Amyloid beta-Peptides/radiation effects , Angiotensin I/metabolism , Angiotensin I/radiation effects , Animals , Carcinoma, Ehrlich Tumor/metabolism , Histones/metabolism , Histones/radiation effects , Hydrolysis , Insulin/metabolism , Insulin/radiation effects , Mice , Mice, Transgenic , Neoplasm Transplantation , Planarians/physiology , Proteins/metabolismABSTRACT
The parameters of the low-frequency (1, 4.4, 16.5 Hz or the sum of these frequencies) extremely weak (300, 100, 150-300 nT, according to frequencies) alternating component of combined magnetic fields have been found, which in combination with a weak collinear static constant field of 42 nT (the induction corresponds to the range of the geomagnetic field) has a marked antitumor activity. The exposure to these magnetic fields inhibits the tumor growth in mice with the intraperitoneally transplanted Ehrlich ascites carcinoma. The effect manifests itself in an increase in the life of tumor-bearing animals and in the content of damaged tumor cells. It was found that the death of tumor cells by the action of weak fields occurs predominantly by the mechanism of necrosis.
