Molecular dynamics of rhodopsin and free opsin: Computer simulation

Kholmurodov, Kholmirzo; Feldman, T. B.; Ostrovskii, M. A.

doi:10.1007/s11055-007-0164-7

Cited by 8 publications

(7 citation statements)

References 49 publications

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“…It is also known that in the dark-adapted visual pigment, the chromophore, as an ligand antagonist, stabilizes the dynamics of α-helix H-VI, restricts its mobility, and prevents spontaneous activation of rhodopsin due to strong electrostatic interactions with Trp265 [3, 15, 29]. It follows from our model that not only Trp265 but also Tyr268 and Leu266 participate in the prevention of spontaneous activation of rhodopsin [26, 27]. …”

Section: Resultsmentioning

confidence: 74%

“…The time of 0.4 ns (viz., 400000 time steps) perhaps characterizes an adaptation time for the 11- cis -retinal inside the chromophore pocket and determines all subsequent events of rhodopin conformation. We have observed [26, 27] that the beta-ionone ring of the 11- cis -retinal begun to rotate with regard to the polyene chain axis to approximately 65º. This “twisting degree” we have calculated by comparing all the rotational torsion angles of all methyl groups C16-C20 of the 11- cis -retinal within the 3-ns dynamical changes.…”

Section: Resultsmentioning

confidence: 99%

“…It was found that the behavior of 11- cis -retinal correlates with both the displacements of the amino acid residues in the chromophore center and the structural deformations in the rhodopsin cytoplasmic domain, which is far enough from the chromophore center [26]. So we have performed the molecular dynamics simulation of amino acid residues not only in the chromophore center, but also in the rhodopsin cytoplasmic domain.…”

Section: Resultsmentioning

confidence: 99%

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Model of Abnormal Chromophore-Protein Interaction for E181K Rhodopsin Mutation: Computer Molecular Dynamics Study

Feldman¹

2012

TOBIOCJ

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The interaction of the 11-cis-retinal chromophore with the surrounding amino acid residues in the chromophore center of the rhodopsin protein has been investigated for the Е181К mutant form using molecular dynamics simulation. A comparative analysis of the arrangement of the amino acid residues in the chromophore center has been performed for both wild (native) and mutant rhodopsins. It is shown that for the Е181К mutant rhodopsin there is no proper binding of 11-cis-retinal with the surrounding amino acid residues. The distortion of the conformation states in the mutant rhodopsin molecule takes place in both the chromophore center and cytoplasmic domain. Our simulations suggest that a stable covalent linkage of 11-cis-retinal with the protein part (viz. opsin) of the rhodopsin molecule will not form. This, on the other hand, implies that the protein’s active site in the cytoplasmic domain, which is responsible for the G-protein binding (so-called transducin), may not be completely blocked.Based on our molecular simulation data, we discuss the possible correlation between retinitis pigmentosa pathogenesis and the structural and functional properties of the rhodopsin protein.

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Section: Resultsmentioning

confidence: 74%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Model of Abnormal Chromophore-Protein Interaction for E181K Rhodopsin Mutation: Computer Molecular Dynamics Study

Feldman¹

2012

TOBIOCJ

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“…The FAD chromophore binding inside the DNA photolyase pocket has many similarities with 11-cis retinal chromophore in opsin proteins [29][30][31][32][33][34][35]. Opsins are expressed in rods and cones in the back (outer) part of the retina; photolyase/cryptochrome proteins are expressed in the front (inner) part of the retina.…”

Section: Resultsmentioning

confidence: 99%

Molecular dynamics simulations of a DNA photolyase protein: High-mobility and conformational changes of the FAD molecule at low temperatures

Kholmurodov¹,

Dushanov²,

Yasuoka³

2012

ABB

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A molecular dynamics (MD) simulation is performed on a DNA photolyase to study the conformational behavior of the photoactive cofactor flavin adenine dinucleotide (FAD) inside the enzyme pocket. A DNA photolyase is a highly efficient light-driven enzyme that repairs the UV-induced cyclobutane pyrimidine dimer in damaged DNA. In this work, the FAD conformational and dynamic changes were studied within the total complex structure of a DNA photolyase protein (containing FADH–, MTHF, and DNA molecules) embedded in a water solvent. We aimed to compare the conformational changes of the FAD cofactor and other constituent fragments of the molecular system under consideration. The obtained results were discussed to gain insight into the light-driven mechanism of DNA repair by a DNA photolyase enzyme—based on the enzyme structure, the FAD mobility, and conformation shape

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“…Based on advanced molecular dynamics methods and visualization techniques, we simulate here the behavior of wild-type and mutated proteins in water and ionic solvents at physiological conditions. The obtained molecular dynamics (MD) simulation results are discussed in terms of their strong correlation with different diseases of a radiobiological nature [1][2][3][4].…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics Study of the Effect of Induced Mutations on the Protein Structures Associated with Diseases of A Radiobiological Nature

Kholmurodov¹

2013

BIO

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The induced mutations in biological molecules, such as DNA and proteins, have quite a different nature (environmental factors, viruses, ionizing radiation, mutagenic chemicals, inherited genetic alterations, etc.). Induced mutations can destroy the existing chemical (hydrogen) bonds in the native molecular structures or, on the contrary, create new chemical (hydrogen) bonds that do not normally exist there. In protein structures, the cause of such changes might be the substitution of one or several specific amino acid residues (point mutations). At the atomic level, the replacement of one amino acid residue by another causes essential modifications of the molecular force fields of the environment, which can break important hydrogen bonds underlying the structural stability of biological molecules. In this work, based on molecular dynamics (MD) method, we demonstrate the effect of mutational structure changes on several biological protein models (the p53 oncoprotein, visual pigment rhodopsin, cyclin-dependent kinase, and recA protein). Molecular dynamics simulation is a powerful tool in investigating the structure properties of biological molecules on the atomic and molecular levels, and it has been widely used to study the structural conformational behavior of proteins. We also discuss the scenario of the mutation effects associated with different kinds of diseases that could develop and take place in physiological conditions.

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Molecular dynamics of rhodopsin and free opsin: Computer simulation

Cited by 8 publications

References 49 publications

Model of Abnormal Chromophore-Protein Interaction for E181K Rhodopsin Mutation: Computer Molecular Dynamics Study

Model of Abnormal Chromophore-Protein Interaction for E181K Rhodopsin Mutation: Computer Molecular Dynamics Study

Molecular dynamics simulations of a DNA photolyase protein: High-mobility and conformational changes of the FAD molecule at low temperatures

Molecular Dynamics Study of the Effect of Induced Mutations on the Protein Structures Associated with Diseases of A Radiobiological Nature

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