Proton transfer in the primary process of vision.
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Animals↗
Biomedical subjects
A Sarai
Publications and source records attributed to A Sarai.
Possible role of protein in photosynthetic electron transfer.
Photosynthetic electron transfer is discussed from a theoretical viewpoint. Theoretical description of electron transfer including the effect of low-frequency mode of protein is first discussed briefly. Then typical electron transfers in the primary photosynthesis are discussed as examples for the comparison between the theory and experiments. Attention is focussed on the fact that the photosynthetic system organizes a variety of electron transfers in a systematic manner to achieve a vary efficient energy conversion, and it is suggested that the protein environment plays an important role in controlling the rate of electron transfer and maximizing the efficiency of the primary reaction. We emphasize that not only the electronic but also vibrational interactions are important for the regulation of electron transfer. Some novel processes such as activationless and negative activation transfers are shown to be connected with the significance of vibrational factor.
Bacterial Physiological Phenomena↗
A backflow of electrons around photosystem II in Chlorella cells.
A study was made with a modulated oxygen electrode of the effect of variations of oxygen concentration on photosynthetic oxygen evolution from algal cells. When Chlorella vulgaris is examined with a modulated 650 nm light at 22 degrees C, both the oxygen yield and the phase lag between the modulated oxygen signal and the light modulations have virtually constant values between 800 and 120 ergs . cm-1 . s-1 if the bathing medium is in equilibrium with the air. Similar results are obtained at 32 degrees C between 1600 and 120 ergs . cm-2 . s-1. Under anaerobic conditions both the oxygen yield and the phase lag decrease if the light intensity is lowered below about 500 ergs . cm-2 . s-1 at 22 degrees C or about 1000 ergs . cm-2 . s-1 at 32 degrees C. A modulated 706 nm beam also gives rise to these phenomena but only at significantly lower rates of oxygen evolution. The cells of Anacystis nidulans and Porphyridium cruentum appear to react in the same way to anaerobic conditions as C. vulgaris. An examination of possible mechanisms to explain these results was performed using a computer simulation of photosynthetic electron transport. The simulation suggests that a backflow of electrons from a redox pool between the Photosystems to the rate-limiting reaction between Photosystem II and the water-splitting act can cause a decrease in oxygen yield and phase lag. If the pool between the Photosystems is in a very reduced state a significant cyclic flow is expected, whereas if the pool is largely oxidized little or no cyclic flow should occur. It is shown that the effects of 706 nm illumination and removal of oxygen can be interpreted in accordance with these proposals. Since a partial inhibition of oxygen evolution by 3-(3.4-dichlorophenyl)-1,1-dimethylurea (10(-8) M) magnifies the decreases in oxygen yield and phase lag, it is proposed that the pool which cycles back electrons is in front of the site of 3-(3,4-dichlorophenyl)-1,1-dimethylurea inhibition and is probably the initial electron acceptor pool after Photosystem II.
Anaerobiosis↗
Orientational changes of the transition dipole moment of retinal chromophore on the disk membrane due to the conversion of rhodopsin to bathorhodopsin and to isorhodopsin.
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Animals↗
Variations in photosynthetic electron-transport pathways in Chlorella vulgaris.
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Chlorella↗
Evaluation of free energy landscape for base-amino acid interactions using ab initio force field and extensive sampling.
Structural data of protein-DNA complex show redundancy and flexibility in base-amino acid interactions. To understand the origin of the specificity in protein-DNA recognition, we calculated the interaction free energy, enthalpy, entropy, and minimum energy maps for AT-Asn, GC-Asn, AT-Ser, and GC-Ser by means of a set of ab initio force field with extensive conformational sampling. We found that the most preferable interactions in these pairs are stabilized by hydrogen bonding, and are mainly enthalpy driven. However, minima in the free energy maps are not necessarily the same as those in the minimum energy map or enthalpy maps, due to the entropic effect. The effect of entropy is particularly important in the case of GC-Asn. Experimentally observed structures of base-amino acid interactions are within preferable regions in the calculated free energy maps, where there are many different interaction configurations with similar energy. The full geometry optimization procedure using ab initio molecular orbital method was applied to get the optimal interaction geometries for AT-Asn, GC-Asn, AT-Ser, and GC-Ser. We found that there are various base-amino acid combinations with similar interaction energies. These results suggest that the redundancy and conformational flexibility in the base-amino acid interactions play an important role in the protein-DNA recognition.
Adenine↗
Thermodynamic databases for proteins and protein-nucleic acid interactions.
Thermodynamic data regarding proteins and their interactions are important for understanding the mechanisms of protein folding, protein stability, and molecular recognition. Although there are several structural databases available for proteins and their complexes with other molecules, databases for experimental thermodynamic data on protein stability and interactions are rather scarce. Thus, we have developed two electronically accessible thermodynamic databases. ProTherm, Thermodynamic Database for Proteins and Mutants, contains numerical data of several thermodynamic parameters of protein stability, experimental methods and conditions, along with structural, functional, and literature information. ProNIT, Thermodynamic Database for Protein-Nucleic Acid Interactions, contains thermodynamic data for protein-nucleic acid binding, experimental conditions, structural information of proteins, nucleic acids and the complex, and literature information. These data have been incorporated into 3DinSight, an integrated database for structure, function, and properties of biomolecules. A WWW interface allows users to search for data based on various conditions, with different display and sorting options, and to visualize molecular structures and their interactions. These thermodynamic databases, together with structural databases, help researchers gain insight into the relationship among structure, function, and thermodynamics of proteins and their interactions, and will become useful resources for studying proteins in the postgenomic era.
DNA↗
Introduction of 6-formylcytidine into a Myb binding sequence.
Single 6-formylcytidine was introduced into a oligonucleotide duplex (23 mers) as a substitute for thymidine in the Myb binding sequence of 3'-TTGAC-5'. The modified duplex showed Tm of 67 degrees C, which was six degrees lower than the Tm of the native duplex. Binding affinity of the 23-mers to the Myb protein was estimated by electrophoretic mobility shift assays, and the binding was almost completely abolished.
Binding Sites↗
[mRNA-FAST (mRNA-Function, Activity, STructure) computer system].
Computer system mRNA-FAST (mRNA--Function, Activity, STructure; http://wwwmgs.bionet.nsc.ru/mgs/dbases/trsig/) is described. The system has been developed to analyze nucleotide sequences of mRNA and to measure their essential properties. The system compiles the data base on translation signals including nucleotide sequences of the regulatory regions with structural and experimental information on their specific activities. It also contains programs to search for local homology between mRNA and translation signals, to search for potential signals basing on analysis of the oligonucleotide dictionaries, and to model secondary RNA structure. Possible applications of the system mRNA-FAST are discussed.
Base Sequence↗
[Analysis of structural motifs of proteins using sets of codes, describing local structures].
An amino acid sequence pattern conserved among a family of proteins is called motif. It is usually related to the specific function of the family. On the other hand, functions of proteins are achieved by their 3D structures. Specific local structures, called structural motifs, are considered related to their functions. However, searching for common structural motifs in different proteins is much more difficult than for common sequence motifs. We are attempting in this study to convert the information about the structural motifs into a set of one-dimensional digital strings, i.e., a set of codes, to compare them more easily by computer and to investigate their relationship to functions more quantitatively. By applying the Delaunay tessellation to a 3D structure of a protein, we can assign each local structure to a unique code that is defined so as to reflect its structural feature. Since a structural motif is defined as a set of the local structures in this paper, the structural motif is represented by a set of the codes. In order to examine the ability of the set of the codes to distinguish differences among the sets of local structures with a given PROSITE pattern that contain both true and false positives, we clustered them by introducing a similarity measure among the set of the codes. The obtained clustering shows a good agreement with other results by direct structural comparison methods such as a superposition method. The structural motifs in homologous proteins are also properly clustered according to their sources. These results suggest that the structural motifs can be well characterized by these sets of the codes, and that the method can be utilized in comparing structural motifs and relating them with function.
Amino Acid Motifs↗
[The context organization of functional regions in yeast genes with high-level expression].
With the example of yeast genes, context organization was compared for functional gene regions (promoter, 5'-UTR, 3'-UTR) and tested for association with the level of gene expression. Several parameters (nucleotide composition, dinucletoide content bias) proved to correlate with expression level, each functional region having its specific features. Context optimization of a functional region was assumed to be essential for highly efficient interaction with the expression system of the cell. Specific context features were considered as dispersed signals important for high-level gene expression.
3' Untranslated Regions↗
[Conformational effects of DNA stretching].
DNA is an extensible molecule, and an extended conformation of DNA is involved in some biological processes. We have examined the effect of elongation stress on the conformational properties of DNA base pairs by conformational analysis. The calculations show that stretching does significantly affect the conformational properties and flexibilities of base pairs. In particular, we have found that the propeller twist in base pairs reverses its sign upon stretching. The energy profile analysis indicates that electrostatic interactions make a major contribution to the stabilization of the positive-propeller-twist configuration in stretched DNA. This stretching also results in a monotonic decrease in the helical twist angle, tending to unwind the double helix. Fluctuations in most variables initially increase upon stretching, because of unstacking of base pairs, but then the fluctuations decrease as DNA is stretched further, owing to the formation of specific interactions between base pairs induced by the positive propeller twist. Thus, the stretching of DNA has particularly significant effects upon DNA flexibility. These changes in both the conformation and flexibility of base pairs probably have a role in functional interactions with proteins.
Base Pairing↗