Advances in Biophysics最新文献

{"title":"Structure-mutation analysis of the ATPase site of Dictyostelium discoideum myosin II.","authors":"N Sasaki,&nbsp;K Sutoh","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Three loop structures called the P-loop, switch I loop and switch II loop of myosin are major components of its ATPase site, and share structural and functional homology with the loop structures in other ATPases and GTPases such as kinesin and G-protein. Using the alanine scanning mutagenesis, structure-function relationship of the switch I and switch II loops in Dictyostelium myosin II was examined. Based on crystal structures of Dictyostelium myosin motor domain, functions of each residue in those loops are discussed.</p>","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"35 ","pages":"1-24"},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20855002","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The structural study of membrane proteins by electron crystallography","authors":"Yoshinori Fujiyoshi","doi":"10.1016/S0065-227X(98)80003-8","DOIUrl":"10.1016/S0065-227X(98)80003-8","url":null,"abstract":"<div><p>A high-resolution electron cryo-microscope equipped with a top-entry specimen stage has been refined by modifying a previously described superfluid helium stage. Instruments equipped with such a cryo-stage achieve a resolution of better than 2.0 Å and have proved extremely powerful in the high-resolution structure analysis of membrane proteins. Improvement of the electron microscopic system in combination with improved specimen preparation techniques allowed the structure of bR to be analyzed to a resolution of 3.0 Å. The 3D structure of bR, especially the surface features, revealed the structural basis for the efficient guidance of protons to the entrance of the transmembrane channel. Based on the characteristic difference of the atomic scattering factors for electrons of ionized atoms versus neutral atoms as well as the data analysis, charged and uncharged amino acid residues could be discriminated. Thus, electron crystallography is providing us with new and exciting insights into the structure of membrane proteins because it not only enables us to determine the structure of a membrane protein, but allows us to study its interaction with the surrounding lipid molecules and to determine its ionization state.</p></div>","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"35 ","pages":"Pages 25-80"},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-227X(98)80003-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"55849878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The neuronal basis of visual memory and imagery in the primate: A neurophysiological approach","authors":"Kiyoshi Nakahara ,&nbsp;Machiko Ohbayashi ,&nbsp;Hyoe Tomita ,&nbsp;Yasushi Miyashita","doi":"10.1016/S0065-227X(98)80005-1","DOIUrl":"10.1016/S0065-227X(98)80005-1","url":null,"abstract":"<div><p>To understand the biological basis of memory is one of the most exciting frontiers of science. Single unit recording is a powerful method to investigate neuronal correlates of various brain functions such as memory in awake animals. Anatomical, neuropsychological, and neurophysiological evidence indicates that the IT has an important role not only for synthesizing the analyzed visual attribute into a unique configuration, but also for the storehouse of visual memory in humans and primates. We performed single unit recordings in the primate IT, and found neuronal correlates of visual long-term memory: the IT neurons could reflect learned associative relations among stimuli. The findings reviewed here support the hypothesis that the IT is a region of the brain where visual perception meets memory and imagery.</p></div>","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"35 ","pages":"Pages 103-119"},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-227X(98)80005-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"55849904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Neural systems for control of voluntary action--a hypothesis.","authors":"O Hikosaka","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Action is the means by which we and animals survive. It consists of a complex combination of movements which are either innately endowed or acquired by learning. In this article, I propose a hypothesis on the relationship between the organization of action and the organization of the brain. Innate and learned actions are controlled by different levels of neural networks: innate actions are controlled by reflex mechanisms and pattern generators in the spinal cord and brainstem, while learned actions are controlled by the cerebral cortex, basal ganglia, and cerebellum. However, these mechanisms are by no means independent. Phylogenetically, animals have acquired progressively more complex actions by gaining neural connections between different neural mechanisms. This is accomplished by the connection from newly evolving brain structures, particularly the cerebral cortex, to reflex or pattern generator mechanisms, as typically observed in the neural mechanism for saccadic eye movement. The cerebral cortex is a general purpose device which can be used in different ways depending on biological demands; in other words, it is used for learned actions. In consequence, a given movement (e.g., saccade) can be produced by different neural circuits, all converging onto the movement generation mechanism (e.g., s.c.) in an excitatory manner. However, such converging inputs that promote actions are likely to produce a chaotic explosion of neural signals. There must be some way to prevent the explosion and select signals that are most appropriate for the current behavioral context. The basal ganglia system evolved to accomplish this goal. It exerts a powerful inhibition on its targets in the brainstem (e.g., s.c.) and the thalamo-cortical system, thereby closing the gate for the action-promoting excitatory inputs; it also removes the sustained inhibition using another inhibition originating in the striatum (input structure of the basal ganglia), thereby opening the gate so that an appropriate action is executed. There are at least two additional functions of the basal ganglia. First, the selection mechanism of the basal ganglia is used also for the selection of simulated actions (e.g., thoughts) which are largely controlled by the association cortices. Second, it is used for learning of behavioral procedures: various kinds of signals from the cerebral cortex converge onto neurons in the basal ganglia to generate temporary association of neural signals, whose behavioral significance is evaluated by signals from the limbic system via dopaminergic neurons. The procedural memories thus created (perhaps in the cerebral cortex, particularly premotor cortices) are then used to guide learning of individual movements in which the cerebellum plays a crucial role. Thus, the implementation of learned actions is carried out by two distinct neural systems, each forming a loop circuit: 1) cerebral cortex and basal ganglia; 2) cerebral cortex and cerebellum. Although thes","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"35 ","pages":"81-102"},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20855004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design of protein function by physical perturbation method","authors":"Shun-Ichi Kidokoro","doi":"10.1016/S0065-227X(98)80006-3","DOIUrl":"10.1016/S0065-227X(98)80006-3","url":null,"abstract":"<div><p>Based on three-dimensional structure of proteins, a rational strategy to design the protein function by physical perturbation method was proposed and tested on one of the well-examined enzymes, thermolysin for higher catalytic activity. An attempt was made to change the electrostatic potential and the dynamic property of three-dimensional structure around the active sites by single-amino-acid mutations, and the physical property of the mutants was then evaluated. Several mutants were found to have remarkably higher enzymatic activity than wild type. The multiple mutation was introduced and the logarithm of the activity was found to be almost additive. A ten times higher active mutant was realized by simultaneously introducing three single-mutations. This strategy can be easily extended to not only other enzymes but also other kinds of proteins than enzymes to modify or control the protein function based on their three-dimensional structures.</p></div>","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"35 ","pages":"Pages 121-143"},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-227X(98)80006-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"55849919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure-mutation analysis of the ATPase site of Dictyostelium discoideum myosin II","authors":"Naoya Sasaki,&nbsp;Kazuo Sutoh","doi":"10.1016/S0065-227X(98)80002-6","DOIUrl":"10.1016/S0065-227X(98)80002-6","url":null,"abstract":"<div><p>Three loop structures called the P-loop, switch I loop and switch II loop of myosin are major components of its ATPase site, and share structural and functional homology with the loop structures in other ATPases and GTPases such as kinesin and G-protein. Using the alanine scanning mutagenesis, structure-function relationship of the switch I and switch II loops in <em>Dictyostelium</em> myosin II was examined. Based on crystal structures of <em>Dictyostelium</em> myosin motor domain, functions of each residue in those loops are discussed.</p></div>","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"35 ","pages":"Pages 1-24"},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-227X(98)80002-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"55849868","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure-mutation analysis of the ATPase site of Dictyostelium discoideum myosin II.","authors":"N. Sasaki, K. Sutoh","doi":"10.1016/S0065-227X(98)90003-X","DOIUrl":"https://doi.org/10.1016/S0065-227X(98)90003-X","url":null,"abstract":"","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"35 1","pages":"1-24"},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"55849928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Contributor sketches","authors":"","doi":"10.1016/S0065-227X(98)90002-8","DOIUrl":"https://doi.org/10.1016/S0065-227X(98)90002-8","url":null,"abstract":"","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"35 ","pages":"Pages 145-147"},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-227X(98)90002-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136719825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The structural study of membrane proteins by electron crystallography.","authors":"Y Fujiyoshi","doi":"10.1016/s0065-227x(98)90004-1","DOIUrl":"https://doi.org/10.1016/s0065-227x(98)90004-1","url":null,"abstract":"<p><p>A high-resolution electron cryo-microscope equipped with a top-entry specimen stage has been refined by modifying a previously described superfluid helium stage. Instruments equipped with such a cryo-stage achieve a resolution of better than 2.0 A and have proved extremely powerful in the high-resolution structure analysis of membrane proteins. Improvement of the electron microscopic system in combination with improved specimen preparation techniques allowed the structure of bR to be analyzed to a resolution of 3.0 A. The 3D structure of bR, especially the surface features, revealed the structural basis for the efficient guidance of protons to the entrance of the transmembrane channel. Based on the characteristic difference of the atomic scattering factors for electrons of ionized atoms versus neutral atoms as well as the data analysis, charged and uncharged amino acid residues could be discriminated. Thus, electron crystallography is providing us with new and exciting insights into the structure of membrane proteins because it not only enables us to determine the structure of a membrane protein, but allows us to study its interaction with the surrounding lipid molecules and to determine its ionization state.</p>","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"35 ","pages":"25-80"},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/s0065-227x(98)90004-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20855003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design of protein function by physical perturbation method.","authors":"S Kidokoro","doi":"10.1016/s0065-227x(98)90007-7","DOIUrl":"https://doi.org/10.1016/s0065-227x(98)90007-7","url":null,"abstract":"<p><p>Based on three-dimensional structure of proteins, a rational strategy to design the protein function by physical perturbation method was proposed and tested on one of the well-examined enzymes, thermolysin for higher catalytic activity. An attempt was made to change the electrostatic potential and the dynamic property of three-dimensional structure around the active sites by single-amino-acid mutations, and the physical property of the mutants was then evaluated. Several mutants were found to have remarkably higher enzymatic activity than wild type. The multiple mutation was introduced and the logarithm of the activity was found to be almost additive. A ten times higher active mutant was realized by simultaneously introducing three single-mutations. This strategy can be easily extended to not only other enzymes but also other kinds of proteins than enzymes to modify or control the protein function based on their three-dimensional structures.</p>","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"35 ","pages":"121-43"},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/s0065-227x(98)90007-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20854933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}