Quarterly Reviews of Biophysics最新文献_第9页

Photosynthetic water splitting by the Mn4Ca2+OX catalyst of photosystem II: its structure, robustness and mechanism. 光系统II中Mn4Ca2+OX催化剂的光合水分解:结构、稳健性和机理

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2017-01-01 DOI: 10.1017/S0033583517000105

James Barber

{"title":"Photosynthetic water splitting by the Mn4Ca2+OX catalyst of photosystem II: its structure, robustness and mechanism.","authors":"James Barber","doi":"10.1017/S0033583517000105","DOIUrl":"https://doi.org/10.1017/S0033583517000105","url":null,"abstract":"The biological energy cycle of our planet is driven by photosynthesis whereby sunlight is absorbed by chlorophyll and other accessory pigments. The excitation energy is then efficiently transferred to a reaction centre where charge separation occurs in a few picoseconds. In the case of photosystem II (PSII), the energy of the charge transfer state is used to split water into oxygen and reducing equivalents. This is accomplished by the relatively low energy content of four photons of visible light. PSII is a large multi-subunit membrane protein complex embedded in the lipid environment of the thylakoid membranes of plants, algae and cyanobacteria. Four high energy electrons, together with four protons (4H+), are used to reduce plastoquinone (PQ), the terminal electron acceptor of PSII, to plastoquinol (PQH2). PQH2 passes its reducing equivalents to an electron transfer chain which feeds into photosystem I (PSI) where they gain additional reducing potential from a second light reaction which is necessary to drive CO2 reduction. The catalytic centre of PSII consists of a cluster of four Mn ions and a Ca2+ linked by oxo bonds. In addition, there are seven amino acid ligands. In this Article, I discuss the structure of this metal cluster, its stability and the probability that an acid-base (nucleophilic-electrophilic) mechanism catalyses the water splitting reaction on the surface of the metal-cluster. Evidence for this mechanism is presented from studies on water splitting catalysts consisting of organo-complexes of ruthenium and manganese and also by comparison with the enzymology of carbon monoxide dehydrogenase (CODH). Finally the relevance of our understanding of PSII is discussed in terms of artificial photosynthesis with emphasis on inorganic water splitting catalysts as oxygen generating photoelectrodes.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"50 ","pages":"e13"},"PeriodicalIF":6.1,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583517000105","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35245132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 13

Nucleic acids: function and potential for abiogenesis. 核酸:自然发生的功能和潜力。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2017-01-01 DOI: 10.1017/S0033583517000038

Falk Wachowius, James Attwater, Philipp Holliger

{"title":"Nucleic acids: function and potential for abiogenesis.","authors":"Falk Wachowius, James Attwater, Philipp Holliger","doi":"10.1017/S0033583517000038","DOIUrl":"https://doi.org/10.1017/S0033583517000038","url":null,"abstract":"The emergence of functional cooperation between the three main classes of biomolecules - nucleic acids, peptides and lipids - defines life at the molecular level. However, how such mutually interdependent molecular systems emerged from prebiotic chemistry remains a mystery. A key hypothesis, formulated by Crick, Orgel and Woese over 40 year ago, posits that early life must have been simpler. Specifically, it proposed that an early primordial biology lacked proteins and DNA but instead relied on RNA as the key biopolymer responsible not just for genetic information storage and propagation, but also for catalysis, i.e. metabolism. Indeed, there is compelling evidence for such an 'RNA world', notably in the structure of the ribosome as a likely molecular fossil from that time. Nevertheless, one might justifiably ask whether RNA alone would be up to the task. From a purely chemical perspective, RNA is a molecule of rather uniform composition with all four bases comprising organic heterocycles of similar size and comparable polarity and pK a values. Thus, RNA molecules cover a much narrower range of steric, electronic and physicochemical properties than, e.g. the 20 amino acid side-chains of proteins. Herein we will examine the functional potential of RNA (and other nucleic acids) with respect to self-replication, catalysis and assembly into simple protocellular entities.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"50 ","pages":"e4"},"PeriodicalIF":6.1,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583517000038","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35245188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 45

A molecular engineering toolbox for the structural biologist. 结构生物学家的分子工程工具箱。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2017-01-01 DOI: 10.1017/S0033583517000051

Galia T Debelouchina, Tom W Muir

{"title":"A molecular engineering toolbox for the structural biologist.","authors":"Galia T Debelouchina, Tom W Muir","doi":"10.1017/S0033583517000051","DOIUrl":"https://doi.org/10.1017/S0033583517000051","url":null,"abstract":"Exciting new technological developments have pushed the boundaries of structural biology, and have enabled studies of biological macromolecules and assemblies that would have been unthinkable not long ago. Yet, the enhanced capabilities of structural biologists to pry into the complex molecular world have also placed new demands on the abilities of protein engineers to reproduce this complexity into the test tube. With this challenge in mind, we review the contents of the modern molecular engineering toolbox that allow the manipulation of proteins in a site-specific and chemically well-defined fashion. Thus, we cover concepts related to the modification of cysteines and other natural amino acids, native chemical ligation, intein and sortase-based approaches, amber suppression, as well as chemical and enzymatic bio-conjugation strategies. We also describe how these tools can be used to aid methodology development in X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy and in the studies of dynamic interactions. It is our hope that this monograph will inspire structural biologists and protein engineers alike to apply these tools to novel systems, and to enhance and broaden their scope to meet the outstanding challenges in understanding the molecular basis of cellular processes and disease.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"50 ","pages":"e7"},"PeriodicalIF":6.1,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583517000051","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35245131","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 42

DNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase. 在有机阳离子存在下，DNA在张力下分裂成三胞胎，序列进化年龄预测三胞胎阶段的稳定性。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2017-01-01 DOI: 10.1017/S0033583517000130

Amirhossein Taghavi, Paul van der Schoot, Joshua T Berryman

{"title":"DNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase.","authors":"Amirhossein Taghavi, Paul van der Schoot, Joshua T Berryman","doi":"10.1017/S0033583517000130","DOIUrl":"https://doi.org/10.1017/S0033583517000130","url":null,"abstract":"Using atomistic simulations, we show the formation of stable triplet structure when particular GC-rich DNA duplexes are extended in solution over a timescale of hundreds of nanoseconds, in the presence of organic salt. We present planar-stacked triplet disproportionated DNA (Σ DNA) as a possible solution phase of the double helix under tension, subject to sequence and the presence of stabilising co-factors. Considering the partitioning of the duplexes into triplets of base pairs as the first step of operation of recombinase enzymes like RecA, we emphasise the structure-function relationship in Σ DNA. We supplement atomistic calculations with thermodynamic arguments to show that codons for 'phase 1' amino acids (those appearing early in evolution) are more likely than a lower entropy GC-rich sequence to form triplets under tension. We further observe that the four amino acids supposed (in the 'GADV world' hypothesis) to constitute the minimal set to produce functional globular proteins have the strongest triplet-forming propensity within the phase 1 set, showing a series of decreasing triplet propensity with evolutionary newness. The weak form of our observation provides a physical mechanism to minimise read frame and recombination alignment errors in the early evolution of the genetic code.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"50 ","pages":"e15"},"PeriodicalIF":6.1,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583517000130","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35245134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 12

Microdroplet fusion mass spectrometry: accelerated kinetics of acid-induced chlorophyll demetallation. 微滴融合质谱法:酸诱导叶绿素脱金属的加速动力学。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2017-01-01 DOI: 10.1017/S0033583517000014

Jae Kyoo Lee, Hong Gil Nam, Richard N Zare

{"title":"Microdroplet fusion mass spectrometry: accelerated kinetics of acid-induced chlorophyll demetallation.","authors":"Jae Kyoo Lee, Hong Gil Nam, Richard N Zare","doi":"10.1017/S0033583517000014","DOIUrl":"https://doi.org/10.1017/S0033583517000014","url":null,"abstract":"Kinetics of acid-induced chlorophyll demetallation was recorded in microdroplets by fusing a stream of microdroplets containing 40 µM chlorophyll a or b dissolved in methanol with a stream of aqueous microdroplets containing 35 mM hydrochloric acid (pH = 1·46). The kinetics of the demetallation of chlorophyll in the fused microdroplets (14 ± 6 µm diameter; 84 ± 18 m s-1 velocity) was recorded by controlling the traveling distance of the fused microdroplets between the fusion region and the inlet of a mass spectrometer. The rate of acid-induced chlorophyll demetallation was about 960 ± 120 times faster in the charged microdroplets compared with that reported in bulk solution. If no voltage was applied to the sprayed microdroplets, then the acceleration factor was about 580 ± 90, suggesting that the applied voltage is not a major factor determining the acceleration. Chlorophyll a was more rapidly demetallated than chlorophyll b by a factor of ~26 in bulk solution and ~5 in charged microdroplets. The demetallation kinetics was second order in the H+ concentration, but the acceleration factor of microdroplets compared with bulk solution appeared to be unchanged in going from pH = 1·3 to 7·0. The water:methanol ratio of the fused microdroplets was varied from 7:3 to 3:7 causing an increase in the reaction rate of chlorophyll a demetallation by 20%. This observation demonstrates that the solvent composition, which has different evaporation rates, does not significantly affect the acceleration. We believe that a major portion of the acceleration can be attributed to confinement effects involving surface reactions rather than either to evaporation of solvents or to the introduction of charges to the microdroplets.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"50 ","pages":"e2"},"PeriodicalIF":6.1,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583517000014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35245186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 29

Unraveling amyloid formation paths of Parkinson's disease protein α-synuclein triggered by anionic vesicles. 揭示由阴离子囊泡引发的帕金森病蛋白α-突触核蛋白淀粉样蛋白形成途径。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2017-01-01 DOI: 10.1017/S0033583517000026

Juris Kiskis, Istvan Horvath, Pernilla Wittung-Stafshede, Sandra Rocha

{"title":"Unraveling amyloid formation paths of Parkinson's disease protein α-synuclein triggered by anionic vesicles.","authors":"Juris Kiskis, Istvan Horvath, Pernilla Wittung-Stafshede, Sandra Rocha","doi":"10.1017/S0033583517000026","DOIUrl":"https://doi.org/10.1017/S0033583517000026","url":null,"abstract":"Amyloid formation of the synaptic brain protein α-synuclein (αS) is related to degeneration of dopaminergic neurons in Parkinson's disease patients. αS is thought to function in vesicle transport and fusion and it binds strongly to negatively charged vesicles in vitro. Here we combined circular dichroism, fluorescence and imaging methods in vitro to characterize the interaction of αS with negatively charged vesicles of DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, sodium salt) and DOPG (1,2-dioleoyl-sn-glycero-3-phospho-(1'-rac-glycerol), sodium salt) and the consequences of such interactions on αS amyloid formation. We found that lipid head-group chemistry modulates αS interactions and also affects amyloid fiber formation. During the course of the experiments, we made the unexpected discovery that pre-formed αS oligomers, typically present in a small amount in the αS starting material, acted as templates for linear growth of anomalous amyloid fibers in the presence of vesicles. At the same time, the remaining αS monomers were restricted from vesicle-mediated nucleation of amyloid fibers. Although not a dominant process in bulk experiments, this hidden αS aggregation pathway may be of importance in vivo.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"50 ","pages":"e3"},"PeriodicalIF":6.1,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583517000026","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35245187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 17

What can be learned about the enzyme ATPase from single-molecule studies of its subunit F1? 从对atp酶亚基F1的单分子研究中可以了解到什么?

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2017-01-01 DOI: 10.1017/S0033583517000129

Sándor Volkán-Kacso, Rudolph A Marcus

引用次数: 7

Understanding membrane-active antimicrobial peptides. 了解膜活性抗菌肽。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2017-01-01 DOI: 10.1017/S0033583517000087

Huey W Huang, Nicholas E Charron

{"title":"Understanding membrane-active antimicrobial peptides.","authors":"Huey W Huang, Nicholas E Charron","doi":"10.1017/S0033583517000087","DOIUrl":"https://doi.org/10.1017/S0033583517000087","url":null,"abstract":"Bacterial membranes represent an attractive target for the design of new antibiotics to combat widespread bacterial resistance to traditional inhibitor-based antibiotics. Understanding how antimicrobial peptides (AMPs) and other membrane-active agents attack membranes could facilitate the design of new, effective antimicrobials. AMPs, which are small, gene-encoded host defense proteins, offer a promising basis for the study of membrane-active antimicrobial agents. These peptides are cationic and amphipathic, spontaneously binding to bacterial membranes and inducing transmembrane permeability to small molecules. Yet there are often confusions surrounding the details of the molecular mechanisms of AMPs. Following the doctrine of structure-function relationship, AMPs are often viewed as the molecular scaffolding of pores in membranes. Instead we believe that the full mechanism of AMPs is understandable if we consider the interactions of AMPs with the whole membrane domain, where interactions induce structural transformations of the entire membrane, rather than forming localized molecular structures. We believe that it is necessary to consider the entire soft matter peptide-membrane system as it evolves through several distinct states. Accordingly, we have developed experimental techniques to investigate the state and structure of the membrane as a function of the bound peptide to lipid ratio, exactly as AMPs in solution progressively bind to the membrane and induce structural changes to the entire system. The results from these studies suggest that global interactions of AMPs with the membrane domain are of fundamental importance to understanding the antimicrobial mechanisms of AMPs.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"50 ","pages":"e10"},"PeriodicalIF":6.1,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583517000087","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35245193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 43

Spatially-controlled illumination microscopy 空间控制照明显微镜

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2016-12-12 DOI: 10.1017/S0033583516000135

V. Krishnaswami, C. V. van Noorden, E. Manders, R. Hoebe

{"title":"Spatially-controlled illumination microscopy","authors":"V. Krishnaswami, C. V. van Noorden, E. Manders, R. Hoebe","doi":"10.1017/S0033583516000135","DOIUrl":"https://doi.org/10.1017/S0033583516000135","url":null,"abstract":"Abstract Live-cell and live-tissue imaging using fluorescence optical microscopes presents an inherent trade-off between image quality and photodamage. Spatially-controlled illumination microscopy (SCIM) aims to strike the right balance between obtaining good image quality and minimizing the risk of photodamage. In traditional imaging, illumination is performed with a spatially-uniform light dose resulting in spatially-variable detected signals. SCIM adopts an alternative imaging approach where illumination is performed with a spatially-variable light dose resulting in spatially-uniform detected signals. The actual image information of the biological specimen in SCIM is predominantly encoded in the illumination profile. SCIM uses real-time spatial control of illumination in the imaging of fluorescent biological specimens. This alternative imaging paradigm reduces the overall illumination light dose during imaging, which facilitates prolonged imaging of live biological specimens by minimizing photodamage without compromising image quality. Additionally, the dynamic range of a SCIM image is no longer limited by the dynamic range of the detector (or camera), since it employs a uniform detection strategy. The large dynamic range of SCIM is predominantly determined by the illumination profile, and is advantageous for imaging both live and fixed biological specimens. In the present review, the concept and working mechanisms of SCIM are discussed, together with its application in various types of optical microscopes.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"20 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2016-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83574215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Frontier methods in coherent X-ray diffraction for high-resolution structure determination 相干x射线衍射高分辨率结构测定的前沿方法

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2016-12-12 DOI: 10.1017/S0033583516000147

M. Gallagher-Jones, José A. Rodríguez, J. Miao

引用次数: 11