Quarterly Reviews of Biophysics最新文献_第9页

Lysozyme's lectin-like characteristics facilitates its immune defense function. 溶菌酶的凝集素样特性有利于其免疫防御功能。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2017-01-01 DOI: 10.1017/S0033583517000075

Ruiyan Zhang, Lisha Wu, Thomas Eckert, Monika Burg-Roderfeld, Miguel A Rojas-Macias, Thomas Lütteke, Vadim B Krylov, Dmitry A Argunov, Aritreyee Datta, Philipp Markart, Andreas Guenther, Bengt Norden, Roland Schauer, Anirban Bhunia, Mushira Abdelaziz Enani, Martin Billeter, Axel J Scheidig, Nikolay E Nifantiev, Hans-Christian Siebert

{"title":"Lysozyme's lectin-like characteristics facilitates its immune defense function.","authors":"Ruiyan Zhang, Lisha Wu, Thomas Eckert, Monika Burg-Roderfeld, Miguel A Rojas-Macias, Thomas Lütteke, Vadim B Krylov, Dmitry A Argunov, Aritreyee Datta, Philipp Markart, Andreas Guenther, Bengt Norden, Roland Schauer, Anirban Bhunia, Mushira Abdelaziz Enani, Martin Billeter, Axel J Scheidig, Nikolay E Nifantiev, Hans-Christian Siebert","doi":"10.1017/S0033583517000075","DOIUrl":"https://doi.org/10.1017/S0033583517000075","url":null,"abstract":"Interactions between human lysozyme (HL) and the lipopolysaccharide (LPS) of Klebsiella pneumoniae O1, a causative agent of lung infection, were identified by surface plasmon resonance. To characterize the molecular mechanism of this interaction, HL binding to synthetic disaccharides and tetrasaccharides representing one and two repeating units, respectively, of the O-chain of this LPS were studied. pH-dependent structural rearrangements of HL after interaction with the disaccharide were observed through nuclear magnetic resonance. The crystal structure of the HL-tetrasaccharide complex revealed carbohydrate chain packing into the A, B, C, and D binding sites of HL, which primarily occurred through residue-specific, direct or water-mediated hydrogen bonds and hydrophobic contacts. Overall, these results support a crucial role of the Glu35/Asp53/Trp63/Asp102 residues in HL binding to the tetrasaccharide. These observations suggest an unknown glycan-guided mechanism that underlies recognition of the bacterial cell wall by lysozyme and may complement the HL immune defense function.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583517000075","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35245192","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: 38

Ribosome structural dynamics in translocation: yet another functional role for ribosomal RNA. 易位中的核糖体结构动力学:核糖体RNA的另一个功能角色。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2017-01-01 DOI: 10.1017/S0033583517000117

Harry F Noller, Laura Lancaster, Srividya Mohan, Jie Zhou

引用次数: 33

A new paradigm for atomically detailed simulations of kinetics in biophysical systems. 生物物理系统动力学原子详细模拟的新范例。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2017-01-01 DOI: 10.1017/S0033583517000063

Ron Elber

{"title":"A new paradigm for atomically detailed simulations of kinetics in biophysical systems.","authors":"Ron Elber","doi":"10.1017/S0033583517000063","DOIUrl":"https://doi.org/10.1017/S0033583517000063","url":null,"abstract":"The kinetics of biochemical and biophysical events determined the course of life processes and attracted considerable interest and research. For example, modeling of biological networks and cellular responses relies on the availability of information on rate coefficients. Atomically detailed simulations hold the promise of supplementing experimental data to obtain a more complete kinetic picture. However, simulations at biological time scales are challenging. Typical computer resources are insufficient to provide the ensemble of trajectories at the correct length that is required for straightforward calculations of time scales. In the last years, new technologies emerged that make atomically detailed simulations of rate coefficients possible. Instead of computing complete trajectories from reactants to products, these approaches launch a large number of short trajectories at different positions. Since the trajectories are short, they are computed trivially in parallel on modern computer architecture. The starting and termination positions of the short trajectories are chosen, following statistical mechanics theory, to enhance efficiency. These trajectories are analyzed. The analysis produces accurate estimates of time scales as long as hours. The theory of Milestoning that exploits the use of short trajectories is discussed, and several applications are described.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583517000063","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35245191","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: 32

Chromatin-remodeling for transcription. 染色质重塑转录。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2017-01-01 DOI: 10.1017/S003358351700004X

Yahli Lorch, Roger D Kornberg

{"title":"Chromatin-remodeling for transcription.","authors":"Yahli Lorch, Roger D Kornberg","doi":"10.1017/S003358351700004X","DOIUrl":"https://doi.org/10.1017/S003358351700004X","url":null,"abstract":"The nucleosome serves as a general gene repressor, preventing all initiation of transcription except that which is brought about by specific positive regulatory mechanisms. The positive mechanisms begin with chromatin-remodeling by complexes that slide, disrupt, or otherwise alter the structure and organization of nucleosomes. RSC in yeast and its counterpart PBAF in human cells are the major remodeling complexes for transcription. RSC creates a nucleosome-free region in front of a gene, flanked by strongly positioned +1 and -1 nucleosomes, with the transcription start site typically 10-15 bp inside the border of the +1 nucleosome. RSC also binds stably to nucleosomes harboring regulatory elements and to +1 nucleosomes, perturbing their structures in a manner that partially exposes their DNA sequences. The cryo-electron microscope structure of a RSC-nucleosome complex reveals such a structural perturbation, with the DNA largely unwrapped from the nucleosome and likely interacting with a positively charged surface of RSC. Such unwrapping both exposes the DNA and enables its translocation across the histone octamer of the nucleosome by an ATP-dependent activity of RSC. Genetic studies have revealed additional roles of RSC in DNA repair, chromosome segregation, and other chromosomal DNA transactions. These functions of RSC likely involve the same fundamental activities, DNA unwrapping and DNA translocation.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S003358351700004X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35245189","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: 49

Structural biology of supramolecular assemblies by magic-angle spinning NMR spectroscopy. 利用魔角自旋核磁共振光谱对超分子组装体进行结构生物学研究。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2017-01-01 DOI: 10.1017/S0033583516000159

Caitlin M Quinn, Tatyana Polenova

{"title":"Structural biology of supramolecular assemblies by magic-angle spinning NMR spectroscopy.","authors":"Caitlin M Quinn, Tatyana Polenova","doi":"10.1017/S0033583516000159","DOIUrl":"10.1017/S0033583516000159","url":null,"abstract":"In recent years, exciting developments in instrument technology and experimental methodology have advanced the field of magic-angle spinning (MAS) nuclear magnetic resonance (NMR) to new heights. Contemporary MAS NMR yields atomic-level insights into structure and dynamics of an astounding range of biological systems, many of which cannot be studied by other methods. With the advent of fast MAS, proton detection, and novel pulse sequences, large supramolecular assemblies, such as cytoskeletal proteins and intact viruses, are now accessible for detailed analysis. In this review, we will discuss the current MAS NMR methodologies that enable characterization of complex biomolecular systems and will present examples of applications to several classes of assemblies comprising bacterial and mammalian cytoskeleton as well as human immunodeficiency virus 1 and bacteriophage viruses. The body of work reviewed herein is representative of the recent advancements in the field, with respect to the complexity of the systems studied, the quality of the data, and the significance to the biology.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5483179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77516984","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: 0

A stretched conformation of DNA with a biological role? DNA的延伸构象具有生物学作用?

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2017-01-01 DOI: 10.1017/S0033583517000099

Niklas Bosaeus, Anna Reymer, Tamás Beke-Somfai, Tom Brown, Masayuki Takahashi, Pernilla Wittung-Stafshede, Sandra Rocha, Bengt Nordén

{"title":"A stretched conformation of DNA with a biological role?","authors":"Niklas Bosaeus, Anna Reymer, Tamás Beke-Somfai, Tom Brown, Masayuki Takahashi, Pernilla Wittung-Stafshede, Sandra Rocha, Bengt Nordén","doi":"10.1017/S0033583517000099","DOIUrl":"https://doi.org/10.1017/S0033583517000099","url":null,"abstract":"We have discovered a well-defined extended conformation of double-stranded DNA, which we call Σ-DNA, using laser-tweezers force-spectroscopy experiments. At a transition force corresponding to free energy change ΔG = 1·57 ± 0·12 kcal (mol base pair)-1 60 or 122 base-pair long synthetic GC-rich sequences, when pulled by the 3'-3' strands, undergo a sharp transition to the 1·52 ± 0·04 times longer Σ-DNA. Intriguingly, the same degree of extension is also found in DNA complexes with recombinase proteins, such as bacterial RecA and eukaryotic Rad51. Despite vital importance to all biological organisms for survival, genome maintenance and evolution, the recombination reaction is not yet understood at atomic level. We here propose that the structural distortion represented by Σ-DNA, which is thus physically inherent to the nucleic acid, is related to how recombination proteins mediate recognition of sequence homology and execute strand exchange. Our hypothesis is that a homogeneously stretched DNA undergoes a 'disproportionation' into an inhomogeneous Σ-form consisting of triplets of locally B-like perpendicularly stacked bases. This structure may ensure improved fidelity of base-pair recognition and promote rejection in case of mismatch during homologous recombination reaction. Because a triplet is the length of a gene codon, we speculate that the structural physics of nucleic acids may have biased the evolution of recombinase proteins to exploit triplet base stacks and also the genetic code.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583517000099","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35245129","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: 15

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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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