Current Research in Structural Biology最新文献

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Crystal structure of the BREX phage defence protein BrxA BREX噬菌体防御蛋白BrxA的晶体结构
IF 2.8
Current Research in Structural Biology Pub Date : 2022-01-01 DOI: 10.1016/j.crstbi.2022.06.001
Izaak N. Beck , David M. Picton , Tim R. Blower
{"title":"Crystal structure of the BREX phage defence protein BrxA","authors":"Izaak N. Beck ,&nbsp;David M. Picton ,&nbsp;Tim R. Blower","doi":"10.1016/j.crstbi.2022.06.001","DOIUrl":"10.1016/j.crstbi.2022.06.001","url":null,"abstract":"<div><p>Bacteria are constantly challenged by bacteriophage (phage) infection and have developed multitudinous and varied resistance mechanisms. Bacteriophage Exclusion (BREX) systems protect from phage infection by generating methylation patterns at non-palindromic 6 bp sites in host bacterial DNA, to distinguish and block replication of non-self DNA. Type 1 BREX systems are comprised of six conserved core genes. Here, we present the first reported structure of a BREX core protein, BrxA from the phage defence island of <em>Escherichia fergusonii</em> ATCC 35469 plasmid pEFER, solved to 2.09 ​Å. BrxA is a monomeric protein in solution, with an all α-helical globular fold. Conservation of surface charges and structural homology modelling against known phage defence systems highlighted that BrxA contains two helix-turn-helix motifs, juxtaposed by 180°, positioned to bind opposite sides of a DNA major groove. BrxA was subsequently shown to bind dsDNA. This new understanding of BrxA structure, and first indication of BrxA biological activity, suggests a conserved mode of DNA-recognition has become widespread and implemented by diverse phage defence systems.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9240713/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40559392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Metabolically-incorporated deuterium in myelin localized by neutron diffraction and identified by mass spectrometry 髓鞘代谢合并氘经中子衍射定位,质谱鉴定
IF 2.8
Current Research in Structural Biology Pub Date : 2021-12-20 DOI: 10.1101/2021.12.17.473245
A. Baumann, A. Denninger, M. Domin, B. Demé, D. Kirschner
{"title":"Metabolically-incorporated deuterium in myelin localized by neutron diffraction and identified by mass spectrometry","authors":"A. Baumann, A. Denninger, M. Domin, B. Demé, D. Kirschner","doi":"10.1101/2021.12.17.473245","DOIUrl":"https://doi.org/10.1101/2021.12.17.473245","url":null,"abstract":"Myelin is a natural and dynamic multilamellar membrane structure that continues to be of significant biological and neurological interest, especially with respect to its biosynthesis and assembly during its normal formation, maintenance, and pathological breakdown. To explore the usefulness of neutron diffraction in the structural analysis of myelin, we investigated the use of in vivo labeling by metabolically incorporating non-toxic levels of deuterium (2H; D) via drinking water into a pregnant dam (D-dam) and her developing embryos. All of the mice were sacrificed when the pups (D-pups) were 55 days old. Myelinated sciatic nerves were dissected, fixed in glutaraldehyde and examined by neutron diffraction. Parallel samples that were unfixed (trigeminal nerves) were frozen for mass spectrometry (MS). The diffraction patterns of the nerves from deuterium-fed mice (D-mice) vs. the controls (H-mice) had major differences in the intensities of the Bragg peaks but no appreciable differences in myelin periodicity. Neutron scattering density profiles showed an appreciable increase in density at the center of the lipid-rich membrane bilayer. This increase was greater in D-pups than in D-dam, and its localization was consistent with deuteration of lipid hydrocarbon, which predominates over transmembrane protein in myelin. MS analysis of the lipids isolated from the trigeminal nerves demonstrated that in the pups the percentage of lipids that had one or more deuterium atoms was uniformly high across lipid species (97.6% ± 2.0%), whereas in the mother the lipids were substantially less deuterated (60.6% ± 26.4%) with levels varying among lipid species and subspecies. The mass distribution pattern of deuterium-containing isotopologues indicated the fraction (in %) of each lipid (sub-)species having one or more deuteriums incorporated: in the D-pups, the pattern was always bell-shaped, and the average number of D atoms ranged from a low of ∼4 in fatty acid to a high of ∼9 in cerebroside. By contrast, in D-dam most lipids had more complex, overlapping distributions that were weighted toward a lower average number of deuteriums, which ranged from a low of ∼3–4 in fatty acid and in one species of sulfatide to a high of 6–7 in cerebroside and sphingomyelin. The consistently high level of deuteration in D-pups can be attributed to their de novo lipogenesis during gestation and rapid, postnatal myelination. The widely varying levels of deuteration in D-dam, by contrast, likely depends on the relative metabolic stability of the particular lipid species during myelin maintenance. Our current findings demonstrate that stably-incorporated D label can be detected and localized using neutron diffraction in a complex tissue such as myelin; and moreover, that MS can be used to screen a broad range of deuterated lipid species to monitor differential rates of lipid turnover. In addition to helping to develop a comprehensive understanding of the de novo synthesis and turnover","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2021-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42516335","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}
引用次数: 1
De novo crystal structure determination of double stranded RNA binding domain using only the sulfur anomalous diffraction in SAD phasing 双链RNA结合域的重新晶体结构测定仅使用硫异常衍射在SAD相位
IF 2.8
Current Research in Structural Biology Pub Date : 2021-01-01 DOI: 10.1016/j.crstbi.2021.05.002
Beatriz Gomes Guimarães , Béatrice Golinelli-Pimpaneau
{"title":"De novo crystal structure determination of double stranded RNA binding domain using only the sulfur anomalous diffraction in SAD phasing","authors":"Beatriz Gomes Guimarães ,&nbsp;Béatrice Golinelli-Pimpaneau","doi":"10.1016/j.crstbi.2021.05.002","DOIUrl":"10.1016/j.crstbi.2021.05.002","url":null,"abstract":"<div><p>Single-wavelength anomalous dispersion (SAD)-phasing using sulfur as the unique anomalous scatterer is a powerful method to solve the phase problem in protein crystallography. However, it is not yet widely used by non-expert crystallographers. We report here the structure determination of the double stranded RNA binding domain of human dihydrouridine synthase using the sulfur-SAD method and highly redundant data collected at 1.8 ​Å (“off-edge”), at which the estimated overall anomalous signal was 1.08%. High multiplicity data were collected on a single crystal rotated along the ϕ or ω axis at different κ angles, with the primary beam intensity being attenuated from 50% to 95%, compared to data collection at 0.98 ​Å, to reduce radiation damage. <em>SHELXD</em> succeeded to locate 14 out 15 sulfur sites only using the data sets recorded with highest beam attenuation, which provided phases sufficient for structure solving. In an attempt to stimulate the use of sulfur-SAD phasing by a broader community of crystallographers, we describe our experimental strategy together with a compilation of previous successful cases, suggesting that sulfur-SAD phasing should be attempted for determining the <em>de novo</em> structure of any protein with average sulfur content diffracting better than 3 ​Å resolution.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.crstbi.2021.05.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39163170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Spatially restricted substrate-binding site of cortisol-synthesizing CYP11B1 limits multiple hydroxylations and hinders aldosterone synthesis 空间限制的皮质醇合成底物结合位点CYP11B1限制多次羟基化并阻碍醛固酮合成
IF 2.8
Current Research in Structural Biology Pub Date : 2021-01-01 DOI: 10.1016/j.crstbi.2021.08.001
Kuniaki Mukai , Hiroshi Sugimoto , Katsumasa Kamiya , Reiko Suzuki , Tomomi Matsuura , Takako Hishiki , Hideo Shimada , Yoshitsugu Shiro , Makoto Suematsu , Norio Kagawa
{"title":"Spatially restricted substrate-binding site of cortisol-synthesizing CYP11B1 limits multiple hydroxylations and hinders aldosterone synthesis","authors":"Kuniaki Mukai ,&nbsp;Hiroshi Sugimoto ,&nbsp;Katsumasa Kamiya ,&nbsp;Reiko Suzuki ,&nbsp;Tomomi Matsuura ,&nbsp;Takako Hishiki ,&nbsp;Hideo Shimada ,&nbsp;Yoshitsugu Shiro ,&nbsp;Makoto Suematsu ,&nbsp;Norio Kagawa","doi":"10.1016/j.crstbi.2021.08.001","DOIUrl":"10.1016/j.crstbi.2021.08.001","url":null,"abstract":"<div><p>Human cytochromes P450<sub>11β</sub> (CYP11B1) and P450<sub>aldo</sub> (CYP11B2) are monooxygenases that synthesize cortisol through steroid 11β-hydroxylation and aldosterone through a three-step process comprising 11β-hydroxylation and two 18-hydroxylations, respectively. CYP11B1 also catalyzes 18-monohydroxylation and 11β,18-dihydroxylation. To study the molecular basis of such catalytic divergence of the two enzymes, we examined a CYP11B1 mutant (Mt-CYP11B1) with amino acid replacements on the distal surface by determining the catalytic activities and crystal structure in the metyrapone-bound form at 1.4-Å resolution. Mt-CY11B1 retained both 11β-hydroxylase and 18-hydroxylase activities of the wild type (Wt-CYP11B1) but lacked 11β,18-dihydroxylase activity. Comparisons of the crystal structure of Mt-CYP11B1 to those of Wt-CYP11B1 and CYP11B2 that were already reported show that the mutation reduced the innermost space putatively surrounding the C3 side of substrate 11-deoxycorticosterone (DOC) bound to Wt-CYP11B1, while the corresponding space in CYP11B2 is enlarged markedly and accessible to bulk water through a channel. Molecular dynamics simulations of their DOC-bound forms supported the above findings and revealed that the enlarged space of CYP11B2 had a hydrogen bonding network involving water molecules that position DOC. Thus, upon positioning 11β-hydroxysteroid for 18-hydroxylation in their substrate-binding sites, steric hindrance could occur more strongly in Mt-CYP11B1 than in Wt-CYP11B1 but less in CYP11B2. Our investigation employing Mt-CYP11B1 sheds light on the divergence in structure and function between CYP11B1 and CYP11B2 and suggests that CYP11B1 with spatially-restricted substrate-binding site serves as 11β-hydroxylase, while CYP11B2 with spatially-extended substrate-binding site successively processes additional 18-hydroxylations to produce aldosterone.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.crstbi.2021.08.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39387459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Folded domain charge properties influence the conformational behavior of disordered tails 折叠畴电荷性质影响无序尾的构象行为
IF 2.8
Current Research in Structural Biology Pub Date : 2021-01-01 DOI: 10.1016/j.crstbi.2021.08.002
Ishan Taneja , Alex S. Holehouse
{"title":"Folded domain charge properties influence the conformational behavior of disordered tails","authors":"Ishan Taneja ,&nbsp;Alex S. Holehouse","doi":"10.1016/j.crstbi.2021.08.002","DOIUrl":"10.1016/j.crstbi.2021.08.002","url":null,"abstract":"<div><p>Intrinsically disordered proteins and protein regions (IDRs) make up around 30% of the human proteome where they play essential roles in dictating and regulating many core biological processes. While IDRs are often studied as isolated domains, in naturally occurring proteins most IDRs are found adjacent to folded domains, where they exist as either N- or C-terminal tails or as linkers connecting two folded domains. Prior work has shown that charge properties of IDRs can influence their conformational behavior, both in isolation and in the context of folded domains. In contrast, the converse scenario is less well-explored: how do the charge properties of folded domains influence IDR conformational behavior? To answer this question, we combined a large-scale structural bioinformatics analysis with all-atom implicit solvent simulations of both rationally designed and naturally occurring proteins. Our results reveal three key takeaways. Firstly, the relative position and accessibility of charged residues across the surface of a folded domain can dictate IDR conformational behavior, overriding expectations based on net surface charge properties. Secondly, naturally occurring proteins possess multiple charge patches that are physically accessible to local IDRs. Finally, even modest changes in the local electrostatic environment of a folded domain can substantially modulate IDR-folded domain interactions. Taken together, our results suggest that folded domain surfaces can act as local determinants of IDR conformational behavior.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.crstbi.2021.08.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39445424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 12
Role of actin cytoskeleton in the organization and function of ionotropic glutamate receptors 肌动蛋白细胞骨架在嗜离子谷氨酸受体的组织和功能中的作用
IF 2.8
Current Research in Structural Biology Pub Date : 2021-01-01 DOI: 10.1016/j.crstbi.2021.10.001
Priyanka Dutta , Pratibha Bharti , Janesh Kumar , Sankar Maiti
{"title":"Role of actin cytoskeleton in the organization and function of ionotropic glutamate receptors","authors":"Priyanka Dutta ,&nbsp;Pratibha Bharti ,&nbsp;Janesh Kumar ,&nbsp;Sankar Maiti","doi":"10.1016/j.crstbi.2021.10.001","DOIUrl":"10.1016/j.crstbi.2021.10.001","url":null,"abstract":"<div><p>Neural networks with precise connection are compulsory for learning and memory. Various cellular events occur during the genesis of dendritic spines to their maturation, synapse formation, stabilization of the synapse, and proper signal transmission. The cortical actin cytoskeleton and its multiple regulatory proteins are crucial for the above cellular events. The different types of ionotropic glutamate receptors (iGluRs) present on the postsynaptic density (PSD) are also essential for learning and memory. Interaction of the iGluRs in association of their auxiliary proteins with actin cytoskeleton regulated by actin-binding proteins (ABPs) are required for precise long-term potentiation (LTP) and long-term depression (LTD). There has been a quest to understand the mechanistic detail of synapse function involving these receptors with dynamic actin cytoskeleton. A major, emerging area of investigation is the relationship between ABPs and iGluRs in synapse development. In this review we have summarized the current understanding of iGluRs functioning with respect to the actin cytoskeleton, scaffolding proteins, and their regulators. The AMPA, NMDA, Delta and Kainate receptors need the stable underlying actin cytoskeleton to anchor through synaptic proteins for precise synapse formation. The different types of ABPs present in neurons play a critical role in dynamizing/stabilizing the actin cytoskeleton needed for iGluRs function.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/7e/13/main.PMC8569634.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39721762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Structure of the Mycobacterium tuberculosis cPknF and conformational changes induced in forkhead-associated regulatory domains 结核分枝杆菌cPknF的结构和叉头相关调控域诱导的构象变化
IF 2.8
Current Research in Structural Biology Pub Date : 2021-01-01 DOI: 10.1016/j.crstbi.2021.07.001
Sindy Cabarca , Maximilia Frazão de Souza , Andrew Albert de Oliveira , Gabriel S. Vignoli Muniz , M. Teresa Lamy , Caio Vinicius dos Reis , Jessica Takarada , Brian Effer , Lucas Santos Souza , Lilia Iriarte de la Torre , Rafael Couñago , Cristiano Luis Pinto Oliveira , Andrea Balan
{"title":"Structure of the Mycobacterium tuberculosis cPknF and conformational changes induced in forkhead-associated regulatory domains","authors":"Sindy Cabarca ,&nbsp;Maximilia Frazão de Souza ,&nbsp;Andrew Albert de Oliveira ,&nbsp;Gabriel S. Vignoli Muniz ,&nbsp;M. Teresa Lamy ,&nbsp;Caio Vinicius dos Reis ,&nbsp;Jessica Takarada ,&nbsp;Brian Effer ,&nbsp;Lucas Santos Souza ,&nbsp;Lilia Iriarte de la Torre ,&nbsp;Rafael Couñago ,&nbsp;Cristiano Luis Pinto Oliveira ,&nbsp;Andrea Balan","doi":"10.1016/j.crstbi.2021.07.001","DOIUrl":"10.1016/j.crstbi.2021.07.001","url":null,"abstract":"<div><p><em>Mycobacterium tuberculosis</em> (<em>Mtb</em>) has 11 Serine-Threonine Protein Kinases (STPK) that control numerous physiological processes, including cell growth, cell division, metabolic flow, and transcription. PknF is one of the 11 Mtb STPKs that has, among other substrates, two FHA domains (FHA-1 and FHA-2) of the ATP-Binding Cassette (ABC) transporter Rv1747. Phosphorylation in T152 and T210 located in a non-structured linker that connects Rv1747 FHA domains is considerate to be the regulatory mechanism of the transporter. In this work, we resolved the three-dimensional structure of the PknF catalytic domain (cPknF) in complex with the human kinase inhibitor IKK16. cPknF is conserved when compared to other STPKs but shows specific residues in the binding site where the inhibitor is positioned. In addition, using Small Angle X-Ray Scattering analysis we monitored the behavior of the wild type and three FHA-phosphomimetic mutants in solution, and measured the cPknF affinity for these domains. The kinase showed higher affinity for the non-phosphorylated wild type domain and preference for phosphorylation of T152 inducing the rapprochement of the domains and significant structural changes. The results shed some light on the process of regulating the transporter's activity by phosphorylation and arises important questions about evolution and importance of this mechanism for the bacillus.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.crstbi.2021.07.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39302817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
“Protein” no longer means what it used to "蛋白质"不再像以前那样有意义了
IF 2.8
Current Research in Structural Biology Pub Date : 2021-01-01 DOI: 10.1016/j.crstbi.2021.06.002
Gustavo Parisi , Nicolas Palopoli , Silvio C.E. Tosatto , María Silvina Fornasari , Peter Tompa
{"title":"“Protein” no longer means what it used to","authors":"Gustavo Parisi ,&nbsp;Nicolas Palopoli ,&nbsp;Silvio C.E. Tosatto ,&nbsp;María Silvina Fornasari ,&nbsp;Peter Tompa","doi":"10.1016/j.crstbi.2021.06.002","DOIUrl":"10.1016/j.crstbi.2021.06.002","url":null,"abstract":"<div><p>Every biologist knows that the word <em>protein</em> describes a group of macromolecules essential to sustain life on Earth. As biologists, we are invariably trained under a protein paradigm established since the early twentieth century. However, in recent years, the term <em>protein</em> unveiled itself as an euphemism to describe the overwhelming heterogeneity of these compounds. Most of our current studies are targeted on carefully selected subsets of proteins, but we tend to think and write about these as representative of the whole population. Here we discuss how seeking for universal definitions and general rules in any arbitrarily segmented study would be misleading about the conclusions. Of course, it is not our purpose to discourage the use of the word <em>protein</em>. Instead, we suggest to embrace the extended universe of proteins to reach a deeper understanding of their full potential, realizing that the term encompasses a group of molecules very heterogeneous in terms of size, shape, chemistry and functions, i.e. the term <em>protein</em> no longer means what it used to.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.crstbi.2021.06.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39221195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Current approaches to flexible loop modeling 柔性环建模的当前方法
IF 2.8
Current Research in Structural Biology Pub Date : 2021-01-01 DOI: 10.1016/j.crstbi.2021.07.002
Amélie Barozet , Pablo Chacón , Juan Cortés
{"title":"Current approaches to flexible loop modeling","authors":"Amélie Barozet ,&nbsp;Pablo Chacón ,&nbsp;Juan Cortés","doi":"10.1016/j.crstbi.2021.07.002","DOIUrl":"10.1016/j.crstbi.2021.07.002","url":null,"abstract":"<div><p>Loops are key components of protein structures, involved in many biological functions. Due to their conformational variability, the structural investigation of loops is a difficult topic, requiring a combination of experimental and computational methods. This paper provides a brief overview of current computational approaches to flexible loop modeling, and presents the main ingredients of the most standard protocols. Despite great progress in recent years, accurately modeling the conformational variability of long flexible loops remains a challenging problem. Future advances in this field will likely come from a tight coupling of experimental and computational techniques, which would enable a better understanding of the relationships between loop sequence, structural flexibility, and functional roles. <em>In fine</em>, accurate loop modeling will open the road to loop design problems of interest for applications in biomedicine and biotechnology.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.crstbi.2021.07.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39324312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 14
Peptide bond planarity constrains hydrogen bond geometry and influences secondary structure conformations 肽键的平面性限制了氢键的几何形状并影响了二级结构的构象
IF 2.8
Current Research in Structural Biology Pub Date : 2021-01-01 DOI: 10.1016/j.crstbi.2020.11.002
Kuan Pern Tan , Khushboo Singh , Anirban Hazra , M.S. Madhusudhan
{"title":"Peptide bond planarity constrains hydrogen bond geometry and influences secondary structure conformations","authors":"Kuan Pern Tan ,&nbsp;Khushboo Singh ,&nbsp;Anirban Hazra ,&nbsp;M.S. Madhusudhan","doi":"10.1016/j.crstbi.2020.11.002","DOIUrl":"10.1016/j.crstbi.2020.11.002","url":null,"abstract":"<div><p>An extensive database study of hydrogen bonds in different protein environments showed systematic variations in donor-acceptor-acceptor antecedent angle (<em>Ĥ</em>) and donor-acceptor distance. Protein environments were characterized by depth (distance of amino acids from bulk solvent), secondary structure, and whether the donor/acceptor belongs to the main chain (MC) or side chain (SC) of amino acids. The MC-MC hydrogen bonds (whether in secondary structures or not) have <em>Ĥ</em> angles tightly restricted to a value of around 155°, which was distinctly different from other <em>Ĥ</em> angles. Quantum chemical calculations attribute this characteristic MC-MC <em>Ĥ</em> angle to the nature of the electron density distribution around the planar peptide bond. Additional classical simulations suggest a causal link between MC-MC <em>Ĥ</em> angle and the conformation of secondary structures in proteins. We also showed that donor-acceptor distances are environment dependent, which has implications on protein stability. Our results redefine hydrogen bond geometries in proteins and suggest useful refinements to existing molecular mechanics force fields.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.crstbi.2020.11.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39302816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 11
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