scholarly journals Structural basis for client recognition and activity of Hsp40 chaperones

Science ◽  
2019 ◽  
Vol 365 (6459) ◽  
pp. 1313-1319 ◽  
Author(s):  
Yajun Jiang ◽  
Paolo Rossi ◽  
Charalampos G. Kalodimos
Keyword(s):  
Binding Sites ◽  
Solution Structure ◽  
Structural Basis ◽  
Resonance Spectroscopy ◽  
Dynamic Features ◽  
Atomic Structures ◽  
Binding Domains ◽  
Wide Range ◽  
Distinct Sequence ◽  
And Function

Hsp70 and Hsp40 chaperones work synergistically in a wide range of biological processes including protein synthesis, membrane translocation, and folding. We used nuclear magnetic resonance spectroscopy to determine the solution structure and dynamic features of an Hsp40 in complex with an unfolded client protein. Atomic structures of the various binding sites in the client complexed to the binding domains of the Hsp40 reveal the recognition pattern. Hsp40 engages the client in a highly dynamic fashion using a multivalent binding mechanism that alters the folding properties of the client. Different Hsp40 family members have different numbers of client-binding sites with distinct sequence selectivity, providing additional mechanisms for activity regulation and function modification. Hsp70 binding to Hsp40 displaces the unfolded client. The activity of Hsp40 is altered in its complex with Hsp70, further regulating client binding and release.

scholarly journals The solution structure of pGolemi, a high affinity Mena EVH1 binding miniature protein, suggests explanations for paralog-specific binding to Ena/VASP homology (EVH) 1 domains

2009 ◽  
Vol 390 (5/6) ◽  
Author(s):  
Nina M. Link ◽  
Cornelia Hunke ◽  
Jonathan W. Mueller ◽  
Jutta Eichler ◽  
Peter Bayer
Keyword(s):  
Solution Structure ◽  
Specific Binding ◽  
Transmembrane Protein ◽  
Structural Data ◽  
Adaptor Proteins ◽  
Axonal Guidance ◽  
High Affinity ◽  
Binding Domains ◽  
Wide Range ◽  
Pancreatic Peptide

Abstract Ena/VASP homology 1 (EVH1) domains are polyproline binding domains that are present in a wide range of adaptor proteins, among them Ena/VASP proteins involved in actin remodeling and axonal guidance. The interaction of ActA, a transmembrane protein from the food-borne pathogen Listeria monocytogenes, with EVH1 domains has been shown to be crucial for recruitment of the host's actin skeleton and, as a consequence, for the infectivity of this bacterium. We present the structure of a synthetic high-affinity Mena EVH1 ligand, pGolemi, capable of paralog-specific binding, solved by NMR spectroscopy. This peptide shares the common pancreatic peptide fold with its scaffold, avian pancreatic peptide, but shows pivotal differences in the amino-terminus. The interplay of spatial fixation and flexibility appears to be the reason for its high affinity towards Mena EVH1. Combined with earlier investigations, our structural data shed light on the specificity determinants of pGolemi and the importance of additional binding epitopes around the residues Thr74 and Phe32 on EVH1 domains regulating paralog specificity. Our results are expected to facilitate the design of other high-affinity, paralog-specific EVH1 domain ligands, and serve as a fundament for the investigation of the molecular mode of action of EVH1 domains.

scholarly journals Design principles of hair-like structures as biological machines

2018 ◽  
Vol 15 (142) ◽  
pp. 20180206 ◽  
Author(s):  
Madeleine Seale ◽  
Cathal Cummins ◽  
Ignazio Maria Viola ◽  
Enrico Mastropaolo ◽  
Naomi Nakayama
Keyword(s):  
Mechanical Properties ◽  
Surface Area ◽  
Large Surface Area ◽  
Structural Basis ◽  
Basic Design ◽  
Form And Function ◽  
Mechanical Unit ◽  
Wide Range ◽  
Range Of Functions ◽  
And Function

Hair-like structures are prevalent throughout biology and frequently act to sense or alter interactions with an organism's environment. The overall shape of a hair is simple: a long, filamentous object that protrudes from the surface of an organism. This basic design, however, can confer a wide range of functions, owing largely to the flexibility and large surface area that it usually possesses. From this simple structural basis, small changes in geometry, such as diameter, curvature and inter-hair spacing, can have considerable effects on mechanical properties, allowing functions such as mechanosensing, attachment, movement and protection. Here, we explore how passive features of hair-like structures, both individually and within arrays, enable diverse functions across biology. Understanding the relationships between form and function can provide biologists with an appreciation for the constraints and possibilities on hair-like structures. Additionally, such structures have already been used in biomimetic engineering with applications in sensing, water capture and adhesion. By examining hairs as a functional mechanical unit, geometry and arrangement can be rationally designed to generate new engineering devices and ideas.

scholarly journals Structure-Based Functional Analysis of a Hormone Belonging to an Ecdysozoan Peptide Superfamily: Revelation of a Common Molecular Architecture and Residues Possibly for Receptor Interaction

2021 ◽  
Vol 22 (20) ◽  
pp. 11142
Author(s):  
Yun-Ru Chen ◽  
Nai-Wan Hsiao ◽  
Yi-Zong Lee ◽  
Shiau-Shan Huang ◽  
Chih-Chun Chang ◽  
...  
Keyword(s):  
Atpase Activity ◽  
Receptor Binding ◽  
Binding Sites ◽  
Disulfide Bonds ◽  
Solution Structure ◽  
Receptor Interaction ◽  
Resonance Spectroscopy ◽  
Molecular Architecture ◽  
Major Factors

A neuropeptide (Sco-CHH-L), belonging to the crustacean hyperglycemic hormone (CHH) superfamily and preferentially expressed in the pericardial organs (POs) of the mud crab Scylla olivacea, was functionally and structurally studied. Its expression levels were significantly higher than the alternative splice form (Sco-CHH) in the POs, and increased significantly after the animals were subjected to a hypo-osmotic stress. Sco-CHH-L, but not Sco-CHH, significantly stimulated in vitro the Na+, K+-ATPase activity in the posterior (6th) gills. Furthermore, the solution structure of Sco-CHH-L was resolved using nuclear magnetic resonance spectroscopy, revealing that it has an N-terminal tail, three α-helices (α2, Gly9−Asn28; α3, His34−Gly38; and α5, Glu62−Arg72), and a π-helix (π4, Cys43−Tyr54), and is structurally constrained by a pattern of disulfide bonds (Cys7–Cys43, Cys23–Cys39, and Cys26–Cys52), which is characteristic of the CHH superfamily-peptides. Sco-CHH-L is topologically most similar to the molt-inhibiting hormone from the Kuruma prawn Marsupenaeus japonicus with a backbone root-mean-square-deviation of 3.12 Å. Ten residues of Sco-CHH-L were chosen for alanine-substitution, and the resulting mutants were functionally tested using the gill Na+, K+-ATPase activity assay, showing that the functionally important residues (I2, F3, E45, D69, I71, and G73) are located at either end of the sequence, which are sterically close to each other and presumably constitute the receptor binding sites. Sco-CHH-L was compared with other members of the superfamily, revealing a folding pattern, which is suggested to be common for the crustacean members of the superfamily, with the properties of the residues constituting the presumed receptor binding sites being the major factors dictating the ligand–receptor binding specificity.

scholarly journals LimF is a versatile prenyltransferase catalyzing histidine-C-geranylation on diverse nonnatural substrates

2021 ◽  
Author(s):  
Yuchen Zhang ◽  
Keisuke Hamada ◽  
Dinh Thanh Nguyen ◽  
Sumika Inoue ◽  
Masayuki Satake ◽  
...  
Keyword(s):  
Crystallographic Analysis ◽  
Structure And Function ◽  
Bioactive Molecules ◽  
Structural Basis ◽  
Peptide Substrate ◽  
Site Specific ◽  
Native Peptide ◽  
Wide Range ◽  
Secondary Function ◽  
And Function

Prenylation plays an important role in diversifying structure and function of secondary metabolites. Although several cyanobactin prenyltransferases have been characterized, their modes of action are mainly limited to the modification of electron-rich hetero atoms. Here we report a unique prenyltransferase originating from Limnothrix sp. CACIAM 69d, referred to as LimF, which catalyzes an unprecedented His-C-geranylation. Interestingly, LimF executes the geranylation on not only its native peptide substrate but also a wide range of exotic peptides, including thioether-closed macrocycles. We have also serendipitously uncovered an ability of Tyr-O-geranylation as the secondary function of LimF, indicating it is an unusual bifunctional prenyltransferase. Crystallographic analysis of LimF complexed with a pentapeptide substrate and a prenyl donor analog provides structural basis for its unique His recognition and its bifunctionality. Lastly, we show the LimF’s prenylation ability on various bioactive molecules containing an imidazole group, highlighting its potential as a versatile biocatalyst for site-specific geranylation.

scholarly journals SuhB is an integral part of the ribosomal antitermination complex and interacts with NusA

2019 ◽  
Vol 47 (12) ◽  
pp. 6504-6518 ◽  
Author(s):  
Benjamin R Dudenhoeffer ◽  
Hans Schneider ◽  
Kristian Schweimer ◽  
Stefan H Knauer
Keyword(s):  
Ribosomal Rna ◽  
Binding Sites ◽  
Structural Basis ◽  
Resonance Spectroscopy ◽  
Inositol Monophosphatase ◽  
Central Process ◽  
Α Subunit ◽  
Terminal Domain ◽  
N Utilization ◽  
Efficient Expression

AbstractThe synthesis of ribosomal RNA (rRNA) is a tightly regulated central process in all cells. In bacteria efficient expression of all seven rRNA operons relies on the suppression of termination signals (antitermination) and the proper maturation of the synthesized rRNA. These processes depend on N-utilization substance (Nus) factors A, B, E and G, as well as ribosomal protein S4 and inositol monophosphatase SuhB, but their structural basis is only poorly understood. Combining nuclear magnetic resonance spectroscopy and biochemical approaches we show that Escherichia coli SuhB can be integrated into a Nus factor-, and optionally S4-, containing antitermination complex halted at a ribosomal antitermination signal. We further demonstrate that SuhB specifically binds to the acidic repeat 2 (AR2) domain of the multi-domain protein NusA, an interaction that may be involved in antitermination or posttranscriptional processes. Moreover, we show that SuhB interacts with RNA and weakly associates with RNA polymerase (RNAP). We finally present evidence that SuhB, the C-terminal domain of the RNAP α-subunit, and the N-terminal domain of NusG share binding sites on NusA-AR2 and that all three can release autoinhibition of NusA, indicating that NusA-AR2 serves as versatile recruitment platform for various factors in transcription regulation.

MONOCLONAL ANTIBODY (ANTI-2B6D4) TO PLASMA FIBRONECTIN INHIBITS COLLAGEN AND THROMBIN INDUCED AGGREGATION OF WASHED PLATELETS

1987 ◽  
Author(s):  
D A Kenneally ◽  
P J Thurlow ◽  
J M Cornellan
Keyword(s):  
Monoclonal Antibody ◽  
Platelet Aggregation ◽  
Binding Sites ◽  
Low Dose ◽  
Solid Phase ◽  
Functional Studies ◽  
Binding Domains ◽  
Wide Range ◽  
Platelet Binding ◽  
Induced Aggregation

Fibronectins(Fns) constitute a family of large glycoproteins which are known to bind to a wide range of biological molecules eg.collagen, gelatin, fibrin, heparin and DNA,and to many cells including platelets via discrete structural domains. A murine monoclonal antibody (anti-2B6D4) produced by imnunizing BALB/c mice with plasma fn, was used to study the structure and function of fn and its platelet interaction Anti-2B6D4 reacted specifically with plasma fn was unreactive with FVIII/vWF,BTG,PF4 collagen and fibrinogen nor was it reactive with platelets (unstiraulated), human PBLs or a range of tumour cell lines. Iirmuno-blotting studies( 8% SDS-PAGE) using thermolysin-digested plasma fn with anti-2B6D4 indicated that the 2B6D4 epitope was present on only 2 of the 7 fragments detected by Indian ink. The 2 fragments had an Mr of 145 and 155 K dal tons and have been reported to each contain domains which bind cells, DNA and heparin. These fragments were studied further by examining the effect of anti-2B6D4 (Fabs) on the binding of 125I-fn to thrombin-stimulated platelets and demonstrated that anti-2B6D4 binding was inhibited by 50% thus implicating the 2B6D4 epitope as a platelet binding site within the two cell binding domains. Competitive binding analysis of 125I-fn to solid-phase macromolecules i.e.collagen, gelatin, fibrin, heparin, DNA and Con A demonstrated that anti-2B6D4 (Fabs) inhibited the binding of fn to DNA by 50%,but not to the other macromolecules. Therefore, either the DNA and platelet binding sites are shared or the inhibition is due to steric hindrance. However, as Fab fragments of anti-2B6D4 were used, it is more likely that the binding sites are shared. Functional studies were performed to investigate the role of 2B6D4 in platelet-platelet interaction. Anti-2B6D4 totally blocked the aggregation of washed platelets stimulated by low dose collagen (1.6ug/ml) and thrombin (0.05U/ml), partially inhibited arachidonic acid (250ugs/ml) induced platelet aggregation and had no effect on aggregation induced by A23187 (30uM). One other report had demonstrated that fn is a requirement for A23187 and low dose thrombin induced platelet aggregation. We conclude that fn plays an essential role in platelet aggregation induced by low dose collagen and thrombin.

Mercury(I) chemistry. Part I. Complexes of the mercurous ion with some arenes

1976 ◽  
Vol 54 (1) ◽  
pp. 166-176 ◽  
Author(s):  
Philip A. W. Dean ◽  
David G. Ibbott ◽  
J. B. Stothers
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Sulfur Dioxide ◽  
Binding Sites ◽  
Chemical Shifts ◽  
Formation Constants ◽  
Resonance Spectroscopy ◽  
Arene Complexes ◽  
Liquid Sulfur ◽  
Wide Range ◽  
Mercurous Ion

A wide range of arene complexes of the mercurous ion has been prepared from mercurous hexafluoroarsenate and the appropriate arene in liquid sulfur dioxide. Raman spectroscopy confirmed the integrity of the dimeric Hg22+ cation in these complexes. 13C nuclear magnetic resonance spectroscopy showed that Hg22+–arene complexes exist in sulfur dioxide solution. The 13C data allowed the estimation of formation constants for the hexamethylbenzene, p-xylene, and p-dichlorobenzene complexes together with the 13C chemical shifts for the bound substrates in these cases. The 13C chemical shift changes (relative to the free substrate) on addition of Hg22+ to SO2 solutions of various methylated benzenes are compared with those occurring on complexation of the same arenes by the argentous ion and the Cr(CO)3 moiety. In mercurous ion–arene complexes, it is concluded that the cation is involved in a localized interaction with the arene and that there are preferred binding sites. These sites may be identified by the complexation shifts for the Ag+– and Hg22+–arene complexes.

scholarly journals Structure-based functional study of a peptide of an ecdysozoan superfamily: reveling a common molecular architecture and receptor-interacting residues

2020 ◽  
Author(s):  
Yun-Ru Chen ◽  
Nai-Wan Hsiao ◽  
Shiau-Shan Huang ◽  
Chih-Chun Chang ◽  
Yi-Zong Lee ◽  
...  
Keyword(s):  
Atpase Activity ◽  
Receptor Binding ◽  
Binding Sites ◽  
Disulfide Bonds ◽  
Solution Structure ◽  
Functional Study ◽  
Resonance Spectroscopy ◽  
Molecular Architecture ◽  
Major Factors

ABSTRACTA neuropeptide (Sco-CHH-L), belonging to the crustacean hyperglycemic hormone (CHH) superfamily and preferentially expressed in the pericardial organs (POs) of the mud crab Scylla olivacea, was functionally and structurally studied. Its expression levels were significantly higher than the alternative splice form (Sco-CHH) in the POs and increased significantly after animals were subjected to a hypo-osmotic stress. Sco-CHH-L, but not Sco-CHH, significantly stimulated in vitro the Na+, K+-ATPase activity in the posterior (6th) gills. Furthermore, solution structure of Sco-CHH-L was resolved using nuclear magnetic resonance spectroscopy revealing that it has an N-terminal tail, three α-helices (α2, Gly9−Asn28; α3, His34−Gly38; α5, Glu62−Arg72), and a π-helix (π4, Cys43−Tyr53) and is structurally constrained by a pattern of disulfide bonds (Cys7-Cys43, Cys23-Cys39, Cys26-Cys52), which is characteristic of the CHH superfamily-peptides. Sco-CHH-L is topologically most similar to the molt-inhibiting hormone from the Kuruma prawn Marsupenaeus japonicus with a backbone root-mean-square-deviation of 3.12 Å. Ten residues of Sco-CHH-L were chosen for alanine-substituted and the resulting mutants were functionally tested using the gill Na+, K+-ATPase activity assay, showing that the functionally important residues (I2, F3, E45, D69, I71, G73) are located at either end of the sequence, which are sterically close to each other and presumably constitutes the receptor binding sites. Sco-CHH-L was compared with other members of the superfamily revealing a molecular architecture, which is suggested to be common for the crustacean members of the superfamily, with the properties of the residues constituting the presumed receptor binding sites being the major factors dictating the ligand-receptor binding specificity.

Solution structure of TbCentrin4 from Trypanosoma brucei and its interactions with Ca2+ and other centrins

2018 ◽  
Vol 475 (23) ◽  
pp. 3763-3778 ◽  
Author(s):  
Fangzhen Shan ◽  
Kaiqin Ye ◽  
Jiahai Zhang ◽  
Shanhui Liao ◽  
Xuecheng Zhang ◽  
...  
Keyword(s):  
Trypanosoma Brucei ◽  
Calcium Binding ◽  
Solution Structure ◽  
Structural Basis ◽  
Titration Calorimetry ◽  
Resonance Spectroscopy ◽  
Basal Bodies ◽  
High Concentration ◽  
Ef Hand

Centrin is a conserved calcium-binding protein that plays an important role in diverse cellular biological processes such as ciliogenesis, gene expression, DNA repair and signal transduction. In Trypanosoma brucei, TbCentrin4 is mainly localized in basal bodies and bi-lobe structure, and is involved in the processes coordinating karyokinesis and cytokinesis. In the present study, we solved the solution structure of TbCentrin4 using NMR (nuclear magnetic resonance) spectroscopy. TbCentrin4 contains four EF-hand motifs consisting of eight α-helices. Isothermal titration calorimetry experiment showed that TbCentrin4 has a strong Ca2+ binding ability. NMR chemical shift perturbation indicated that TbCentrin4 binds to Ca2+ through its C-terminal domain composed of EF-hand 3 and 4. Meanwhile, we revealed that TbCentrin4 undergoes a conformational change and self-assembly induced by high concentration of Ca2+. Intriguingly, localization of TbCentrin4 was dispersed or disappeared from basal bodies and the bi-lobe structure when the cells were treated with Ca2+in vivo, implying the influence of Ca2+ on the cellular functions of TbCentrin4. Besides, we observed the interactions between TbCentrin4 and other Tbcentrins and revealed that the interactions are Ca2+ dependent. Our findings provide a structural basis for better understanding the biological functions of TbCentrin4 in the relevant cellular processes.

scholarly journals Probing the Dynamic Distribution of Bound States for Methylcytosine-binding Domains on DNA

2013 ◽  
Vol 289 (3) ◽  
pp. 1294-1302 ◽  
Author(s):  
Jason M. Cramer ◽  
J. Neel Scarsdale ◽  
Ninad M. Walavalkar ◽  
William A. Buchwald ◽  
Gordon D. Ginder ◽  
...  
Keyword(s):  
Bound States ◽  
Solution Structure ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Structural Basis ◽  
Relative Distribution ◽  
Binding Modes ◽  
Nonspecific Binding ◽  
Methylated Dna ◽  
Binding Domains

Although highly homologous to other methylcytosine-binding domain (MBD) proteins, MBD3 does not selectively bind methylated DNA, and thus the functional role of MBD3 remains in question. To explore the structural basis of its binding properties and potential function, we characterized the solution structure and binding distribution of the MBD3 MBD on hydroxymethylated, methylated, and unmethylated DNA. The overall fold of this domain is very similar to other MBDs, yet a key loop involved in DNA binding is more disordered than previously observed. Specific recognition of methylated DNA constrains the structure of this loop and results in large chemical shift changes in NMR spectra. Based on these spectral changes, we show that MBD3 preferentially localizes to methylated and, to a lesser degree, unmethylated cytosine-guanosine dinucleotides (CpGs), yet does not distinguish between hydroxymethylated and unmethylated sites. Measuring residual dipolar couplings for the different bound states clearly shows that the MBD3 structure does not change between methylation-specific and nonspecific binding modes. Furthermore, residual dipolar couplings measured for MBD3 bound to methylated DNA can be described by a linear combination of those for the methylation and nonspecific binding modes, confirming the preferential localization to methylated sites. The highly homologous MBD2 protein shows similar but much stronger localization to methylated as well as unmethylated CpGs. Together, these data establish the structural basis for the relative distribution of MBD2 and MBD3 on genomic DNA and their observed occupancy at active and inactive CpG-rich promoters.

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