scholarly journals Molecular recognition of M1-linked ubiquitin chains by native and phosphorylated UBAN domains

2019 ◽  
Author(s):  
Lina Herhaus ◽  
Henry van den Bedem ◽  
Sean Tang ◽  
Soichi Wakatsuki ◽  
Ivan Dikic ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Binding Sites ◽  
Coiled Coil ◽  
Domain Specificity ◽  
Binding Properties ◽  
Post Translational Modifications ◽  
Binding Characteristics ◽  
Binding Stoichiometry ◽  
Coil Structure ◽  
Concentration Dependency

AbstractAlthough the Ub-binding domain in ABIN proteins and NEMO (UBAN) is highly conserved, UBAN-containing proteins exhibit different Ub-binding properties, resulting in their diverse biological roles. Post-translational modifications further control UBAN domain specificity for poly-Ub chains. However, precisely, how the UBAN domain structurally confers such functional diversity remains poorly understood. Here we report crystal structures of ABIN-1 alone and in complex with one or two M1-linked di-Ub chains. ABIN-1 UBAN forms a homo-dimer that provides two symmetrical Ub-binding sites on either side of the coiled-coil structure. Moreover, crystal structures of ABIN1 UBAN in complex with di-Ub chains reveal a concentration-dependency of UBAN/di-Ub binding stoichiometry. Analysis of UBAN/M1-linked di-Ub binding characteristics indicates that phosphorylated S473 in OPTN and its corresponding phospho-mimetic residue in ABIN-1 (E484) are essential for high affinity interactions with M1-linked Ub chains. Also, a phospho-mimetic mutation of A303 in NEMO, corresponding to S473 of OPTN, increases binding affinity for M1-linked Ub chains. These findings are in line with the diverse physiological roles of UBAN domains, as phosphorylation of OPTN UBAN is required to enhance its binding to Ub during mitophagy.

Species differences between male rat and ram pituitary somatostatin receptors involved in the inhibition of growth hormone secretion

1997 ◽  
pp. 545-555 ◽  
Author(s):  
N Briard ◽  
A Dutour ◽  
J Epelbaum ◽  
N Sauze ◽  
A Slama ◽  
...  
Keyword(s):  
Binding Sites ◽  
Hormone Secretion ◽  
Somatostatin Receptors ◽  
Growth Hormone Secretion ◽  
Male Rat ◽  
Receptor Subtype ◽  
Binding Properties ◽  
Binding Characteristics ◽  
Gh Secretion ◽  
Inhibition Of Growth

The sheep is a valuable model in which to study GH neuroregulation as its pattern of GH secretion is very close to that in humans. Furthermore, important differences in somatostatin (SRIH) action between rats and sheep have been found previously. Our goal was to compare in male rat and ram pituitaries the binding characteristics of somatostatin receptors and the effect of SRIH and 17 analogues on GH release. Using radioautography, SRIH binding was seen to be evenly distributed over the anterior pituitary of both species. In the binding assay, binding sites were three times more concentrated in rats than in sheep. Important interspecies differences in the action of SRIH and its analogues were found: they inhibited GH at lower concentrations in rats than in sheep. Seven peptides displayed greater inhibitory ability in sheep than in rats while three were more potent in rats. Agonistic potencies to inhibit GH release in rats were correlated with somatostatin receptors subtype 2 (sst2) affinities. Our data confirm and extend the quantitative differences between rat and sheep in SRIH inhibitory action on GH secretion and confirm that ligand-binding properties of a given receptor subtype cannot be extrapolated across species.

scholarly journals Molecular architecture of a dynamin adaptor: implications for assembly of mitochondrial fission complexes

2010 ◽  
Vol 191 (6) ◽  
pp. 1127-1139 ◽  
Author(s):  
Sajjan Koirala ◽  
Huyen T. Bui ◽  
Heidi L. Schubert ◽  
Debra M. Eckert ◽  
Christopher P. Hill ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Crystal Structures ◽  
Binding Sites ◽  
Mitochondrial Fission ◽  
Coiled Coil ◽  
Adaptor Proteins ◽  
Molecular Architecture ◽  
Cellular Membranes ◽  
Membrane Scission ◽  
Antiparallel Coiled Coil

Recruitment and assembly of some dynamin-related guanosine triphosphatases depends on adaptor proteins restricted to distinct cellular membranes. The yeast Mdv1 adaptor localizes to mitochondria by binding to the membrane protein Fis1. Subsequent Mdv1 binding to the mitochondrial dynamin Dnm1 stimulates Dnm1 assembly into spirals, which encircle and divide the mitochondrial compartment. In this study, we report that dimeric Mdv1 is joined at its center by a 92-Å antiparallel coiled coil (CC). Modeling of the Fis1–Mdv1 complex using available crystal structures suggests that the Mdv1 CC lies parallel to the bilayer with N termini at opposite ends bound to Fis1 and C-terminal β-propeller domains (Dnm1-binding sites) extending into the cytoplasm. A CC length of appropriate length and sequence is necessary for optimal Mdv1 interaction with Fis1 and Dnm1 and is important for proper Dnm1 assembly before membrane scission. Our results provide a framework for understanding how adaptors act as scaffolds to orient and stabilize the assembly of dynamins on membranes.

scholarly journals Distinct effects of Q925 mutation on intracellular and extracellular Na+ and K+ binding to the Na+, K+-ATPase

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hang N. Nielsen ◽  
Kerri Spontarelli ◽  
Rikke Holm ◽  
Jens Peter Andersen ◽  
Anja P. Einholm ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Binding Sites ◽  
Functional Role ◽  
Transmembrane Helix ◽  
Binding Properties ◽  
Ion Translocation ◽  
Extracellular Side ◽  
Insight Into

Abstract Three Na+ sites are defined in the Na+-bound crystal structure of Na+, K+-ATPase. Sites I and II overlap with two K+ sites in the K+-bound structure, whereas site III is unique and Na+ specific. A glutamine in transmembrane helix M8 (Q925) appears from the crystal structures to coordinate Na+ at site III, but does not contribute to K+ coordination at sites I and II. Here we address the functional role of Q925 in the various conformational states of Na+, K+-ATPase by examining the mutants Q925A/G/E/N/L/I/Y. We characterized these mutants both enzymatically and electrophysiologically, thereby revealing their Na+ and K+ binding properties. Remarkably, Q925 substitutions had minor effects on Na+ binding from the intracellular side of the membrane – in fact, mutations Q925A and Q925G increased the apparent Na+ affinity – but caused dramatic reductions of the binding of K+ as well as Na+ from the extracellular side of the membrane. These results provide insight into the changes taking place in the Na+-binding sites, when they are transformed from intracellular- to extracellular-facing orientation in relation to the ion translocation process, and demonstrate the interaction between sites III and I and a possible gating function of Q925 in the release of Na+ at the extracellular side.

scholarly journals Routine phasing of coiled-coil protein crystal structures withAMPLE

IUCrJ ◽  
2015 ◽  
Vol 2 (2) ◽  
pp. 198-206 ◽  
Author(s):  
Jens M. H. Thomas ◽  
Ronan M. Keegan ◽  
Jaclyn Bibby ◽  
Martyn D. Winn ◽  
Olga Mayans ◽  
...  
Keyword(s):  
Ab Initio ◽  
Crystal Structures ◽  
Coiled Coil ◽  
Protein Crystal ◽  
Molecular Replacement ◽  
Search Models ◽  
Homologous Protein ◽  
Coil Structure ◽  
Convenient Route ◽  
Chain Lengths

Coiled-coil protein folds are among the most abundant in nature. These folds consist of long wound α-helices and are architecturally simple, but paradoxically their crystallographic structures are notoriously difficult to solve with molecular-replacement techniques. The programAMPLEcan solve crystal structures by molecular replacement usingab initiosearch models in the absence of an existent homologous protein structure.AMPLEhas been benchmarked on a large and diverse test set of coiled-coil crystal structures and has been found to solve 80% of all cases. Successes included structures with chain lengths of up to 253 residues and resolutions down to 2.9 Å, considerably extending the limits on size and resolution that are typically tractable byab initiomethodologies. The structures of two macromolecular complexes, one including DNA, were also successfully solved using their coiled-coil components. It is demonstrated that both theab initiomodelling and the use of ensemble search models contribute to the success ofAMPLEby comparison with phasing attempts using single structures or ideal polyalanine helices. These successes suggest that molecular replacement withAMPLEshould be the method of choice for the crystallographic elucidation of a coiled-coil structure. Furthermore,AMPLEmay be able to exploit the presence of a coiled coil in a complex to provide a convenient route for phasing.

scholarly journals Location of the head-tail junction of myosin.

1989 ◽  
Vol 108 (5) ◽  
pp. 1783-1789 ◽  
Author(s):  
D L Rimm ◽  
J H Sinard ◽  
T D Pollard
Keyword(s):  
Electron Microscopy ◽  
Amino Acids ◽  
Monoclonal Antibodies ◽  
Binding Sites ◽  
Myosin Ii ◽  
Coiled Coil ◽  
Heptad Repeat ◽  
Coil Structure ◽  
Hydrophobic Amino Acids ◽  
Lines Of Evidence

The tails of double-headed myosin molecules consist of an alpha-helical/coiled-coil structure composed of two identical polypeptides with a heptad repeat of hydrophobic amino acids that starts immediately after a conserved proline near position 847. Both muscle and nonmuscle myosins have this heptad repeat and it has been assumed that proline 847 is physically located at the head-tail junction. We present two lines of evidence that this assumption is incorrect. First, we localized the binding sites of several monoclonal antibodies on Acanthamoeba myosin-II both physically, by electron microscopy, and chemically, with a series of truncated myosin-II peptides produced in bacteria. These data indicate that the head-tail junction is located near residue 900. Second, we compared the lengths of two truncated recombinant myosin-II tails with native myosin-II. The distances from the NH2 termini to the tips of these short tails confirms the rise per residue (0.148 nm/residue) and establishes that the 86-nm tail of myosin-II must start near residue 900. We propose that the first 53 residues of heptad repeat of Acanthamoeba myosin-II and other myosins are located in the heads and the proteolytic separation of S-1 from rod occurs within the heads.

scholarly journals Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Seiya Watanabe ◽  
Yohsuke Murase ◽  
Yasunori Watanabe ◽  
Yasuhiro Sakurai ◽  
Kunihiko Tajima
Keyword(s):  
Molecular Evolution ◽  
Agrobacterium Tumefaciens ◽  
Crystal Structures ◽  
Epr Spectroscopy ◽  
Binding Sites ◽  
Active Sites ◽  
Type I ◽  
Type Ii ◽  
Thermococcus Kodakarensis ◽  
Evolutionary Scenario

AbstractAconitase superfamily members catalyze the homologous isomerization of specific substrates by sequential dehydration and hydration and contain a [4Fe-4S] cluster. However, monomeric and heterodimeric types of function unknown aconitase X (AcnX) have recently been characterized as a cis-3-hydroxy-L-proline dehydratase (AcnXType-I) and mevalonate 5-phosphate dehydratase (AcnXType-II), respectively. We herein elucidated the crystal structures of AcnXType-I from Agrobacterium tumefaciens (AtAcnX) and AcnXType-II from Thermococcus kodakarensis (TkAcnX) without a ligand and in complex with substrates. AtAcnX and TkAcnX contained the [2Fe-2S] and [3Fe-4S] clusters, respectively, conforming to UV and EPR spectroscopy analyses. The binding sites of the [Fe-S] cluster and substrate were clearlydifferent from those that were completely conserved in other aconitase enzymes; however, theoverall structural frameworks and locations of active sites were partially similar to each other.These results provide novel insights into the evolutionary scenario of the aconitase superfamilybased on the recruitment hypothesis.

scholarly journals Diversity in the structures and ligand-binding sites of nematode fatty acid and retinol-binding proteins revealed by Na-FAR-1 from Necator americanus

2015 ◽  
Vol 471 (3) ◽  
pp. 403-414 ◽  
Author(s):  
M. Florencia Rey-Burusco ◽  
Marina Ibáñez-Shimabukuro ◽  
Mads Gabrielsen ◽  
Gisela R. Franchini ◽  
Andrew J. Roe ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Ligand Binding ◽  
Tissue Distribution ◽  
Binding Sites ◽  
Binding Proteins ◽  
Retinol Binding Protein ◽  
Internal Cavity ◽  
Binding Characteristics ◽  
Necator Americanus ◽  
Ligand Binding Sites

Necator americanus fatty acid and retinol-binding protein-1 (Na-FAR-1) is an abundantly expressed FAR from a parasitic hookworm. The present work describes its tissue distribution, structure and ligand-binding characteristics and shows that Na-FAR-1 expands to transport multiple FA molecules in its internal cavity.

scholarly journals Crystal Structures of Ral-GppNHp and Ral-GDP Reveal Two Binding Sites that Are Also Present in Ras and Rap

Structure ◽  
2004 ◽  
Vol 12 (11) ◽  
pp. 2025-2036 ◽  
Author(s):  
Nathan I. Nicely ◽  
Justin Kosak ◽  
Vesna de Serrano ◽  
Carla Mattos
Keyword(s):  
Crystal Structures ◽  
Binding Sites

scholarly journals Binding Properties of a Dinuclear Zinc(II) Salen-Type Molecular Tweezer with a Flexible Spacer in the Formation of Lewis Acid-Base Adducts with Diamines

Inorganics ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 49
Author(s):  
Gabriella Munzi ◽  
Giuseppe Consiglio ◽  
Salvatore Failla ◽  
Santo Di Bella
Keyword(s):  
Lewis Acid ◽  
Degrees Of Freedom ◽  
Binding Constants ◽  
Molecular Structures ◽  
Acid Base ◽  
Binding Properties ◽  
Binding Characteristics ◽  
Fluorescence Studies ◽  
Flexible Spacer ◽  
Molecular Tweezer

In this paper we report the binding properties, by combined 1H NMR, optical absorption, and fluorescence studies, of a molecular tweezer composed of two Zn(salen)-type Schiff-base units connected by a flexible spacer, towards a series of ditopic diamines having a strong Lewis basicity, with different chain length and rigidity. Except for the 1,2-diaminoethane, in all other cases the formation of stable 1:1 Lewis acid-base adducts with large binding constants is demonstrated. For α,ω-aliphatic diamines, binding constants progressively increase with the increasing length of the alkyl chain, thanks to the flexible nature of the spacer and the parallel decreased conformational strain upon binding. Stable adducts are also found even for short diamines with rigid molecular structures. Given their preorganized structure, these latter species are not subjected to loss of degrees of freedom. The binding characteristics of the tweezer have been exploited for the colorimetric and fluorometric selective and sensitive detection of piperazine.

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