scholarly journals Self-association configures the NAD+-binding site of plant NLR TIR domains

2021 ◽  
Author(s):  
Hayden Burdett ◽  
Xiahao Hu ◽  
Maxwell X Rank ◽  
Natsumi Maruta ◽  
Bostjan Kobe
Keyword(s):  
Binding Site ◽  
Conformational Changes ◽  
Active Site ◽  
Binding Sites ◽  
Molecular Mechanisms ◽  
Structural Features ◽  
Active Conformation ◽  
Effector Triggered Immunity ◽  
Self Association ◽  
Tir Domains

TIR domains are signalling domains present in plant nucleotide-binding leucine-rich repeat receptors (NLRs), with key roles in plant innate immunity. They are required for the induction of a hypersensitive response (HR) in effector-triggered immunity, but the mechanism by which this occurs is not yet fully understood. It has been recently shown that the TIR domains from several plant NLRs possess NADase activity. The oligomeric structure of TIR-containing NLRs ROQ1 and RPP1 reveals how the TIR domains arrange into an active conformation, but low resolution around the NAD+ binding sites leaves questions unanswered about the molecular mechanisms linking self-association and NADase activity. In this study, a number of crystal structures of the TIR domain from the grapevine NLR RUN1 reveal how self-association and enzymatic activity may be linked. Structural features previously proposed to play roles involve the ″AE interface″ (mediated by helices A and E), the ″BB-loop″ (connecting β-strand B and helix B in the structure), and the ″BE interface″ (mediated by the BB-loop from one TIR and the ″DE surface″ of another). We demonstrate that self-association through the AE interface induces conformational changes in the NAD+-binding site, shifting the BB-loop away from the catalytic site and allowing NAD+ to access the active site. We propose that an intact ″DE surface″ is necessary for production of the signalling product (variant cyclic ADPR), as it constitutes part of the active site. Addition of NAD+ or NADP+ is not sufficient to induce self-association, suggesting that NAD+ binding occurs after TIR self-association. Our study identifies a mechanistic link between TIR self-association and NADase activity.

Molecular mechanisms of initiation of fibrinolysis by fibrin

2003 ◽  
Vol 89 (03) ◽  
pp. 409-419 ◽  
Author(s):  
Willem Nieuwenhuizen ◽  
Leonid Medved
Keyword(s):  
Binding Site ◽  
Conformational Changes ◽  
Binding Sites ◽  
Molecular Mechanisms ◽  
Intramolecular Interaction ◽  
Affinity Binding ◽  
Fibrin Deposition ◽  
High Affinity ◽  
Physiological Processes ◽  
D Region

SummaryFibrinogen is rather inert in the circulation, however, after conversion into fibrin it participates in various physiological processes including fibrinolysis. Initiation of fibrinolysis occurs through a number of orchestrated interactions between fibrin, plasminogen and its activator tPA which result in generation of plasmin. Numerous studies localized a set of specific low affinity tPA- and plasminogen-binding sites in each D region of fibrin(ogen). The tPA-binding site includes residues γ312-324 and the plasminogen-binding site includes residues Aα148-160; they bind tPA and plasminogen with a Kd of about 1 μM. Another set of high affinity tPA- and plasminogen-binding sites (Kds = 16-33 nM) was identified in the compact portion of each fibrin(ogen) αC-domain within residues Aα392-610. All these sites are cryptic in fibrinogen and become exposed in fibrin. Recent studies with recombinant and proteolytic fibrin(ogen) fragments clarified the molecular mechanisms by which these sites become exposed. Namely, upon fibrin assembly, the interaction between the D and E regions causes conformational changes in the former that expose the low affinity binding sites. The exposure of the high affinity binding sites in the αC-domains is connected most probably with their switch from an intramolecular interaction in fibrinogen to an intermolecular one in fibrin. These mechanisms serve to minimize degradation of circulating fibrinogen and confine fibrinolysis to places of fibrin deposition.

scholarly journals Positive co-operative binding at two weak lysine-binding sites governs the Glu-plasminogen conformational change

1992 ◽  
Vol 285 (2) ◽  
pp. 419-425 ◽  
Author(s):  
U Christensen ◽  
L Mølgaard
Keyword(s):  
Ligand Binding ◽  
Binding Site ◽  
Conformational Change ◽  
Conformational Changes ◽  
Binding Sites ◽  
High Specificity ◽  
Stopped Flow ◽  
Protein Fluorescence ◽  
Lysine Residues ◽  
Kinetics Of

The kinetics of a series of Glu-plasminogen ligand-binding processes were investigated at pH 7.8 and 25 degrees C (in 0.1 M-NaCl). The ligands include compounds analogous to C-terminal lysine residues and to normal lysine residues. Changes of the Glu-plasminogen protein fluorescence were measured in a stopped-flow instrument as a function of time after rapid mixing of Glu-plasminogen and ligand at various concentrations. Large positive fluorescence changes (approximately 10%) accompany the ligand-induced conformational changes of Glu-plasminogen resulting from binding at weak lysine-binding sites. Detailed studies of the concentration-dependencies of the equilibrium signals and the rate constants of the process induced by various ligands showed the conformational change to involve two sites in a concerted positive co-operative process with three steps: (i) binding of a ligand at a very weak lysine-binding site that preferentially, but not exclusively, binds C-terminal-type lysine ligands, (ii) the rate-determining actual-conformational-change step and (iii) binding of one more lysine ligand at a second weak lysine-binding site that then binds the ligand more tightly. Further, totally independent initial small negative fluorescence changes (approximately 2-4%) corresponding to binding at the strong lysine-binding site of kringle 1 [Sottrup-Jensen, Claeys, Zajdel, Petersen & Magnusson (1978) Prog. Chem. Fibrinolysis Thrombolysis 3, 191-209] were observed for the C-terminal-type ligands. The finding that the conformational change in Glu-plasminogen involves two weak lysine-binding sites indicates that the effect cannot be assigned to any single kringle and that the problem of whether kringle 4 or kringle 5 is responsible for the process resolves itself. Probably kringle 4 and 5 are both participating. The involvement of two lysine binding-sites further makes the high specificity of Glu-plasminogen effectors more conceivable.

scholarly journals Computational Analysis of the Soluble Form of the Intracellular Chloride Ion Channel Protein CLIC1

2013 ◽  
Vol 2013 ◽  
pp. 1-14 ◽  
Author(s):  
Peter M. Jones ◽  
Paul M. G. Curmi ◽  
Stella M. Valenzuela ◽  
Anthony M. George
Keyword(s):  
Ion Channel ◽  
Binding Site ◽  
Conformational Changes ◽  
Active Site ◽  
Bound States ◽  
Covalent Binding ◽  
Chloride Ion ◽  
Soluble Form ◽  
Active Site Cysteine ◽  
Dynamics Simulations

The chloride intracellular channel (CLIC) family of proteins has the remarkable property of maintaining both a soluble form and an integral membrane form acting as an ion channel. The soluble form is structurally related to the glutathione-S-transferase family, and CLIC can covalently bind glutathione via an active site cysteine. We report approximately 0.6 μs of molecular dynamics simulations, encompassing the three possible ligand-bound states of CLIC1, using the structure of GSH-bound human CLIC1. Noncovalently bound GSH was rapidly released from the protein, whereas the covalently ligand-bound protein remained close to the starting structure over 0.25 μs of simulation. In the unliganded state, conformational changes in the vicinity of the glutathione-binding site resulted in reduced reactivity of the active site thiol. Elastic network analysis indicated that the changes in the unliganded state are intrinsic to the protein architecture and likely represent functional transitions. Overall, our results are consistent with a model of CLIC function in which covalent binding of glutathione does not occur spontaneously but requires interaction with another protein to stabilise the GSH binding site and/or transfer of the ligand. The results do not indicate how CLIC1 undergoes a radical conformational change to form a transmembrane chloride channel but further elucidate the mechanism by which CLICs are redox controlled.

Circulating IgG-LD complex, dissociable by addition of NAD+.

1982 ◽  
Vol 28 (1) ◽  
pp. 236-239 ◽  
Author(s):  
F Gorus ◽  
W Aelbrecht ◽  
B Van Camp
Keyword(s):  
Lactate Dehydrogenase ◽  
Autoimmune Disease ◽  
Complex Formation ◽  
Affinity Chromatography ◽  
Conformational Changes ◽  
Active Site ◽  
Nicotinamide Adenine Dinucleotide ◽  
Binding Sites ◽  
Gel Filtration ◽  
Binding Studies

Abstract Macromolecular LD (lactate dehydrogenase, EC 1.1.1.27) was present in the serum of a patient suffering from idiopathic fibrosis of the lung and presenting signs of autoimmune disease. By using gel filtration and affinity chromatography techniques, the vast majority of the patient's serum LD activity was shown to consist of LD-IgG complexes, which dissociated in the presence of added nicotinamide adenine dinucleotide (NAD+). Binding studies with tritiated NAD+ indicated that complex formation was not ascribable to a lack of circulating cofactor. The most likely explanation for the complex formation was the existence of LD binding sites on IgG molecules. The disruption of the complex by NAD+ might be explained by a competition between IgG molecules and NAD+ for the LD active site or by conformational changes induced in the LD molecules on binding of NAD+.

scholarly journals The genome of a Bacteroidetes inhabitant of the human gut encodes a structurally distinct enoyl-acyl carrier protein reductase (FabI)

2020 ◽  
Vol 295 (22) ◽  
pp. 7635-7652
Author(s):  
Christopher D. Radka ◽  
Matthew W. Frank ◽  
Jiangwei Yao ◽  
Jayaraman Seetharaman ◽  
Darcie J. Miller ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Change ◽  
Conformational Changes ◽  
Active Site ◽  
Acyl Carrier Protein ◽  
Acid Synthesis ◽  
Binding Pocket ◽  
Structural Features ◽  
Antibacterial Drug ◽  
Carrier Protein

Enoyl-acyl carrier protein reductase (FabI) catalyzes a rate-controlling step in bacterial fatty-acid synthesis and is a target for antibacterial drug development. A phylogenetic analysis shows that FabIs fall into four divergent clades. Members of clades 1–3 have been structurally and biochemically characterized, but the fourth clade, found in members of phylum Bacteroidetes, is uncharacterized. Here, we identified the unique structure and conformational changes that distinguish clade 4 FabIs. Alistipes finegoldii is a prototypical Bacteroidetes inhabitant of the gut microbiome. We found that A. finegoldii FabI (AfFabI) displays cooperative kinetics and uses NADH as a cofactor, and its crystal structure at 1.72 Å resolution showed that it adopts a Rossmann fold as do other characterized FabIs. It also disclosed a carboxyl-terminal extension that forms a helix–helix interaction that links the protomers as a unique feature of AfFabI. An AfFabI·NADH crystal structure at 1.86 Å resolution revealed that this feature undergoes a large conformational change to participate in covering the NADH-binding pocket and establishing the water channels that connect the active site to the central water well. Progressive deletion of these interactions led to catalytically compromised proteins that fail to bind NADH. This unique conformational change imparted a distinct shape to the AfFabI active site that renders it refractory to a FabI drug that targets clade 1 and 3 pathogens. We conclude that the clade 4 FabI, found in the Bacteroidetes inhabitants of the gut, have several structural features and conformational transitions that distinguish them from other bacterial FabIs.

DNA shape complements sequence-based representations of transcription factor binding sites

2019 ◽  
Author(s):  
Peter DeFord ◽  
James Taylor
Keyword(s):  
Transcription Factor ◽  
Binding Site ◽  
Binding Sites ◽  
Structural Features ◽  
Structural Motif ◽  
Dna Motif ◽  
Binding Site Identification ◽  
Encoding Strategies ◽  
Encoding Strategy ◽  
Site Identification

AbstractThe position weight matrix (PWM) has long been a useful tool for describing variation in the composition of regions of DNA such as transcription factor (TF) binding sites. It is difficult, however, to relate the sequence-based representation of a DNA motif to the biological features of the interaction of a TF with its binding site. Here we present an alternative strategy for representing DNA motifs – called Structural Motif (StruM) – that can easily represent different sets of structural features. Structural features are inferred from dinucleotide properties listed in the Dinucleotide Property Database. StruMs are able to specifically model TF binding sites, using an encoding strategy that is distinct from sequence-based models. This difference in encoding strategies makes StruMs complementary to sequence-based methods of TF binding site identification.

scholarly journals Mutations in penicillin-binding protein 2 from cephalosporin-resistant Neisseria gonorrhoeae hinder ceftriaxone acylation by restricting protein dynamics

2020 ◽  
Vol 295 (21) ◽  
pp. 7529-7543
Author(s):  
Avinash Singh ◽  
Jonathan M. Turner ◽  
Joshua Tomberg ◽  
Alena Fedarovich ◽  
Magnus Unemo ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Protein Dynamics ◽  
Conformational Changes ◽  
Active Site ◽  
Molecular Mechanisms ◽  
Binding Protein ◽  
Transmitted Disease ◽  
Penicillin Binding Protein ◽  
Sexually Transmitted ◽  
Diminished Capacity

The global incidence of the sexually transmitted disease gonorrhea is expected to rise due to the spread of Neisseria gonorrhoeae strains with decreased susceptibility to extended-spectrum cephalosporins (ESCs). ESC resistance is conferred by mosaic variants of penicillin-binding protein 2 (PBP2) that have diminished capacity to form acylated adducts with cephalosporins. To elucidate the molecular mechanisms of ESC resistance, we conducted a biochemical and high-resolution structural analysis of PBP2 variants derived from the decreased-susceptibility N. gonorrhoeae strain 35/02 and ESC-resistant strain H041. Our data reveal that mutations both lower affinity of PBP2 for ceftriaxone and restrict conformational changes that normally accompany acylation. Specifically, we observe that a G545S substitution hinders rotation of the β3 strand necessary to form the oxyanion hole for acylation and also traps ceftriaxone in a noncanonical configuration. In addition, F504L and N512Y substitutions appear to prevent bending of the β3–β4 loop that is required to contact the R1 group of ceftriaxone in the active site. Other mutations also appear to act by reducing flexibility in the protein. Overall, our findings reveal that restriction of protein dynamics in PBP2 underpins the ESC resistance of N. gonorrhoeae.

scholarly journals Discovery and mechanism of a pH-dependent dual-binding-site switch in the interaction of a pair of protein modules

2020 ◽  
Vol 6 (43) ◽  
pp. eabd7182
Author(s):  
Xingzhe Yao ◽  
Chao Chen ◽  
Yefei Wang ◽  
Sheng Dong ◽  
Ya-Jun Liu ◽  
...  
Keyword(s):  
Binding Site ◽  
Conformational Changes ◽  
Binding Sites ◽  
Protein Function ◽  
Titration Calorimetry ◽  
Resonance Spectroscopy ◽  
Biological Regulation ◽  
Structural Mechanism ◽  
Functional Sites ◽  
Ph Dependent

Many important proteins undergo pH-dependent conformational changes resulting in “on-off” switches for protein function, which are essential for regulation of life processes and have wide application potential. Here, we report a pair of cellulosomal assembly modules, comprising a cohesin and a dockerin from Clostridium acetobutylicum, which interact together following a unique pH-dependent switch between two functional sites rather than on-off states. The two cohesin-binding sites on the dockerin are switched from one to the other at pH 4.8 and 7.5 with a 180° rotation of the bound dockerin. Combined analysis by nuclear magnetic resonance spectroscopy, crystal structure determination, mutagenesis, and isothermal titration calorimetry elucidates the chemical and structural mechanism of the pH-dependent switching of the binding sites. The pH-dependent dual-binding-site switch not only represents an elegant example of biological regulation but also provides a new approach for developing pH-dependent protein devices and biomaterials beyond an on-off switch for biotechnological applications.

scholarly journals Proposed Mechanism for Monomethylarsonate Reductase Activity of Human Omega-class Glutathione Transferase GSTO1

2021 ◽  
Author(s):  
Aaron J Oakley
Keyword(s):  
Binding Site ◽  
Active Site ◽  
Binding Sites ◽  
Glutathione Transferase ◽  
Reductase Activity ◽  
Inorganic Arsenic ◽  
Glutathione Transferases ◽  
Public Health Issue ◽  
Major Public Health Issue ◽  
Glutathione Binding

Contamination of drinking water with toxic inorganic arsenic is a major public health issue. The mechanisms of enzymes and transporters in arsenic elimination are therefore of interest. The human omega-class glutathione transferases have been previously shown to possess monomethylarsonate (V) reductase activity. To further understanding of this activity, molecular dynamics of human GSTO1-1 bound to glutathione with a monomethylarsonate isostere were simulated to reveal putative monomethylarsonate binding sites on the enzyme. The major binding site is in the active site, adjacent to the glutathione binding site. Based on this and previously reported biochemical data, a reaction mechanism for this enzyme is proposed. Further insights were gained from comparison of the human omega-class GSTs to homologs from a range of animals.

Papain-like lysosomal cysteine proteases and their inhibitors: drug discovery targets?

2003 ◽  
Vol 70 ◽  
pp. 15-30 ◽  
Author(s):  
Dŭsan Turk ◽  
Boris Turk ◽  
Vito Turk
Keyword(s):  
Drug Discovery ◽  
Active Site ◽  
Binding Sites ◽  
Substrate Binding ◽  
Cysteine Proteases ◽  
Structural Features ◽  
Discovery Research ◽  
Drug Discovery Research ◽  
Lysosomal Cysteine Proteases ◽  
Substrate Binding Sites

Papain-like lysosomal cysteine proteases are processive and digestive enzymes that are expressed in organisms from bacteria to humans. Increasing knowledge about the physiological and pathological roles of cysteine proteases is bringing them into the focus of drug discovery research. These proteases have rather short active-site clefts, comprising three well defined substrate-binding subsites (S2, S1 and S1') and additional broad binding areas (S4, S3, S2' and S3'). The geometry of the active site distinguishes cysteine proteases from other protease classes, such as serine and aspartic proteases, which have six and eight substrate-binding sites respectively. Exopeptidases (cathepsins B, C, H and X), in contrast with endopeptidases (such as cathepsins L, S, V and F), possess structural features that facilitate the binding of N- and C-terminal groups of substrates into the active-site cleft. Other than a clear preference for free chain termini in the case of exopeptidases, the substrate-binding sites exhibit no strict specificities. Instead, their subsite preferences arise more from the specific exclusion of substrate types. This presents a challenge for the design of inhibitors to target a specific cathepsin: only the cumulative effect of an assembly of inhibitor fragments will bring the desired result.

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