scholarly journals Conformational changes involving ammonia tunnel formation and allosteric control in GMP synthetase

2014 ◽  
Vol 545 ◽  
pp. 22-32 ◽  
Author(s):  
Justin C. Oliver ◽  
Ravidra Gudihal ◽  
John W. Burgner ◽  
Anthony M. Pedley ◽  
Alexander T. Zwierko ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Allosteric Control ◽  
Ammonia Tunnel ◽  
Gmp Synthetase

scholarly journals Role of allosteric switches and adaptor domains in long-distance cross-talk and transient tunnel formation

2020 ◽  
Vol 6 (14) ◽  
pp. eaay7919
Author(s):  
Nandini Sharma ◽  
Navjeet Ahalawat ◽  
Padmani Sandhu ◽  
Erick Strauss ◽  
Jagannath Mondal ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Active Sites ◽  
Long Distance ◽  
Dynamic Interactions ◽  
Interface Control ◽  
Protein Energy ◽  
Catalytic Loop ◽  
Ammonia Tunnel ◽  
Dynamics Simulations

Transient tunnels that assemble and disassemble to facilitate passage of unstable intermediates in enzymes containing multiple reaction centers are controlled by allosteric cues. Using the 140-kDa purine biosynthetic enzyme PurL as a model system and a combination of biochemical and x-ray crystallographic studies, we show that long-distance communication between ~25-Å distal active sites is initiated by an allosteric switch, residing in a conserved catalytic loop, adjacent to the synthetase active site. Further, combinatory experiments seeded from molecular dynamics simulations help to delineate transient states that bring out the central role of nonfunctional adaptor domains. We show that carefully orchestrated conformational changes, facilitated by interplay of dynamic interactions at the allosteric switch and adaptor-domain interface, control reactivity and concomitant formation of the ammonia tunnel. This study asserts that substrate channeling is modulated by allosteric hotspots that alter protein energy landscape, thereby allowing the protein to adopt transient conformations paramount to function.

scholarly journals H3K4me3 induces allosteric conformational changes in the DNA-binding and catalytic regions of the V(D)J recombinase

2017 ◽  
Vol 114 (8) ◽  
pp. 1904-1909 ◽  
Author(s):  
John Bettridge ◽  
Chan Hyun Na ◽  
Akhilesh Pandey ◽  
Stephen Desiderio
Keyword(s):  
Dna Binding ◽  
Conformational Changes ◽  
Solvent Accessibility ◽  
Active Chromatin ◽  
Catalytic Center ◽  
Allosteric Control ◽  
Recombination Activating Gene ◽  
Rag 1 ◽  
Cysteine Thiols ◽  
Conformational Distribution

V(D)J recombination is initiated by the recombination-activating gene (RAG) recombinase, consisting of RAG-1 and RAG-2 subunits. The susceptibility of gene segments to cleavage by RAG is associated with histone modifications characteristic of active chromatin, including trimethylation of histone H3 at lysine 4 (H3K4me3). Binding of H3K4me3 by a plant homeodomain (PHD) in RAG-2 stimulates substrate binding and catalysis, which are functions of RAG-1. This has suggested an allosteric mechanism in which information regarding occupancy of the RAG-2 PHD is transmitted to RAG-1. To determine whether the conformational distribution of RAG is altered by H3K4me3, we mapped changes in solvent accessibility of cysteine thiols by differential isotopic chemical footprinting. Binding of H3K4me3 to the RAG-2 PHD induces conformational changes in RAG-1 within a DNA-binding domain and in the ZnH2 domain, which acts as a scaffold for the catalytic center. Thus, engagement of H3K4me3 by the RAG-2 PHD is associated with dynamic conformational changes in RAG-1, consistent with allosteric control by active chromatin.

scholarly journals The Pharmacological TAILS of Matrix Metalloproteinases and Their Inhibitors

2020 ◽  
Vol 14 (1) ◽  
pp. 31
Author(s):  
Nabangshu Das ◽  
Colette Benko ◽  
Sean E. Gill ◽  
Antoine Dufour
Keyword(s):  
Clinical Trials ◽  
Matrix Metalloproteinases ◽  
Conformational Changes ◽  
Active Sites ◽  
Inflammatory Diseases ◽  
Phase Iii ◽  
Biological Functions ◽  
Mmp Inhibitors ◽  
Allosteric Control ◽  
Phase Iii Clinical Trials

Matrix metalloproteinases (MMPs) have been demonstrated to have both detrimental and protective functions in inflammatory diseases. Several MMP inhibitors, with the exception of Periostat®, have failed in Phase III clinical trials. As an alternative strategy, recent efforts have been focussed on the development of more selective inhibitors or targeting other domains than their active sites through specific small molecule inhibitors or monoclonal antibodies. Here, we present some examples that aim to better understand the mechanisms of conformational changes/allosteric control of MMPs functions. In addition to MMP inhibitors, we discuss unbiased global approaches, such as proteomics and N-terminomics, to identify new MMP substrates. We present some examples of new MMP substrates and their implications in regulating biological functions. By characterizing the roles and substrates of individual MMP, MMP inhibitors could be utilized more effectively in the optimal disease context or in diseases never tested before where MMP activity is elevated and contributing to disease progression.

scholarly journals The Pharmacological Tails of Matrix Metalloproteinases and Their Inhibitors

2021 ◽  
Author(s):  
Nabangshu Das ◽  
Colette Benko ◽  
Sean E. Gill ◽  
Antoine Dufour
Keyword(s):  
Clinical Trials ◽  
Monoclonal Antibodies ◽  
Matrix Metalloproteinases ◽  
Conformational Changes ◽  
Active Sites ◽  
Inflammatory Diseases ◽  
Phase Iii ◽  
Mmp Inhibitors ◽  
Allosteric Control ◽  
Phase Iii Clinical Trials

Matrix metalloproteinases (MMPs) have been demonstrated to have both detrimental and protective functions in inflammatory diseases. Several MMP inhibitors, with the exception of Periostat®, have failed in Phase III clinical trials. As an alternative strategy, recent efforts have been focussed on the development of more selective inhibitors or targeting other domains than their active sites (e.g., exosites, ectosites) through specific small molecule inhibitors or monoclonal antibodies. Here, we present some examples that aim to better understand the mechanisms of conformational changes/allosteric control of MMPs functions. In addition to MMP inhibitors, we discuss unbiased global approaches such as proteomics and N-terminomics to identify new MMP substrates and achieve a better understanding of the roles of these proteases in diseases.

scholarly journals The Pharmacological Tails of Matrix Metalloproteinases and Their Inhibitors

2020 ◽  
Author(s):  
Nabangshu Das ◽  
Colette Benko ◽  
Sean E. Gill ◽  
Antoine Dufour
Keyword(s):  
Clinical Trials ◽  
Monoclonal Antibodies ◽  
Matrix Metalloproteinases ◽  
Conformational Changes ◽  
Active Sites ◽  
Inflammatory Diseases ◽  
Phase Iii ◽  
Mmp Inhibitors ◽  
Allosteric Control ◽  
Phase Iii Clinical Trials

Matrix metalloproteinases (MMPs) have been demonstrated to have both detrimental and protective functions in inflammatory diseases. Several MMP inhibitors, with the exception of Periostat®, have failed in Phase III clinical trials. As an alternative strategy, recent efforts have been focussed on the development of more selective inhibitors or targeting other domains than their active sites (e.g., exosites, ectosites) through specific small molecule inhibitors or monoclonal antibodies. Here, we present some examples that aim to better understand the mechanisms of conformational changes/allosteric control of MMPs functions. In addition to MMP inhibitors, we discuss unbiased global approaches such as proteomics and N-terminomics to identify new MMP substrates and achieve a better understanding of the roles of these proteases in diseases.

scholarly journals Structural basis for ligand binding modes of CTP synthase

2021 ◽  
Vol 118 (30) ◽  
pp. e2026621118
Author(s):  
Xian Zhou ◽  
Chen-Jun Guo ◽  
Chia-Chun Chang ◽  
Jiale Zhong ◽  
Huan-Huan Hu ◽  
...  
Keyword(s):  
Conformational Changes ◽  
De Novo ◽  
Feedback Inhibition ◽  
Structural Basis ◽  
Binding Modes ◽  
Atp Binding Site ◽  
Ctp Synthase ◽  
Ammonia Tunnel ◽  
Underlying Mechanisms ◽  
Allosteric Activator

Cytidine triphosphate synthase (CTPS), which comprises an ammonia ligase domain and a glutamine amidotransferase domain, catalyzes the final step of de novo CTP biosynthesis. The activity of CTPS is regulated by the binding of four nucleotides and glutamine. While glutamine serves as an ammonia donor for the ATP-dependent conversion of UTP to CTP, the fourth nucleotide GTP acts as an allosteric activator. Models have been proposed to explain the mechanisms of action at the active site of the ammonia ligase domain and the conformational changes derived by GTP binding. However, actual GTP/ATP/UTP binding modes and relevant conformational changes have not been revealed fully. Here, we report the discovery of binding modes of four nucleotides and a glutamine analog 6-diazo-5-oxo-L-norleucine in Drosophila CTPS by cryo–electron microscopy with near-atomic resolution. Interactions between GTP and surrounding residues indicate that GTP acts to coordinate reactions at both domains by directly blocking ammonia leakage and stabilizing the ammonia tunnel. Additionally, we observe the ATP-dependent UTP phosphorylation intermediate and determine interacting residues at the ammonia ligase. A noncanonical CTP binding at the ATP binding site suggests another layer of feedback inhibition. Our findings not only delineate the structure of CTPS in the presence of all substrates but also complete our understanding of the underlying mechanisms of the allosteric regulation and CTP synthesis.

Influence of Calcium Ions on the Plant Cell Surface: Membrane Fusions and Conformational Changes

1974 ◽  
Vol 32 ◽  
pp. 154-155
Author(s):  
D. James Morré ◽  
Charles E. Bracker ◽  
William J. VanDerWoude
Keyword(s):  
Cell Wall ◽  
Cell Surface ◽  
Conformational Changes ◽  
Calcium Ions ◽  
Surface Membrane ◽  
Carboxyl Groups ◽  
Cross Linking ◽  
Ultrastructural Evidence ◽  
Glycine Max L ◽  
Wall Extensibility

Calcium ions in the concentration range 5-100 mM inhibit auxin-induced cell elongation and wall extensibility of plant stems. Inhibition of wall extensibility requires that the tissue be living; growth inhibition cannot be explained on the basis of cross-linking of carboxyl groups of cell wall uronides by calcium ions. In this study, ultrastructural evidence was sought for an interaction of calcium ions with some component other than the wall at the cell surface of soybean (Glycine max (L.) Merr.) hypocotyls.

Role of spectrin in membrane fusion and in shape change of human erythrocyte ghost

1978 ◽  
Vol 36 (2) ◽  
pp. 328-329
Author(s):  
Hideo Hayashi ◽  
Yoshikazu Hirai ◽  
John T. Penniston
Keyword(s):  
Conformational Changes ◽  
Human Erythrocyte ◽  
Shape Change ◽  
Membrane Surface ◽  
Slight Modification ◽  
Active Role ◽  
Main Role ◽  
Bank Blood ◽  
Human Erythrocyte Ghost

Spectrin is a membrane associated protein most of which properties have been tentatively elucidated. A main role of the protein has been assumed to give a supporting structure to inside of the membrane. As reported previously, however, the isolated spectrin molecule underwent self assemble to form such as fibrous, meshwork, dispersed or aggregated arrangements depending upon the buffer suspended and was suggested to play an active role in the membrane conformational changes. In this study, the role of spectrin and actin was examined in terms of the molecular arrangements on the erythrocyte membrane surface with correlation to the functional states of the ghosts.Human erythrocyte ghosts were prepared from either freshly drawn or stocked bank blood by the method of Dodge et al with a slight modification as described before. Anti-spectrin antibody was raised against rabbit by injection of purified spectrin and partially purified.

Pinocytotic-Like Forms of Mitochondria From Rat Anterior Pituitary

1968 ◽  
Vol 26 ◽  
pp. 146-147
Author(s):  
Burton B. Silver
Keyword(s):  
Electron Micrographs ◽  
Conformational Changes ◽  
Anterior Pituitary ◽  
Dynamic State ◽  
Surrounding Cell ◽  
The Matrix ◽  
The Moment ◽  
Cell Medium ◽  
Sectioned Tissue ◽  
State Of Activity

Sectioned tissue rarely indicates evidence of what is probably a highly dynamic state of activity in mitochondria which have been reported to undergo a variety of movements such as streaming, divisions and coalescence. Recently, mitochondria from the rat anterior pituitary have been fixed in a variety of configurations which suggest that conformational changes were occurring at the moment of fixation. Pinocytotic-like vacuoles which may be taking in or expelling materials from the surrounding cell medium, appear to be forming in some of the mitochondria. In some cases, pores extend into the matrix of the mitochondria. In other forms, the remains of what seems to be pinched off vacuoles are evident in the mitochondrial interior. Dense materials, resembling secretory droplets, appear at the junction of the pores and the cytoplasm. The droplets are similar to the secretory materials commonly identified in electron micrographs of the anterior pituitary.

Electron Microscopy and image reconstruction reveal the structural basis for spectrin's elastic properties

1992 ◽  
Vol 50 (1) ◽  
pp. 510-511
Author(s):  
Amy M. McGough ◽  
Robert Josephs
Keyword(s):  
Electron Microscopy ◽  
Elastic Properties ◽  
Conformational Changes ◽  
Quaternary Structure ◽  
Three Dimensional ◽  
Membrane Skeleton ◽  
Projection Algorithm ◽  
Structural Basis ◽  
Iterative Approximation ◽  
Membrane Skeletons

The remarkable deformability of the erythrocyte derives in large part from the elastic properties of spectrin, the major component of the membrane skeleton. It is generally accepted that spectrin's elasticity arises from marked conformational changes which include variations in its overall length (1). In this work the structure of spectrin in partially expanded membrane skeletons was studied by electron microscopy to determine the molecular basis for spectrin's elastic properties. Spectrin molecules were analysed with respect to three features: length, conformation, and quaternary structure. The results of these studies lead to a model of how spectrin mediates the elastic deformation of the erythrocyte.Membrane skeletons were isolated from erythrocyte membrane ghosts, negatively stained, and examined by transmission electron microscopy (2). Particle lengths and end-to-end distances were measured from enlarged prints using the computer program MACMEASURE. Spectrin conformation (straightness) was assessed by calculating the particles’ correlation length by iterative approximation (3). Digitised spectrin images were correlation averaged or Fourier filtered to improve their signal-to-noise ratios. Three-dimensional reconstructions were performed using a suite of programs which were based on the filtered back-projection algorithm and executed on a cluster of Microvax 3200 workstations (4).

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