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https://www.readbyqxmd.com/read/28435869/a-dynamic-hydrophobic-core-orchestrates-allostery-in-protein-kinases
#1
Jonggul Kim, Lalima G Ahuja, Fa-An Chao, Youlin Xia, Christopher L McClendon, Alexandr P Kornev, Susan S Taylor, Gianluigi Veglia
Eukaryotic protein kinases (EPKs) constitute a class of allosteric switches that mediate a myriad of signaling events. It has been postulated that EPKs' active and inactive states depend on the structural architecture of their hydrophobic cores, organized around two highly conserved spines: C-spine and R-spine. How the spines orchestrate the transition of the enzyme between catalytically uncommitted and committed states remains elusive. Using relaxation dispersion nuclear magnetic resonance spectroscopy, we found that the hydrophobic core of the catalytic subunit of protein kinase A, a prototypical and ubiquitous EPK, moves synchronously to poise the C subunit for catalysis in response to binding adenosine 5'-triphosphate...
April 2017: Science Advances
https://www.readbyqxmd.com/read/28434917/conformational-dynamics-and-allostery-in-e2-e3-interactions-drive-ubiquitination-gp78-and-ube2g2
#2
Kalyan S Chakrabarti, Jess Li, Ranabir Das, R Andrew Byrd
Conformational dynamics plays a fundamental role in molecular recognition and activity in enzymes. The ubiquitin-conjugating enzyme (E2) Ube2g2 functions with the ubiquitin ligase (E3) gp78 to assemble poly-ubiquitin chains on target substrates. Two domains in gp78, RING and G2BR, bind to two distant regions of Ube2g2, and activate it for ubiquitin (Ub) transfer. G2BR increases the affinity between the RING and Ube2g2 by 50-fold, while the RING catalyzes the transfer of Ub from the Ube2g2∼Ub conjugate. How G2BR and RING activate Ube2g2 is unclear...
April 13, 2017: Structure
https://www.readbyqxmd.com/read/28431259/allosteric-regulation-of-metabolism-in-cancer-endogenous-mechanisms-and-considerations-for-drug-design
#3
REVIEW
Jamie A Macpherson, Dimitrios Anastasiou
Alterations in metabolic processes have been linked to various diseases, including cancer. Although gene expression can dictate long-term metabolic adaptation, many metabolic changes found in cancer are associated with altered allosteric properties of the underlying enzymes. Small molecule-protein interactions and intracellular signalling converge to orchestrate these allosteric mechanisms, which, emerging evidence suggests, constitute a promising therapeutic avenue. In this review we focus on glucose and energy metabolism to illustrate the role of allostery in cancer physiology and we discuss approaches to streamline the process of targeting aberrant allosteric pathways with small molecules...
April 18, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28430446/piecing-together-the-allosteric-patterns-of-chaperonin-groel
#4
Jin Chen, Qian Zhang, Weitong Ren, Wenfei Li
Despite considerable effort, elucidating allostery of large macromolecular assemblies at a molecular level in solution remains technically challenging due to its structural complexity. Here we have employed an approach combining amide backbone hydrogen/deuterium exchange coupled with mass spectrometry, fluorescence spectroscopy and molecular simulations to characterize allosteric patterns of chaperonin GroEL, a ~800 kDa tetradecamer from E. coli. Using available crystal structures of GroEL, we quantitatively map out GroEL allosteric changes in solution by resolving exchange behaviors of 133 overlapping proteolytic peptides with more than 95% sequence coverage...
April 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28428246/key-features-of-an-hsp70-chaperone-allosteric-landscape-revealed-by-ion-mobility-native-mass-spectrometry-and-double-electron-electron-resonance
#5
Alex L Lai, Eugenia M Clerico, Mandy E Blackburn, Nisha A Patel, Carol V Robinson, Peter P Borbat, Jack H Freed, Lila M Gierasch
Proteins are dynamic entities that populate conformational ensembles, and most functions of proteins depend on their dynamic character. Allostery, in particular, relies on ligand-modulated shifts in these conformational ensembles. Hsp70s are allosteric molecular chaperones with conformational landscapes that involve large rearrangements of their two domains (viz, the nucleotide-binding domain and substrate-binding domain) in response to adenine nucleotides and substrates. However, it remains unclear how the Hsp70 conformational ensemble is populated at each point of the allosteric cycle and how ligands control these populations...
April 20, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28425706/allosteric-autoinhibition-pathway-in-transcription-factor-erg-dynamics-network-and-mutant-experimental-evaluations
#6
Wei Ye, Tianle Qian, Hao Liu, Ray Luo, Hai-Feng Chen
Allosteric autoinhibition exists in many transcription factors. The ERG proteins exhibit autoinhibition on DNA binding by the C-terminal and N-terminal inhibitory domains (CID and NID). However, the autoinhibition mechanism and allosteric pathway of ERG are unknown. In this study we intend to elucidate the residue-level allosteric mechanism and pathway via a combined approach of computational and experimental analyses. Specifically computational residue-level fluctuation correlation data was analyzed to reveal detailed dynamics signatures in the allosteric autoinhibition process...
April 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28420785/bringing-disorder-and-dynamics-in-protein-allostery-into-focus
#7
A Joshua Wand
No abstract text is available yet for this article.
April 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28419415/allostery-at-opioid-receptors-modulation-with-small-molecule-ligands
#8
REVIEW
Kathryn E Livingston, John R Traynor
Opioid receptors are 7-transmembrane domain receptors that couple to heterotrimeric G proteins. The endogenous ligands for opioid receptors are peptides which bind to the orthosteric site on the receptors. The μ-opioid receptor is the target for opioid analgesics while the δ-opioid receptor has been suggested as a target for pain management, migraine, and depression. Similarly, κ-opioid receptors are involved in pain and depression and nociceptin receptors in pain and mood behaviors. However, exogenous orthosteric ligands for the opioid receptors cause a myriad of on-target side effects...
April 18, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28416647/identifiability-reducibility-and-adaptability-in-allosteric-macromolecules
#9
Gergő Bohner, Gaurav Venkataraman
The ability of macromolecules to transduce stimulus information at one site into conformational changes at a distant site, termed "allostery," is vital for cellular signaling. Here, we propose a link between the sensitivity of allosteric macromolecules to their underlying biophysical parameters, the interrelationships between these parameters, and macromolecular adaptability. We demonstrate that the parameters of a canonical model of the mSlo large-conductance Ca(2+)-activated K(+) (BK) ion channel are non-identifiable with respect to the equilibrium open probability-voltage relationship, a common functional assay...
April 17, 2017: Journal of General Physiology
https://www.readbyqxmd.com/read/28412959/opportunities-for-developing-therapies-for-rare-genetic-diseases-focus-on-gain-of-function-and-allostery
#10
Binbin Chen, Russ B Altman
BACKGROUND: Advances in next generation sequencing technologies have revolutionized our ability to discover the causes of rare genetic diseases. However, developing treatments for these diseases remains challenging. In fact, when we systematically analyze the US FDA orphan drug list, we find that only 8% of rare diseases have an FDA-designated drug. Our approach leverages three primary insights: first, diseases with gain-of-function mutations and late onset are more likely to have drug options; second, drugs are more often inhibitors than activators; and third, some disease-causing proteins can be rescued by allosteric activators in diseases due to loss-of-function mutations...
April 17, 2017: Orphanet Journal of Rare Diseases
https://www.readbyqxmd.com/read/28411213/allostery-modulates-the-beat-rate-of-a-cardiac-pacemaker
#11
Chung-Jung Tsai, Ruth Nussinov
The S672R mutation in heart cell ion channels leads to low heart rates and arrhythmia by an unknown route. A multifaceted NMR analysis now demonstrates that this mutant impacts allosteric coupling in domains inside of the cell to change channel activation, providing a mechanistic explanation for phenotypic outcomes.
April 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28407397/whole-protein-alanine-scanning-mutagenesis-of-allostery-a-large-percentage-of-a-protein-can-contribute-to-mechanism
#12
Qingling Tang, Aron W Fenton
Many studies of allosteric mechanisms use limited numbers of mutations to test whether residues play "key" roles. However, if a large percentage of the protein contributes to allosteric function, mutating any residue would have a high probability of modifying allostery. Thus, a predicted mechanism that is dependent on only a few residues could erroneously appear to be supported. We used whole-protein alanine-scanning mutagenesis to determine which amino acid side-chains of human liver pyruvate kinase (hL-PYK; approved symbol PKLR) contribute to regulation by fructose-1,6-bisphosphate (activator) and alanine (inhibitor)...
April 13, 2017: Human Mutation
https://www.readbyqxmd.com/read/28402876/mechanistic-models-fit-to-variable-temperature-calorimetric-data-provide-insights-into-cooperativity
#13
Elihu C Ihms, Ian R Kleckner, Paul Gollnick, Mark P Foster
Allostery pervades macromolecular function and drives cooperative binding of ligands to macromolecules. To decipher the mechanisms of cooperative ligand binding it is necessary to define at a microscopic level the structural and thermodynamic consequences of binding of each ligand to its allosterically coupled site(s). However, dynamic sampling of alternative conformations (microstates) in allosteric molecules complicates interpretation of both structural and thermodynamic data. Isothermal titration calorimetry has the potential to directly quantify the thermodynamics of allosteric interactions, but usually falls short of enabling mechanistic insight...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28396388/altering-the-allosteric-pathway-in-igps-suppresses-millisecond-motions-and-catalytic-activity
#14
George P Lisi, Kyle W East, Victor S Batista, J Patrick Loria
Imidazole glycerol phosphate synthase (IGPS) is a V-type allosteric enzyme, meaning that its catalytic rate is critically dependent on activation by its allosteric ligand, N'-[(5'-phosphoribulosyl)formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR). The allosteric mechanism of IGPS is reliant on millisecond conformational motions for efficient catalysis. We engineered four mutants of IGPS designed to disrupt millisecond motions and allosteric coupling to identify regions that are critical to IGPS function...
April 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28375734/high-dimensional-mutant-and-modular-thermodynamic-cycles-molecular-switching-and-free-energy-transduction
#15
Charles W Carter
Understanding how distinct parts of proteins produce coordinated behavior has driven and continues to drive advances in protein science and enzymology. However, despite consensus about the conceptual basis for allostery, the idiosyncratic nature of allosteric mechanisms resists general approaches. Computational methods can identify conformational transition states from structural changes, revealing common switching mechanisms that impose multistate behavior. Thermodynamic cycles use factorial perturbations to measure coupling energies between side chains in molecular switches that mediate shear during domain motion...
March 24, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28370845/benchmarking-predictions-of-allostery-in-liver-pyruvate-kinase-in-cagi4
#16
Qifang Xu, Qingling Tang, Panagiotis Katsonis, Olivier Lichtarge, David Jones, Samuele Bovo, Giulia Babbi, Pier L Martelli, Rita Casadio, Gyu Rie Lee, Chaok Seok, Aron W Fenton, Roland L Dunbrack
Critical Assessment of Genome Interpretation "CAGI" is a global community experiment to objectively assess computational methods for predicting phenotypic impacts of genomic variation. One of the 2015-2016 competitions focused on predicting the influence of mutations on the allosteric regulation of human liver pyruvate kinase. More than 30 different researchers accessed the challenge data. However, only four groups accepted the challenge. Features used for predictions ranged from evolutionary constraints, mutant site locations relative to active and effector binding sites, and computational docking outputs...
March 29, 2017: Human Mutation
https://www.readbyqxmd.com/read/28358030/allosteric-cross-talk-in-chromatin-can-mediate-drug-drug-synergy
#17
Zenita Adhireksan, Giulia Palermo, Tina Riedel, Zhujun Ma, Reyhan Muhammad, Ursula Rothlisberger, Paul J Dyson, Curt A Davey
Exploitation of drug-drug synergism and allostery could yield superior therapies by capitalizing on the immensely diverse, but highly specific, potential associated with the biological macromolecular landscape. Here we describe a drug-drug synergy mediated by allosteric cross-talk in chromatin, whereby the binding of one drug alters the activity of the second. We found two unrelated drugs, RAPTA-T and auranofin, that yield a synergistic activity in killing cancer cells, which coincides with a substantially greater number of chromatin adducts formed by one of the compounds when adducts from the other agent are also present...
March 30, 2017: Nature Communications
https://www.readbyqxmd.com/read/28348247/entropy-redistribution-controls-allostery-in-a-metalloregulatory-protein
#18
Daiana A Capdevila, Joseph J Braymer, Katherine A Edmonds, Hongwei Wu, David P Giedroc
Allosteric communication between two ligand-binding sites in a protein is a central aspect of biological regulation that remains mechanistically unclear. Here we show that perturbations in equilibrium picosecond-nanosecond motions impact zinc (Zn)-induced allosteric inhibition of DNA binding by the Zn efflux repressor CzrA (chromosomal zinc-regulated repressor). DNA binding leads to an unanticipated increase in methyl side-chain flexibility and thus stabilizes the complex entropically; Zn binding redistributes these motions, inhibiting formation of the DNA complex by restricting coupled fast motions and concerted slower motions...
March 27, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28339191/allosteric-activation-of-cytochrome-p450-3a4-via-progesterone-bioconjugation
#19
Vanja Polic, Karine Auclair
Human cytochrome P450 3A4 (CYP3A4) is responsible for the metabolism of the majority of drugs. As such, it is implicated in many adverse drug-drug and food-drug interactions, and is of significant interest to the pharmaceutical industry. This enzyme is known to simultaneously bind multiple ligands and display atypical enzyme kinetics, suggestive of allostery and cooperativity. As well, evidence of a postulated peripheral allosteric binding site has provoked debate around its significance and location. We report the use of bioconjugation to study the significance of substrate binding at the proposed allosteric site and its effect on CYP3A4 activity...
March 29, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28334219/a-network-model-predicts-the-intensity-of-residue-protein-thermal-coupling
#20
Luciano Censoni, Heloisa Dos Santos Muniz, Leandro Martínez
Motivation: The flow of vibrational energy in proteins has been shown not to obey expectations for isotropic media. The existence of preferential pathways for energy transport, with probable connections to allostery mechanisms, has been repeatedly demonstrated. Here, we investigate whether, by representing a set of protein structures as networks of interacting amino acid residues, we are able to model heat diffusion and predict residue-protein vibrational couplings, as measured by the Anisotropic Thermal Diffusion (ATD) computational protocol of modified molecular dynamics simulations...
March 7, 2017: Bioinformatics
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