journal
https://read.qxmd.com/read/38619104/stereospecific-nanog-pest-stabilization-by-pin1
#1
JOURNAL ARTICLE
Josephine C Ferreon, Hai Minh Ta, Hyosuk Yun, Kyoung-Jae Choi, My Diem Quan, Phoebe S Tsoi, Choel Kim, Chul Won Lee, Allan Chris M Ferreon
NANOG protein levels correlate with stem cell pluripotency. NANOG concentrations fluctuate constantly with low NANOG levels leading to spontaneous cell differentiation. Previous literature implicated Pin1, a phosphorylation-dependent prolyl isomerase, as a key player in NANOG stabilization. Here, using NMR spectroscopy, we investigate the molecular interactions of Pin1 with the NANOG unstructured N-terminal domain that contains a PEST sequence with two phosphorylation sites. Phosphorylation of NANOG PEST peptides increases affinity to Pin1...
April 15, 2024: Biochemistry
https://read.qxmd.com/read/38607680/polyethylene-glycol-impacts-conformation-and-dynamics-of-escherichia-coli-prolyl-trna-synthetase-via-crowding-and-confinement-effects
#2
JOURNAL ARTICLE
Jessica Liebau, Bethany F Laatsch, Joshua Rusnak, Keegan Gunderson, Brianna Finke, Kassandra Bargender, Alex Narkiewicz-Jodko, Katelyn Weeks, Murphi T Williams, Irina Shulgina, Karin Musier-Forsyth, Sudeep Bhattacharyya, Sanchita Hati
Polyethylene glycol (PEG) is a flexible, nontoxic polymer commonly used in biological and medical research, and it is generally regarded as biologically inert. PEG molecules of variable sizes are also used as crowding agents to mimic intracellular environments. A recent study with PEG crowders revealed decreased catalytic activity of Escherichia coli prolyl-tRNA synthetase (Ec ProRS), where the smaller molecular weight PEGs had the maximum impact. The molecular mechanism of the crowding effects of PEGs is not clearly understood...
April 12, 2024: Biochemistry
https://read.qxmd.com/read/38603770/cryo-em-structure-of-the-human-amylin-1-receptor-in-complex-with-cgrp-and-gs-protein
#3
JOURNAL ARTICLE
Jianjun Cao, Matthew J Belousoff, Radostin Danev, Arthur Christopoulos, Denise Wootten, Patrick M Sexton
Inhibition of calcitonin gene-related peptide (CGRP) or its cognate CGRP receptor (CGRPR) has arisen as a major breakthrough in the treatment of migraine. However, a second CGRP-responsive receptor exists, the amylin (Amy) 1 receptor (AMY1 R), yet its involvement in the pathology of migraine is poorly understood. AMY1 R and CGRPR are heterodimers consisting of receptor activity-modifying protein 1 (RAMP1) with the calcitonin receptor (CTR) and the calcitonin receptor-like receptor (CLR), respectively. Here, we present the structure of AMY1 R in complex with CGRP and Gs protein and compare it with the reported structures of the AMY1 R complex with rat amylin (rAmy) and the CGRPR in complex with CGRP...
April 11, 2024: Biochemistry
https://read.qxmd.com/read/38602394/contribution-of-a-c-terminal-extension-to-the-substrate-affinity-and-oligomeric-stability-of-aldehyde-dehydrogenase-from-thermus-thermophilus-hb27
#4
JOURNAL ARTICLE
Wiktoria Brytan, Kim Shortall, Francisco Duarte, Tewfik Soulimane, Luis Padrela
Aldehyde dehydrogenase enzymes (ALDHs) are widely studied for their roles in disease propagation and cell metabolism. Their use in biocatalysis applications, for the conversion of aldehydes to carboxylic acids, has also been recognized. Understanding the structural features and functions of both prokaryotic and eukaryotic ALDHs is key to uncovering novel applications of the enzyme and probing its role in disease propagation. The thermostable enzyme ALDH Tt originating from Thermus thermophilus , strain HB27, possesses a unique extension of its C-terminus, which has been evolutionarily excluded from mesophilic counterparts and other thermophilic enzymes in the same genus...
April 11, 2024: Biochemistry
https://read.qxmd.com/read/38598682/correction-to-structural-elucidation-of-the-cell-penetrating-penetratin-peptide-in-model-membranes-at-the-atomic-level-probing-hydrophobic-interactions-in-the-blood-brain-barrier
#5
Swapna Bera, Rajiv K Kar, Susanta Mondal, Kalipada Pahan, Anirban Bhunia
No abstract text is available yet for this article.
April 10, 2024: Biochemistry
https://read.qxmd.com/read/38598681/4-4-difluoroproline-as-a-unique-19-f-nmr-probe-of-proline-conformation
#6
JOURNAL ARTICLE
Himal K Ganguly, Brice A Ludwig, Caitlin M Tressler, Megh R Bhatt, Anil K Pandey, Caitlin M Quinn, Shi Bai, Glenn P A Yap, Neal J Zondlo
Despite the importance of proline conformational equilibria ( trans versus cis amide and exo versus endo ring pucker) on protein structure and function, there is a lack of convenient ways to probe proline conformation. 4,4-Difluoroproline (Dfp) was identified to be a sensitive 19 F NMR-based probe of proline conformational biases and cis-trans isomerism. Within model compounds and disordered peptides, the diastereotopic fluorines of Dfp exhibit similar chemical shifts (ΔδFF = 0-3 ppm) when a trans X-Dfp amide bond is present...
April 10, 2024: Biochemistry
https://read.qxmd.com/read/38598309/substrate-specificities-of-variants-of-barley-1-3-and-1-3-1-4-%C3%AE-d-glucanases-resulting-from-mutagenesis-and-segment-hybridization
#7
JOURNAL ARTICLE
Mu-Rong Kao, Jake Parker, Daniel Oehme, Shu-Chieh Chang, Lin-Chen Cheng, Damao Wang, Vaibhav Srivastava, John M Wagner, Philip J Harris, Yves S Y Hsieh
Barley (1,3;1,4)-β-d-glucanase is believed to have evolved from an ancestral monocotyledon (1,3)-β-d-glucanase, enabling the hydrolysis of (1,3;1,4)-β-d-glucans in the cell walls of leaves and germinating grains. In the present study, we investigated the substrate specificities of variants of the barley enzymes (1,3;1,4)-β-d-glucan endohydrolase [(1,3;1,4)-β-d-glucanase] isoenzyme EII ( Hv EII) and (1,3)-β-d-glucan endohydrolase [(1,3)-β-d-glucanase] isoenzyme GII ( Hv GII) obtained by protein segment hybridization and site-directed mutagenesis...
April 10, 2024: Biochemistry
https://read.qxmd.com/read/38587906/initial-steps-in-methanobactin-biosynthesis-substrate-binding-by-the-mixed-valent-diiron-enzyme-mbnbc
#8
JOURNAL ARTICLE
Richard J Jodts, Madeline B Ho, Reyvin M Reyes, Yun Ji Park, Peter E Doan, Amy C Rosenzweig, Brian M Hoffman
The MbnBC enzyme complex converts cysteine residues in a peptide substrate, MbnA, to oxazolone/thioamide groups during the biosynthesis of copper chelator methanobactin (Mbn). MbnBC belongs to the mixed-valent diiron oxygenase (MVDO) family, of which members use an Fe(II)Fe(III) cofactor to react with dioxygen for substrate modification. Several crystal structures of the inactive Fe(III)Fe(III) form of MbnBC alone and in complex with MbnA have been reported, but a mechanistic understanding requires determination of the oxidation states of the crystallographically observed Fe ions in the catalytically active Fe(II)Fe(III) state, along with the site of MbnA binding...
April 8, 2024: Biochemistry
https://read.qxmd.com/read/38587893/modulation-of-electron-transfer-branches-by-atrazine-and-triazine-herbicides-in-photosynthetic-reaction-centers
#9
JOURNAL ARTICLE
Gai Nishikawa, Keisuke Saito, Hiroshi Ishikita
Quinone analogue molecules, functioning as herbicides, bind to the secondary quinone site, QB , in type-II photosynthetic reaction centers, including those from purple bacteria (PbRC). Here, we investigated the impact of herbicide binding on electron transfer branches, using herbicide-bound PbRC crystal structures and employing the linear Poisson-Boltzmann equation. In contrast to urea and phenolic herbicides [Fufezan, C. Biochemistry 2005, 44, 12780-12789], binding of atrazine and triazine did not cause significant changes in the redox-potential ( E m ) values of the primary quinone (QA ) in these crystal structures...
April 8, 2024: Biochemistry
https://read.qxmd.com/read/38577885/structural-spectroscopic-and-computational-insights-from-canavanine-bound-and-two-catalytically-compromised-variants-of-the-ethylene-forming-enzyme
#10
JOURNAL ARTICLE
Shramana Chatterjee, Matthias Fellner, JoelA Rankin, Midhun G Thomas, Simahudeen Bathir J S Rifayee, Christo Z Christov, Jian Hu, Robert P Hausinger
The ethylene-forming enzyme (EFE) is an Fe(II), 2-oxoglutarate (2OG), and l-arginine (l-Arg)-dependent oxygenase that either forms ethylene and three CO2 /bicarbonate from 2OG or couples the decarboxylation of 2OG to C5 hydroxylation of l-Arg. l-Arg binds with C5 toward the metal center, causing 2OG to change from monodentate to chelate metal interaction and OD1 to OD2 switch of D191 metal coordination. We applied anaerobic UV-visible spectroscopy, X-ray crystallography, and computational approaches to three EFE systems with high-resolution structures...
April 5, 2024: Biochemistry
https://read.qxmd.com/read/38577872/differential-interactions-of-the-proteasome-inhibitor-pi31-with-constitutive-and-immuno-20s-proteasomes
#11
JOURNAL ARTICLE
Jason Wang, Abbey Kjellgren, George N DeMartino
PI31 (<u>P</u>roteasome <u>I</u>nhibitor of <u>31</u>,000 Da) is a 20S proteasome binding protein originally identified as an in vitro inhibitor of 20S proteasome proteolytic activity. Recently reported cryo-electron microscopy structures of 20S-PI31 complexes have revealed that the natively disordered proline-rich C-terminus of PI31 enters the central chamber in the interior of the 20S proteasome and interacts directly with the proteasome's multiple catalytic threonine residues in a manner predicted to inhibit their enzymatic function while evading its own proteolysis...
April 5, 2024: Biochemistry
https://read.qxmd.com/read/38569593/strong-protection-by-4-hydroxyestrone-against-erastin-induced-ferroptotic-cell-death-in-estrogen-receptor-negative-human-breast-cancer-cells-evidence-for-protein-disulfide-isomerase-as-a-mechanistic-target-for-protection
#12
JOURNAL ARTICLE
Hongge Wang, Ming-Jie Hou, Lixi Liao, Peng Li, Tongxiang Chen, Pan Wang, Bao Ting Zhu
Ferroptosis is a recently identified form of regulated cell death, characterized by excessive iron-dependent lipid peroxidation. Recent studies have demonstrated that protein disulfide isomerase (PDI) is an important mediator of chemically induced ferroptosis and also a new target for protection against ferroptosis-associated cell death. In the present study, we identified that 4-hydroxyestrone (4-OH-E1 ), a metabolic derivative of endogenous estrogen, is a potent small-molecule inhibitor of PDI, and can strongly protect against chemically induced ferroptotic cell death in the estrogen receptor-negative MDA-MB-231 human breast cancer cells...
April 3, 2024: Biochemistry
https://read.qxmd.com/read/38564530/kinetics-of-intermediate-release-enhances-p450-11b2-catalyzed-aldosterone-synthesis
#13
JOURNAL ARTICLE
Juan Valentín-Goyco, Sang-Choul Im, Richard J Auchus
The mitochondrial enzyme cytochrome P450 11B2 (aldosterone synthase) catalyzes the 3 terminal transformations in the biosynthesis of aldosterone from 11-deoxycorticosterone (DOC): 11β-hydroxylation to corticosterone, 18-hydroxylation, and 18-oxidation. Prior studies have shown that P450 11B2 produces more aldosterone from DOC than from the intermediate corticosterone and that the reaction sequence is processive, with intermediates remaining bound to the active site between oxygenation reactions. In contrast, P450 11B1 (11β-hydroxylase), which catalyzes the terminal step in cortisol biosynthesis, shares a 93% amino acid sequence identity with P450 11B2, converts DOC to corticosterone, but cannot synthesize aldosterone from DOC...
April 2, 2024: Biochemistry
https://read.qxmd.com/read/38546289/glycerol-3-phosphate-dehydrogenase-role-of-the-protein-conformational-change-in-activation-of-a-readily-reversible-enzyme-catalyzed-hydride-transfer-reaction
#14
JOURNAL ARTICLE
Judith R Cristobal, Rania Hegazy, John P Richard
Kinetic parameters are reported for glycerol 3-phosphate dehydrogenase (GPDH)-catalyzed hydride transfer from the whole substrate glycerol 3-phosphate (G3P) or truncated substrate ethylene glycol (EtG) to NAD, and for activation of the hydride transfer reaction of EtG by phosphite dianion. These kinetic parameters were combined with parameters for enzyme-catalyzed hydride transfer in the microscopic reverse direction to give the reaction equilibrium constants K eq . Hydride transfer from G3P is favored in comparison to EtG because the carbonyl product of the former reaction is stabilized by hyperconjugative electron donation from the -CH2 R keto substituent...
March 28, 2024: Biochemistry
https://read.qxmd.com/read/38545902/drug-design-do-not-forget-the-supramolecular-factor
#15
REVIEW
Steven L Regen
A major challenge currently facing medicinal chemists is designing agents that can selectively destroy drug resistant fungi and bacteria that have begun to emerge. One factor that has been overlooked by virtually all drug discovery/development approaches is the supramolecular factor, in which aggregated forms of a drug candidate exhibit low selectivity in destroying targeted cells while the corresponding monomers exhibit high selectivity. This Perspective discusses how we were led to the supramolecular factor through fundamental studies with simple model systems, how we reasoned that the selectivity of monomers of the antifungal agent amphotericin B should be much greater than the selectivity of the corresponding aggregates, and how we confirmed this hypothesis using derivatives of amphotericin B...
March 28, 2024: Biochemistry
https://read.qxmd.com/read/38533731/poacic-acid-a-plant-derived-stilbenoid-augments-cell-wall-chitin-production-but-its-antifungal-activity-is-hindered-by-this-polysaccharide-and-by-fungal-essential-metals
#16
JOURNAL ARTICLE
Adi Yona, Micha Fridman
Climate and environmental changes have modified the habitats of fungal pathogens, inflicting devastating effects on livestock and crop production. Additionally, drug-resistant fungi are increasing worldwide, driving the urgent need to identify new molecular scaffolds for the development of antifungal agents for humans, animals, and plants. Poacic acid (PA), a plant-derived stilbenoid, was recently discovered to be a novel molecular scaffold that inhibits the growth of several fungi. Its antifungal activity has been associated with perturbation of the production/assembly of the fungal cell wall β-1,3-glucan, but its mode of action is not resolved...
March 27, 2024: Biochemistry
https://read.qxmd.com/read/38507812/in-vitro-and-in-silico-explorations-of-the-protein-conformational-changes-of-corynebacterium-glutamicum-msha-a-model-retaining-gt-b-glycosyltransferase
#17
JOURNAL ARTICLE
Bakar A Hassan, Jozafina Milicaj, Meka Tyson, Ramesh Karki, Yuk Y Sham, Patrick A Frantom, Erika A Taylor
MshA is a GT-B glycosyltransferase catalyzing the first step in the biosynthesis of mycothiol. While many GT-B enzymes undergo an open-to-closed transition, MshA is unique because its 97° rotation is beyond the usual range of 10-25°. Molecular dynamics (MD) simulations were carried out for MshA in both ligand bound and unbound states to investigate the effect of ligand binding on localized protein dynamics and its conformational free energy landscape. Simulations showed that both the unliganded "opened" and liganded "closed" forms of the enzyme sample a wide degree of dihedral angles and interdomain distances with relatively low overlapping populations...
March 20, 2024: Biochemistry
https://read.qxmd.com/read/38501608/cryo-em-of-the-nucleosome-core-particle-bound-to-ran-rcc1-reveals-a-dynamic-complex
#18
JOURNAL ARTICLE
Shuya Kate Huang, John L Rubinstein, Lewis E Kay
Ras-related nuclear protein (Ran) is a member of the Ras superfamily of small guanosine triphosphatases (GTPases) and a regulator of multiple cellular processes. In healthy cells, the GTP-bound form of Ran is concentrated at chromatin, creating a Ran•GTP gradient that provides the driving force for nucleocytoplasmic transport, mitotic spindle assembly, and nuclear envelope formation. The Ran•GTP gradient is maintained by the regulator of chromatin condensation 1 (RCC1), a guanine nucleotide exchange factor that accelerates GDP/GTP exchange in Ran...
March 19, 2024: Biochemistry
https://read.qxmd.com/read/38498885/tryptophan-centric-bioinformatics-identifies-new-lasso-peptide-modifications
#19
JOURNAL ARTICLE
Lonnie A Harris, Hamada Saad, Kyle E Shelton, Lingyang Zhu, Xiaorui Guo, Douglas A Mitchell
Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) defined by a macrolactam linkage between the N-terminus and the side chain of an internal aspartic acid or glutamic acid residue. Instead of adopting a branched-cyclic conformation, lasso peptides are "threaded", with the C-terminal tail passing through the macrocycle to present a kinetically trapped rotaxane conformation. The availability of enhanced bioinformatics methods has led to a significant increase in the number of secondary modifications found on lasso peptides...
March 18, 2024: Biochemistry
https://read.qxmd.com/read/38498694/aqp4-darpin1-a-chimeric-antigen-based-on-scaffold-protein-darpin-for-efficient-detection-of-aqp4-igg-in-nmosd
#20
JOURNAL ARTICLE
Xiaofei Wang, Shubei Ma, Ying Bai, Xinyang Wu, Fangling Ji, Lingyun Jia
AQP4-IgG is an autoantibody associated with neuromyelitis optica spectroscopic disorder (NMOSD), a central nervous system inflammatory disease that requires early diagnosis and treatment. We designed two fusion proteins, AQP4-DARPin1 and AQP4-DARPin2, comprising the complete antigenic epitopes of aquaporin-4 (AQP4) and the constant region of the scaffold protein DARPin. These fusion proteins were expressed and purified from Escherichia coli and coated on microplates to develop an efficient method for detecting AQP4-IgG...
March 18, 2024: Biochemistry
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