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https://www.readbyqxmd.com/read/29150441/co-ii-and-ni-ii-binding-of-the-escherichia-coli-transcriptional-repressor-rcnr-orders-its-n-terminus-alters-helix-dynamics-and-reduces-dna-affinity
#1
Hsin-Ting Huang, Cedric E Bobst, Jeffrey S Iwig, Peter T Chivers, Igor A Kaltashov, Michael J Maroney
RcnR, a transcriptional regulator in Escherichia coli, derepresses the expression of the export proteins RcnAB upon binding Ni(II) or Co(II). Lack of structural information has precluded elucidation of the allosteric basis for the decreased DNA affinity in RcnR's metal-bound states. Here, using hydrogen-deuterium exchange coupled with MS (HDX-MS), we probed the RcnR structure in the presence of DNA, the cognate metal ions Ni(II) and Co(II), or the noncognate metal ion Zn(II). We found that cognate metal binding altered the flexibility from the N-terminus through helix 1 and modulated the RcnR-DNA interaction...
November 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29138428/structural-disorder-and-induced-folding-within-two-cereal-aba-stress-and-ripening-asr-proteins
#2
Karama Hamdi, Edoardo Salladini, Darragh P O'Brien, Sébastien Brier, Alexandre Chenal, Ines Yacoubi, Sonia Longhi
Abscisic acid (ABA), stress and ripening (ASR) proteins are plant-specific proteins involved in plant response to multiple abiotic stresses. We previously isolated the ASR genes and cDNAs from durum wheat (TtASR1) and barley (HvASR1). Here, we show that HvASR1 and TtASR1 are consistently predicted to be disordered and further confirm this experimentally. Addition of glycerol, which mimics dehydration, triggers a gain of structure in both proteins. Limited proteolysis showed that they are highly sensitive to protease degradation...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29135326/hydrogen-deuterium-exchange-mass-spectrometry-and-computational-modeling-reveal-a-discontinuous-epitope-of-an-antibody-tl1a-interaction
#3
Richard Y-C Huang, Stanley R Krystek, Nathan Felix, Robert F Graziano, Mohan Srinivasan, Achal Pashine, Guodong Chen
TL1A, a tumor necrosis factor-like cytokine, is a ligand for the death domain receptor DR3. TL1A, upon binding to DR3, can stimulate lymphocytes and trigger secretion of proinflammatory cytokines. Therefore, blockade of TL1A/DR3 interaction may be a potential therapeutic strategy for autoimmune and inflammatory diseases. Recently, the anti-TL1A monoclonal antibody 1 (mAb1) with a strong potency in blocking the TL1A/DR3 interaction was identified. Here, we report on the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) to obtain molecular-level details of mAb1's binding epitope on TL1A...
November 14, 2017: MAbs
https://www.readbyqxmd.com/read/29131142/a-consensus-model-of-human-apolipoprotein-a-i-in-its-monomeric-and-lipid-free-state
#4
John T Melchior, Ryan G Walker, Allison L Cooke, Jamie Morris, Mark Castleberry, Thomas B Thompson, Martin K Jones, Hyun D Song, Kerry-Anne Rye, Michael N Oda, Mary G Sorci-Thomas, Michael J Thomas, Jay W Heinecke, Xiaohu Mei, David Atkinson, Jere P Segrest, Sissel Lund-Katz, Michael C Phillips, W Sean Davidson
Apolipoprotein (apo)A-I is an organizing scaffold protein that is critical to high-density lipoprotein (HDL) structure and metabolism, probably mediating many of its cardioprotective properties. However, HDL biogenesis is poorly understood, as lipid-free apoA-I has been notoriously resistant to high-resolution structural study. Published models from low-resolution techniques share certain features but vary considerably in shape and secondary structure. To tackle this central issue in lipoprotein biology, we assembled a team of structural biologists specializing in apolipoproteins and set out to build a consensus model of monomeric lipid-free human apoA-I...
November 13, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29129068/structural-and-functional-characterization-of-a-hole-hole-homodimer-variant-in-a-knob-into-hole-bispecific-antibody
#5
Hui-Min Zhang, Charlene Li, Ming Lei, Victor Lundin, Ho Young Lee, Milady Ninonuevo, Kevin Lin, Guanghui Han, Wendy Sandoval, Dongsheng Lei, Gang Ren, Jennifer Zhang, Hongbin Liu
Bispecific antibodies have great potential to be the next-generation biotherapeutics due to their ability to simultaneously recognize two different targets. Compared to conventional monoclonal antibodies, knob-into-hole bispecific antibodies face unique challenges in production and characterization due to the increase in variant possibilities, such as homodimerization in covalent and non-covalent forms. In this study, a storage- and pH-sensitive hydrophobic interaction chromatography (HIC) profile change was observed for the hole-hole homodimer, and the multiple HIC peaks were explored and shown to be conformational isomers...
November 12, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29092908/coordination-and-redox-state-dependent-structural-changes-of-the-heme-based-oxygen-sensor-afgchk-associated-with-intraprotein-signal-transduction
#6
Martin Stranava, Petr Man, Tereza Skalova, Petr Kolenko, Jan Blaha, Veronika Fojtikova, Vaclav Martinek, Jan Dohnalek, Alzbeta Lengalova, Michal Rosulek, Toru Shimizu, Marketa Martinkova
The heme-based oxygen sensor histidine kinase AfGcHK is part of a two-component signal transduction system in bacteria. O2 binding to the Fe(II) heme complex of its N-terminal globin domain strongly stimulates autophosphorylation at His-183 in its C-terminal kinase domain. The 6-coordinate heme Fe(III)-OH- and -CN- complexes of AfGcHK are also active, but the 5-coordinate heme Fe(II) complex and the heme-free apo-form are inactive. Here, we determined the crystal structures of the isolated dimeric globin domains of the active Fe(III)-CN- and inactive 5-coordinate Fe(II) forms, revealing striking structural differences on the heme-proximal side of the globin domain...
November 1, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29080206/structural-dynamics-of-the-gw182-silencing-domain-including-its-rna-recognition-motif-rrm-revealed-by-hydrogen-deuterium-exchange-mass-spectrometry
#7
Maja K Cieplak-Rotowska, Krzysztof Tarnowski, Marcin Rubin, Marc R Fabian, Nahum Sonenberg, Michal Dadlez, Anna Niedzwiecka
The human GW182 protein plays an essential role in micro(mi)RNA-dependent gene silencing. miRNA silencing is mediated, in part, by a GW182 C-terminal region called the silencing domain, which interacts with the poly(A) binding protein and the CCR4-NOT deadenylase complex to repress protein synthesis. Structural studies of this GW182 fragment are challenging due to its predicted intrinsically disordered character, except for its RRM domain. However, detailed insights into the properties of proteins containing disordered regions can be provided by hydrogen-deuterium exchange mass spectrometry (HDX/MS)...
October 27, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29080204/design-and-validation-of-in-source-atmospheric-pressure-photoionization-hydrogen-deuterium-exchange-mass-spectrometry-with-continuous-feeding-of-d2o
#8
Thamina Acter, Seulgidaun Lee, Eunji Cho, Maeng-Joon Jung, Sunghwan Kim
In this study, continuous in-source hydrogen/deuterium exchange (HDX) atmospheric pressure photoionization (APPI) mass spectrometry (MS) with continuous feeding of D2O was developed and validated. D2O was continuously fed using a capillary line placed on the center of a metal plate positioned between the UV lamp and nebulizer. The proposed system overcomes the limitations of previously reported APPI HDX-MS approaches where deuterated solvents were premixed with sample solutions before ionization. This is particularly important for APPI because solvent composition can greatly influence ionization efficiency as well as the solubility of analytes...
October 27, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29078272/ligand-induced-conformational-dynamics-of-the-escherichia-coli-na-h-antiporter-nhaa-revealed-by-hydrogen-deuterium-exchange-mass-spectrometry
#9
Martin Lorenz Eisinger, Aline Ricarda Dörrbaum, Hartmut Michel, Etana Padan, Julian David Langer
Na(+)/H(+) antiporters comprise a family of membrane proteins evolutionarily conserved in all kingdoms of life and play an essential role in cellular ion homeostasis. The NhaA crystal structure of Escherichia coli has become the paradigm for this class of secondary active transporters. However, structural data are only available at low pH, where NhaA is inactive. Here, we adapted hydrogen/deuterium-exchange mass spectrometry (HDX-MS) to analyze conformational changes in NhaA upon Li(+) binding at physiological pH...
October 31, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29056864/understanding-curli-amyloid-protein-aggregation-by-hydrogen-deuterium-exchange-and-mass-spectrometry
#10
Hanliu Wang, Qin Shu, Don L Rempel, Carl Frieden, Michael L Gross
Bacteria within Curli biofilms are protected from environmental pressures (e.g., disinfectants, antibiotics), and this is responsible for intractable infections. Understanding aggregation of the major protein component of Curli, CsgA, may uncover disease-associated amyloidogenesis mechanisms. Here, we report the application of pulsed hydrogen-deuterium exchange and mass spectrometry (HDX-MS) to study CsgA aggregation, thereby obtaining region-specific information. By following time-dependent peptide signal depletion, presumably a result of insoluble fibril formation, we acquired sigmoidal profiles that are specific for regions (region-specific) of the protein...
September 2017: International Journal of Mass Spectrometry
https://www.readbyqxmd.com/read/29049865/interrogating-membrane-protein-conformational-dynamics-within-native-lipid-compositions
#11
Eamonn Reading, Zoe Hall, Chloe Martens, Tabasom Haghighi, Heather Findlay, Zainab Ahdash, Argyris Politis, Paula J Booth
Membrane protein-lipid interplay is important for cellular function, however, tools enabling the interrogation of protein dynamics within native lipid environments are scarce and often invasive. We establish that the styrene-maleic acid anhydride lipid particle (SMALP) technology can be coupled with hydrogen-deuterium exchange mass spectrometry (HDX-MS) to investigate membrane protein conformational dynamics within native lipid bilayers. We demonstrate changes in accessibility and dynamics of the rhomboid protease, GlpG, captured within three different native lipid compositions, and identify protein regions sensitive to changes in the native lipid environment...
October 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29035497/conformational-dynamics-of-dna-binding-and-cas3-recruitment-by-the-crispr-rna-guide-cascade-complex
#12
Paul B G van Erp, Angela Patterson, Ravi Kant, Luke Berry, Sarah M Golden, Brittney L Forsman, Joshua Carter, Ryan N Jackson, Brian Bothner, Blake Wiedenheft
Bacteria and archaea rely on CRISPR (clustered regularly interspaced short palindromic repeats) RNA-guided adaptive immune systems for sequence specific elimination of foreign nucleic acids. In Escherichia coli, short CRISPR-derived RNAs (crRNAs) assemble with Cas (CRISPR-associated) proteins into a 405-kilodalton multi-subunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Cascade binds foreign DNA complementary to the crRNA guide and recruits Cas3, a trans-acting nuclease-helicase required for target degradation...
October 16, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29030554/hdx-reveals-the-conformational-dynamics-of-dna-sequence-specific-vdr-co-activator-interactions
#13
Jie Zheng, Mi Ra Chang, Ryan E Stites, Yong Wang, John B Bruning, Bruce D Pascal, Scott J Novick, Ruben D Garcia-Ordonez, Keith R Stayrook, Michael J Chalmers, Jeffrey A Dodge, Patrick R Griffin
The vitamin D receptor/retinoid X receptor-α heterodimer (VDRRXRα) regulates bone mineralization via transcriptional control of osteocalcin (BGLAP) gene and is the receptor for 1α,25-dihydroxyvitamin D3 (1,25D3). However, supra-physiological levels of 1,25D3 activates the calcium-regulating gene TRPV6 leading to hypercalcemia. An approach to attenuate this adverse effect is to develop selective VDR modulators (VDRMs) that differentially activate BGLAP but not TRPV6. Here we present structural insight for the action of a VDRM compared with agonists by employing hydrogen/deuterium exchange...
October 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29030428/a-retractable-lid-in-lecithin-cholesterol-acyltransferase-provides-a-structural-mechanism-for-activation-by-apolipoprotein-a-i
#14
Kelly A Manthei, Joomi Ahn, Alisa Glukhova, Wenmin Yuan, Christopher Larkin, Taylor D Manett, Louise Chang, James A Shayman, Milton J Axley, Anna Schwendeman, John J G Tesmer
Lecithin:cholesterol acyltransferase (LCAT) plays a key role in reverse cholesterol transport by transferring an acyl group from phosphatidylcholine to cholesterol, promoting the maturation of high density lipoproteins (HDL) from discoidal to spherical particles. LCAT is activated through an unknown mechanism by apolipoprotein A-I (ApoA-I) and other mimetic peptides that form a belt around HDL. Here we report the crystal structure of LCAT with an extended lid that blocks access to the active site, consistent with an inactive conformation...
October 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28993252/h-d-exchange-mass-spectrometry-and-statistical-coupling-analysis-reveal-a-role-for-allostery-in-a-ferredoxin-dependent-bifurcating-transhydrogenase-catalytic-cycle
#15
Luke Berry, Saroj Poudel, Monika Tokmina-Lukaszewska, Daniel R Colman, Diep M N Nguyen, Gerrit J Schut, Michael W W Adams, John W Peters, Eric S Boyd, Brian Bothner
Recent investigations into ferredoxin-dependent transhydrogenases, a class of enzymes responsible for electron transport, have highlighted the biological importance of flavin-based electron bifurcation (FBEB). FBEB generates biomolecules with very low reduction potential by coupling the oxidation of an electron donor with intermediate potential to the reduction of high and low potential molecules. Bifurcating systems can generate biomolecules with very low reduction potentials, such as reduced ferredoxin (Fd), from species such as NADPH...
January 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28990064/gaseous-signalling-molecule-so2-via-hippo%C3%A2-mst-pathway-to-improve-myocardial-fibrosis-of-diabetic-rats
#16
Maojun Liu, Shengquan Liu, Wenting Tan, Fen Tang, Junrong Long, Zining Li, Biao Liang, Chun Chu, Jun Yang
Recent studies have indicated the existence of an endogenous sulfur dioxide (SO2)‑generating system in the cardiovascular system. The present study aimed to discuss the function and regulatory mechanism of gaseous signal molecule SO2 in inhibiting apoptosis and endoplasmic reticulum stress (ERS) via the Hippo‑MST signaling pathway to improve myocardial fibrosis of diabetic rats. A total of 40 male Sprague‑Dawley rats were randomly divided into four groups (10 rats per group): Normal control group (control group), diabetic rats group [streptozotocin (STZ) group], SO2 intervention group (STZ+SO2 group) and diabetes mellitus rats treated with L‑Aspartic acid β‑hydroxamate (HDX) group (HDX group)...
December 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28972141/dissecting-the-molecular-assembly-of-the-toxoplasma-gondii-myoa-motility-complex
#17
Cameron J Powell, Meredith L Jenkins, Michelle L Parker, Raghavendran Ramaswamy, Anne Kelsen, David M Warshaw, Gary E Ward, John E Burke, Martin J Boulanger
Apicomplexan parasites such as Toxoplasma gondii rely on a unique form of locomotion known as gliding motility. Generating the mechanical forces to support motility are divergent class XIV myosins (MyoA) coordinated by accessory proteins known as light chains. While the importance of the MyoA-light chain complex is well established, the detailed mechanisms governing its assembly and regulation are relatively unknown. To establish a molecular blueprint of this dynamic complex, we first mapped the adjacent binding sites of light chains MLC1 and ELC1 on the MyoA neck (residues 775-818) using a combination of hydrogen-deuterium exchange mass spectrometry (HDX-MS) and isothermal titration calorimetry (ITC)...
September 25, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28971440/probing-conformational-dynamics-of-tau-protein-by-hydrogen-deuterium-exchange-mass-spectrometry
#18
Richard Y-C Huang, Roxana E Iacob, Sethu Sankaranarayanan, Ling Yang, Michael Ahlijanian, Li Tao, Adrienne A Tymiak, Guodong Chen
Fibrillization of the microtubule-associated protein tau has been recognized as one of the signature pathologies of the nervous system in Alzheimer's disease, progressive supranuclear palsy, and other tauopathies. The conformational transition of tau in the fibrillization process, tau monomer to soluble aggregates to fibrils in particular, remains unclear. Here we report on the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) in combination with other biochemical approaches, including Thioflavin S fluorescence measurements, enzyme-linked immunosorbent assay (ELISA), and Western blotting to understand the heparin-induced tau's fibrillization...
October 2, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28956290/ion-mobility-spectrometry-mass-spectrometry-coupled-with-gas-phase-hydrogen-deuterium-exchange-for-metabolomics-analyses
#19
Hossein Maleki, Ahmad K Karanji, Sandra Majuta, Megan M Maurer, Stephen J Valentine
Ion mobility spectrometry-mass spectrometry (IMS-MS) in combination with gas-phase hydrogen/deuterium exchange (HDX) and collision-induced dissociation (CID) is evaluated as an analytical method for small-molecule standard and mixture characterization. Experiments show that compound ions exhibit unique HDX reactivities that can be used to distinguish different species. Additionally, it is shown that gas-phase HDX kinetics can be exploited to provide even further distinguishing capabilities by using different partial pressures of reagent gas...
September 27, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28933661/suppressing-allostery-in-epitope-mapping-experiments-using-millisecond-hydrogen-deuterium-exchange-mass-spectrometry
#20
Bin Deng, Shaolong Zhu, Andrew M Macklin, Jianrong Xu, Cristina Lento, Adnan Sljoka, Derek J Wilson
Localization of the interface between the candidate antibody and its antigen target, commonly known as epitope mapping, is a critical component of the development of therapeutic monoclonal antibodies. With the recent availability of commercial automated systems, hydrogen / deuterium eXchange (HDX) is rapidly becoming the tool for mapping epitopes preferred by researchers in both industry and academia. However, this approach has a significant drawback in that it can be confounded by 'allosteric' structural and dynamic changes that result from the interaction, but occur far from the point(s) of contact...
November 2017: MAbs
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