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Tossounian MA, Khanh Truong AC, Buts L, Wahni K, Mourenza Á, Leermakers M, Vertommen D, Mateos LM, Volkov AN, Messens J. Methionine sulfoxide reductase B from Corynebacterium diphtheriae catalyzes sulfoxide reduction via an intramolecular disulfide cascade. J Biol Chem 2020; 295:3664-3677. [PMID: 31992594 DOI: 10.1074/jbc.ra119.012438] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/24/2020] [Indexed: 11/06/2022] Open
Abstract
Corynebacterium diphtheriae is a human pathogen that causes diphtheria. In response to immune system-induced oxidative stress, C. diphtheriae expresses antioxidant enzymes, among which are methionine sulfoxide reductase (Msr) enzymes, which are critical for bacterial survival in the face of oxidative stress. Although some aspects of the catalytic mechanism of the Msr enzymes have been reported, several details still await full elucidation. Here, we solved the solution structure of C. diphtheriae MsrB (Cd-MsrB) and unraveled its catalytic and oxidation-protection mechanisms. Cd-MsrB catalyzes methionine sulfoxide reduction involving three redox-active cysteines. Using NMR heteronuclear single-quantum coherence spectra, kinetics, biochemical assays, and MS analyses, we show that the conserved nucleophilic residue Cys-122 is S-sulfenylated after substrate reduction, which is then resolved by a conserved cysteine, Cys-66, or by the nonconserved residue Cys-127. We noted that the overall structural changes during the disulfide cascade expose the Cys-122-Cys-66 disulfide to recycling through thioredoxin. In the presence of hydrogen peroxide, Cd-MsrB formed reversible intra- and intermolecular disulfides without losing its Cys-coordinated Zn2+, and only the nonconserved Cys-127 reacted with the low-molecular-weight (LMW) thiol mycothiol, protecting it from overoxidation. In summary, our structure-function analyses reveal critical details of the Cd-MsrB catalytic mechanism, including a major structural rearrangement that primes the Cys-122-Cys-66 disulfide for thioredoxin reduction and a reversible protection against excessive oxidation of the catalytic cysteines in Cd-MsrB through intra- and intermolecular disulfide formation and S-mycothiolation.
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Shabaev AR, Kazantsev AN, Tarasov RS, Ruban EV, Lider RI, Iakhnis EI, Solobuev AI, Volkov AN, Mironov AV. [Surgical treatment of a patient with saccular arterial aneurysm of the cavernous-ophthalmic segment]. ANGIOLOGII︠A︡ I SOSUDISTAI︠A︡ KHIRURGII︠A︡ = ANGIOLOGY AND VASCULAR SURGERY 2020; 25:131-138. [PMID: 31855210 DOI: 10.33529/angio2019412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Presented in the article are the results of surgical management of a patient with an extremely rare pathology - a saccular arterial aneurysm of the cavernous-ophthalmic segment of the left internal carotid artery. We performed multistage open surgical intervention in the following scope: osteoplastic pterional craniotomy on the left, creation of a wide-lumen anastomosis between the left external carotid artery and M2 segment of the left middle cerebral artery with the use of the radial artery, ligation of the cervical portion of the left internal carotid artery and clipping of its supraclinoid portion. The chosen surgical policy made it possible to create sufficient volumetric blood flow through the shunt, comparable to the blood flow through the internal carotid artery, which helped avoid ischaemic stroke after exclusion of the aneurysm from circulation. A conclusion was drawn on efficacy of this method of treatment.
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Tarasov RS, Ivanov SV, Kazantsev AN, Volkov AN, Shabayev AR, Bakovskiy KV, Lider RY, Grachev KI. [Long-term outcomes of coronary artery bypass surgery in young patients]. Khirurgiia (Mosk) 2019:57-63. [PMID: 31714531 DOI: 10.17116/hirurgia201911157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To analyze long-term outcomes of CABG in young patients, incidence and structure of adverse cardiovascular events depending on patients' age. MATERIAL AND METHODS There were 175 young patients (up to 44 years old in accordance with WHO classification) who underwent CABG for the period from 2006 to 2016. The control group included 175 patients aged 45 years and older who were randomly selected among patients operated in the same period. Overall long-term follow-up period was 81.9±15.75 months (≈ 6.8 years). Data on long-term survival and adverse cardiovascular events were available in 86.3% of patients in general sample and 72.6% of young patients. RESULTS Young patients undergoing CABG were usually characterized by the absence of severe concomitant diseases, moderate coronary atherosclerosis by SYNTAX Score scale, high percentage of left ventricular aneurysm and previous PCI. Incidence and structure of in-hospital and long-term adverse cardiovascular events in young and older patients confirmed satisfactory results of CABG regardless age.
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Yoon JH, Kulesha AV, Lengyel-Zhand Z, Volkov AN, Rempillo JJ, D'Souza A, Costeas C, Chester C, Caselle ER, Makhlynets OV. Uno Ferro, a de novo Designed Protein, Binds Transition Metals with High Affinity and Stabilizes Semiquinone Radical Anion. Chemistry 2019; 25:15252-15256. [PMID: 31509280 DOI: 10.1002/chem.201904020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Indexed: 11/07/2022]
Abstract
Metalloenzymes often utilize radicals in order to facilitate chemical reactions. Recently, DeGrado and co-workers have discovered that model proteins can efficiently stabilize semiquinone radical anion produced by oxidation of 3,5-di-tert-butylcatechol (DTBC) in the presence of two zinc ions. Here, we show that the number and the nature of metal ions have relatively minor effect on semiquinone stabilization in model proteins, with a single metal ion being sufficient for radical stabilization. The radical is stabilized by both metal ion, hydrophobic sequestration, and interactions with the hydrophilic residues in the protein interior resulting in a remarkable, nearly 500 mV change in the redox potential of the SQ. - /catechol couple compared to bulk aqueous solution. Moreover, we have created 4G-UFsc, a single metal ion-binding protein with pm affinity for zinc that is higher than any other reported model systems and is on par with many natural zinc-containing proteins. We expect that the robust and easy-to-modify DFsc/UFsc family of proteins will become a versatile tool for mechanistic model studies of metalloenzymes.
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Rice HC, de Malmazet D, Schreurs A, Frere S, Van Molle I, Volkov AN, Creemers E, Vertkin I, Nys J, Ranaivoson FM, Comoletti D, Savas JN, Remaut H, Balschun D, Wierda KD, Slutsky I, Farrow K, De Strooper B, de Wit J. Secreted amyloid-β precursor protein functions as a GABA BR1a ligand to modulate synaptic transmission. Science 2019; 363:363/6423/eaao4827. [PMID: 30630900 DOI: 10.1126/science.aao4827] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/30/2018] [Accepted: 11/14/2018] [Indexed: 12/16/2022]
Abstract
Amyloid-β precursor protein (APP) is central to the pathogenesis of Alzheimer's disease, yet its physiological function remains unresolved. Accumulating evidence suggests that APP has a synaptic function mediated by an unidentified receptor for secreted APP (sAPP). Here we show that the sAPP extension domain directly bound the sushi 1 domain specific to the γ-aminobutyric acid type B receptor subunit 1a (GABABR1a). sAPP-GABABR1a binding suppressed synaptic transmission and enhanced short-term facilitation in mouse hippocampal synapses via inhibition of synaptic vesicle release. A 17-amino acid peptide corresponding to the GABABR1a binding region within APP suppressed in vivo spontaneous neuronal activity in the hippocampus of anesthetized Thy1-GCaMP6s mice. Our findings identify GABABR1a as a synaptic receptor for sAPP and reveal a physiological role for sAPP in regulating GABABR1a function to modulate synaptic transmission.
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Volkov AN, Khabieva SM, Smirnova EY, Larionov AV. [The genetic diagnostics of mutations UGT1A1 in practice of modern medicine.]. Klin Lab Diagn 2019; 63:186-192. [PMID: 30673201 DOI: 10.18821/0869-2084-2018-63-3-186-192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 11/22/2017] [Indexed: 11/17/2022]
Abstract
The detection of mutations of the gene of UDF-glucuronyltransferase A1 (UGT1A1) has an important practical value. The carriers of mutant genotypes, mainly *28/*28, are characterized by a reduced function of glucuronidation and excretion of a number of endogenous and exogenous toxins. A precise association of particular forms of benign hyperbilirubinemia (especially Gilbert's syndrome) with mutations in promoter and exonic areas of UGT1A1 is established. On the other hand, carriers of various genotypes of UGT1A1 differ significantly in metabolism characteristics of a number of common medications (irinotecan, belinostat, etc.), that requires a dosage of these medications considering individual genetic status of patient. The analysis of modern technical solutions for genetic diagnostics of UGT1A1 mutations is carried out. The particular attention is paid to discussion of national developments for genetic typing of UGT1A1. The conclusion is made concerning small assortment of corresponding test-systems of Russian production. In some cases, there is no data about their main analytical and diagnostic characteristics. When developing design of diagnosticums, various methodological approaches are applied that allow to potential consumers to choose depending on financial technical capabilities of laboratory, amount of implemented analyses, qualification of personnel. To support UGT1A1 research instrumentally, laboratory equipment of national manufacturers can be sufficient that would permit to organize entire analytical cycle on the basis of import substitution principle.
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Kalyakin AS, Lyagaeva JY, Volkov AN, Medvedev DA. Unusual oxygen detection by means of a solid state sensor based on a CaZr0.9In0.1O3–δ proton-conducting electrolyte. J Electroanal Chem (Lausanne) 2019. [DOI: 10.1016/j.jelechem.2019.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Sedykh DY, Kazantsev AN, Tarasov RS, Kashtalap VV, Volkov AN, Grachev KI, Shabayev AR, Barbarash OL. [Predictors of Progressive Course of Multifocal Atherosclerosis in Patients With Myocardial Infarction]. ACTA ACUST UNITED AC 2019; 59:36-44. [PMID: 31131766 DOI: 10.18087/cardio.2019.5.10257] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 05/25/2019] [Indexed: 11/18/2022]
Abstract
PURPOSE Determination of clinical and instrumental predictors of progressive course of multifocal atherosclerosis (MFA) in patients one year after myocardial infarction (MI), initially having hemodynamically insignificant stenoses of carotid arteries. MATERIALS AND METHODS From database of patients with acute coronary syndrome treated in the Kemerovo Regional Clinical Cardiac Dispensary in 2009-2010 we selected for this study 141 patients with verified diagnosis of MI and hemodynamically insignificant lesions in the internal carotid artery (ICA) (stenosis up ≤ 55 %). All patients had coronary atherosclerosis verified on coronary angiography at admission because of MI. A multivariate analysis of possible predictors of the progressive course of multifocal atherosclerosis was made based on assessment of the development of cardiovascular complications (CVC) (death, MI, stroke and transient cerebral circulatory attacks [TIA]), as well as revascularizations and negative dynamics of parameters of color duplex scanning (CDS) of ICA during one year after MI. RESULTS One year after MI the overall incidence of CVC was 16.3 % (n=23). Structure of registered events was as follows: death from MI 7.1 % (n=10), deaths from stroke 2.1 % (n=3) and other causes 2.1 % (n=3), non-fatal MI 5.0 % (n=7), non-fatal stroke / TIA 2.1 % (n=3), carotid revascularization 2.8 % (n=4), coronary revascularization 14.9 % (n=21). CDC of ICAs was repeated in 125 patients. There were 17 (13.6 %) cases of progression of carotid atherosclerosis in the form of de novo bilateral stenoses in 14 (11.2 %) patients, stenoses in the left and right ICA 1 patient and 2 patients, respectively. The following predictors of progression of atherosclerosis of cerebral arteries were identified: family history of cardiovascular diseases (CVD),ICA stenosis ≥45 %, baseline circular atherosclerotic plaque (ASP). Predictors of high risk of stroke were family history of CVD, history of stroke,ICA stenosis ≥45 %, heterogeneous hypoechoic ASP. As predictors of lethal outcome, we identified history of MI, high functional class of angina preceding the index MI, severe coronary vascular bed involvement (SYNTAX score >23), presence of any bilateral atherosclerotic lesion in ICAs, and heterogeneous hypoechoic ASP. Assessment of the contribution of adherence to therapy in the prognosis 1 year after hospital discharge was fulfilled in 125 alive patients. It allowed to conclude that patients with progression of atherosclerosis and nonfatal CVC were characterized by insufficient adherence to standard therapy. CONCLUSION Predictors of the progressive course of multifocal atherosclerosis during one year after MI were identified in this study. It is necessary to strengthen therapeutic and preventive measures aimed at minimization of the impact of these factors in this category of patients.
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Caselle EA, Yoon JH, Bhattacharya S, Rempillo JJL, Lengyel Z, D'Souza A, Moroz YS, Tolbert PL, Volkov AN, Forconi M, Castañeda CA, Makhlynets OV, Korendovych IV. Front Cover: Kemp Eliminases of the AlleyCat Family Possess High Substrate Promiscuity (ChemCatChem 5/2019). ChemCatChem 2019. [DOI: 10.1002/cctc.201900266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Caselle EA, Yoon JH, Bhattacharya S, Rempillo JJL, Lengyel Z, D'Souza A, Moroz YS, Tolbert PL, Volkov AN, Forconi M, Castañeda CA, Makhlynets OV, Korendovych IV. Kemp Eliminases of the AlleyCat Family Possess High Substrate Promiscuity. ChemCatChem 2019. [DOI: 10.1002/cctc.201900269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Caselle EA, Yoon JH, Bhattacharya S, Rempillo JJ, Lengyel Z, D’Souza A, Moroz YS, Tolbert PL, Volkov AN, Forconi M, Castañeda CA, Makhlynets OV, Korendovych IV. Kemp Eliminases of the AlleyCat Family Possess High Substrate Promiscuity. ChemCatChem 2019; 11:1425-1430. [PMID: 31788134 PMCID: PMC6884320 DOI: 10.1002/cctc.201801994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Indexed: 10/21/2023]
Abstract
Minimalist enzymes designed to catalyze model reactions provide useful starting points for creating catalysts for practically important chemical transformations. We have shown that Kemp eliminases of the AlleyCat family facilitate conversion of leflunomide (an immunosupressor pro-drug) to its active form teriflunomide with outstanding rate enhancement (nearly four orders of magnitude) and catalytic proficiency (more than seven orders of magnitude) without any additional optimization. This remarkable activity is achieved by properly positioning the substrate in close proximity to the catalytic glutamate with very high pKa.
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Kazantsev AN, Tarasov RS, Burkov NN, Volkov AN, Grachev KI, Iakhnis EI, Lider RI, Shabaev AR, Barbarash LS. [In-hospital outcomes of transcutaneous coronary intervention and carotid endarterectomy in hybrid and staged regimens]. ANGIOLOGIIA I SOSUDISTAIA KHIRURGIIA = ANGIOLOGY AND VASCULAR SURGERY 2019; 25:101-107. [PMID: 30994615 DOI: 10.33529/angio2019114] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The aim of this study was comparative assessment of in-hospital outcomes after hybrid and staged surgical management of patients presenting with haemodynamically significant lesions of the coronary (CA) and brachiocephalic arteries (BCA) treated by means of either endovascular or surgical techniques. Over the period from 2010 to 2017, we operated on a total of 197 patients with stenotic lesions of the carotid and coronary arteries. The strategy of revascularization included transcutaneous coronary intervention (TCI) and carotid endarterectomy (CEA). Of these, 73 (37%) patients underwent staged revascularization of the brain and myocardium in various sequence (TCI-CEA or CEA-TCI), with a mean interval between the operations amounting to 9.89±7.36 months. Unfavourable outcomes were regarded as the development of such significant cardiovascular events as myocardial infarction (MI), acute impairment of cerebral circulation, death, repeat unplanned revascularization. For hybrid strategy (TCI+CEA) the index period of assessing the outcomes was the single in-hospital period, whereas for the staged strategy it was the time period beginning from the in-hospital period of the primary operation and ending by the in-hospital period of the second stage. The groups were comparable by the absolute majority of the parameters. More than half of the patients were elderly males. One third had a history of MI. The findings of coronary angiography most often revealed lesions of 1-2 CAs. The average parameters of carotid artery stenosis, according to the BCA angiography varied from 74.9 to 82.6%, with bilateral occlusive stenotic lesions being revealed in every third patient. In connection with more frequent involvement of 1-2 CAs the patients underwent implantation of 1-2 stents. In our sample we used a total of 247 stents. Of these, 119 were uncoated and 128 were drug-eluting stents. No between-group significant differences in the development of unfavourable cardiovascular events during the in-hospital postoperative period were revealed. However, despite this, a pronounced negative tendency of the complication rate was noted in the group of staged revascularization. Non-optimal time intervals between the stages of the operations in a third of cases exceeded one year on the patient's own initiative. Nearly a quarter of patients did not come for the second stage of revascularization. An important finding of our study was no increase in the risk of stent thrombosis in hybrid operations compared with the staged approach, despite administration of a loading dose of clopidogrel after CEA, but not before TCI. Another significant result was the fact of greater availability of revascularization of the myocardium and the brain within the framework of the hybrid strategy as compared with the staged one, which may play an important role in prevention of ischaemic unfavourable events in the remote period of follow up.
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Nguyen HH, Volkov AN, Vandenbussche G, Tompa P, Pauwels K. In vivo biotinylated calpastatin improves the affinity purification of human m-calpain. Protein Expr Purif 2018; 145:77-84. [PMID: 29339216 DOI: 10.1016/j.pep.2018.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/14/2017] [Accepted: 01/05/2018] [Indexed: 12/31/2022]
Abstract
Recently we established a novel affinity purification method for calpain by exploiting the specific and reversible binding properties of its intrinsically disordered protein inhibitor, calpastatin. The immobilization strategy relied on the strength and specificity of the biotin - streptavidin interaction. Here, we report an improved and optimized method that even enables the general applicability of in vivo biotinylated (intrinsically disordered) proteins in any affinity capture strategy. Since in vitro chemical biotinylation is only accomplished with reagents that lack exact site specificity, it can not only cause sample heterogeneity but it can also hamper the functionality of the biotinylated molecules. Therefore, we have developed a recombinant expression protocol to produce in vivo biotinylated human calpastatin domain 1 (hCSD1) in Escherichia coli. We have experimentally verified that the biotinylated polypeptide tag is compatible with the intrinsically disordered state of hCSD1 and that it does not influence the functional properties of this intrinsically disordered protein (IDP). The in vivo biotinylated hCSD1 was then used without the need of any prepurification step prior to the affinity capturing of its substrate, human m-calpain. This leads to a simplified purification strategy that allows capturing the calpain efficiently from a complex biological mixture with only a single chromatogaphic step and in a considerably reduced timeframe. Our approach is generally applicable through the in vivo biotinylation of any IDP of interest, and its practical implementation will showcase the power to exploit the properties of IDPs in affinity capture strategies.
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Volkov AN, Rytenkova OI, Babarykina TA, Lysenko DI. [The cytogenetic diagnostic of chromosome anomalies under non-developing pregnancy.]. Klin Lab Diagn 2017; 62:553-556. [PMID: 30807055 DOI: 10.18821/0869-2084-2017-62-9-553-556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 04/15/2017] [Indexed: 06/09/2023]
Abstract
The purpose of the study is to analyze qualitative and quantitative characteristics of chromosome anomalies in abortus under undeveloped pregnancy. The cytogenetic analysis was implemented concerning embryonic material obtained after artificial abortion of undeveloped pregnancy in 57 women. The percentage of abnormal karyotypes made up to 67.3%. The number abnormalities prevailed among chromosome disorders. The structural alterations of chromosomes occurred significantly rarely. The cytogenetic analysis of abortion material can become a valuable diagnostic tool permitting to establish the role of genetic factors in termination of pregnancy both in cases of natural conception and application of ART.
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Antonik PM, Volkov AN, Broder UN, Re DL, van Nuland NAJ, Crowley PB. Anomer-Specific Recognition and Dynamics in a Fucose-Binding Lectin. Biochemistry 2016; 55:1195-203. [PMID: 26845253 DOI: 10.1021/acs.biochem.5b01212] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Sugar binding by a cell surface ∼29 kDa lectin (RSL) from the bacterium Ralstonia solanacearum was characterized by NMR spectroscopy. The complexes formed with four monosaccharides and four fucosides were studied. Complete resonance assignments and backbone dynamics were determined for RSL in the sugar-free form and when bound to l-fucose or d-mannose. RSL was found to interact with both the α- and the β-anomer of l-fucose and the "fucose like" sugars d-arabinose and l-galactose. Peak splitting was observed for some resonances of the binding site residues. The assignment of the split signals to the α- or β-anomer was confirmed by comparison with the spectra of RSL bound to methyl-α-l-fucoside or methyl-β-l-fucoside. The backbone dynamics of RSL were sensitive to the presence of ligand, with the protein adopting a more compact structure upon binding to l-fucose. Taking advantage of tryptophan residues in the binding sites, we show that the indole resonance is an excellent reporter on ligand binding. Each sugar resulted in a distinct signature of chemical shift perturbations, suggesting that tryptophan signals are a sufficient probe of sugar binding.
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Volkov AN. [The fixed human lymphocytes as a source of DNA for polymerase chain reaction diagnostic.]. Klin Lab Diagn 2016; 61:819-821. [PMID: 31536692 DOI: 10.18821/0869-2084-2016-61-12-819-821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 05/15/2016] [Indexed: 06/10/2023]
Abstract
The article presents the results of studying of quantitative and qualitative characteristics of DNA samples separated by sorbate technique from human lymphocytes went through ethanol acetic fixation for preparation of cytogenetic specimen. The concentration of DNA varied within range 18.9-213.2 ng per mkl. The rate A260/A280 amounted to 1.47-2.53. All samples were found suitable for application of polymerase chain reaction during detection of AZF-deletions of Y-chromosome. The considered mode of separation of DNA is highly efficient in respect of fixed lymphocytes and it can be applied in medical biologic studies.
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Abstract
Many biomolecular interactions proceed via lowly populated, transient intermediates. Believed to facilitate formation of a productive complex, these short-lived species are inaccessible to conventional biophysical and structural techniques and, until recently, could only be studied by theoretical simulations. Recent development of experimental approaches sensitive to the presence of minor species--in particular paramagnetic relaxation enhancement (PRE) NMR spectroscopy--has enabled direct visualization and detailed characterization of such lowly populated states. Collectively referred to as an encounter complex, the binding intermediates are particularly important in transient protein interactions, such as those orchestrating signaling cascades or energy-generating electron transfer (ET) chains. Here I discuss encounter complexes of redox proteins mediating biological ET reactions, which are essential for many vital cellular activities including oxidative phosphorylation and photosynthesis. In particular, this Account focuses on the complex of cytochrome c (Cc) and cytochrome c peroxidase (CcP), which is a paradigm of biomolecular ET and an attractive system for studying protein binding and enzymatic catalysis. The Cc-CcP complex formation proceeds via an encounter state, consisting of multiple protein-protein orientations sampled in the search of the dominant, functionally active bound form and exhibiting a broad spatial distribution, in striking agreement with earlier theoretical simulations. At low ionic strength, CcP binds another Cc molecule to form a weak ternary complex, initially inferred from kinetics experiments and postulated to account for the measured ET activity. Despite strenuous efforts, the ternary complex could not be observed directly and remained eagerly sought for the past two decades. Very recently, we have solved its structure in solution and shown that it consists of two binding forms: the dominant, ET-inactive geometry and an ensemble of lowly populated species with short separations between Cc and CcP cofactors, which summarily account for the measured ET rate. Unlike most protein complexes, which require accurate alignment of the binding surfaces in a single, well-defined orientation to carry out their function, redox proteins can form multiple productive complexes. As fast ET will occur any time the redox centers of the binding partners are close enough to ensure efficient electron tunneling across the interface, many protein-protein orientations are expected to be ET active. The present analysis confirms that the low-occupancy states can support the functional ET activity and contribute to the stability of redox protein complexes. As illustrated here, boundaries between the dominant and the encounter forms become blurred for many dynamic ET systems, which are more aptly described by ensembles of functionally and structurally heterogeneous bound forms.
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Sterckx YGJ, Volkov AN. Cofactor-Dependent Structural and Binding Properties of Yeast Cytochrome c Peroxidase. Biochemistry 2014; 53:4526-36. [DOI: 10.1021/bi500603w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Sterckx YGJ, Volkov AN, Vranken WF, Kragelj J, Jensen MR, Buts L, Garcia-Pino A, Jové T, Van Melderen L, Blackledge M, van Nuland NAJ, Loris R. Small-angle X-ray scattering- and nuclear magnetic resonance-derived conformational ensemble of the highly flexible antitoxin PaaA2. Structure 2014; 22:854-65. [PMID: 24768114 DOI: 10.1016/j.str.2014.03.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 03/14/2014] [Accepted: 03/15/2014] [Indexed: 11/26/2022]
Abstract
Antitoxins from prokaryotic type II toxin-antitoxin modules are characterized by a high degree of intrinsic disorder. The description of such highly flexible proteins is challenging because they cannot be represented by a single structure. Here, we present a combination of SAXS and NMR data to describe the conformational ensemble of the PaaA2 antitoxin from the human pathogen E. coli O157. The method encompasses the use of SAXS data to filter ensembles out of a pool of conformers generated by a custom NMR structure calculation protocol and the subsequent refinement by a block jackknife procedure. The final ensemble obtained through the method is validated by an established residual dipolar coupling analysis. We show that the conformational ensemble of PaaA2 is highly compact and that the protein exists in solution as two preformed helices, connected by a flexible linker, that probably act as molecular recognition elements for toxin inhibition.
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Vanwetswinkel S, Volkov AN, Sterckx YGJ, Garcia-Pino A, Buts L, Vranken WF, Bouckaert J, Roy R, Wyns L, van Nuland NAJ. Study of the structural and dynamic effects in the FimH adhesin upon α-d-heptyl mannose binding. J Med Chem 2014; 57:1416-27. [PMID: 24476493 DOI: 10.1021/jm401666c] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Uropathogenic Escherichia coli cause urinary tract infections by adhering to mannosylated receptors on the human urothelium via the carbohydrate-binding domain of the FimH adhesin (FimHL). Numerous α-d-mannopyranosides, including α-d-heptyl mannose (HM), inhibit this process by interacting with FimHL. To establish the molecular basis of the high-affinity HM binding, we solved the solution structure of the apo form and the crystal structure of the FimHL-HM complex. NMR relaxation analysis revealed that protein dynamics were not affected by the sugar binding, yet HM addition promoted protein dimerization, which was further confirmed by small-angle X-ray scattering. Finally, to address the role of Y48, part of the "tyrosine gate" believed to govern the affinity and specificity of mannoside binding, we characterized the FimHL Y48A mutant, whose conformational, dynamical, and HM binding properties were found to be very similar to those of the wild-type protein.
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Vanwetswinkel S, van Nuland NAJ, Volkov AN. Paramagnetic properties of the low- and high-spin states of yeast cytochrome c peroxidase. JOURNAL OF BIOMOLECULAR NMR 2013; 57:21-26. [PMID: 23832496 DOI: 10.1007/s10858-013-9760-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 06/26/2013] [Indexed: 06/02/2023]
Abstract
Here we describe paramagnetic NMR analysis of the low- and high-spin forms of yeast cytochrome c peroxidase (CcP), a 34 kDa heme enzyme involved in hydroperoxide reduction in mitochondria. Starting from the assigned NMR spectra of a low-spin CN-bound CcP and using a strategy based on paramagnetic pseudocontact shifts, we have obtained backbone resonance assignments for the diamagnetic, iron-free protein and the high-spin, resting-state enzyme. The derived chemical shifts were further used to determine low- and high-spin magnetic susceptibility tensors and the zero-field splitting constant (D) for the high-spin CcP. The D value indicates that the latter contains a hexacoordinate heme species with a weak field ligand, such as water, in the axial position. Being one of the very few high-spin heme proteins analyzed in this fashion, the resting state CcP expands our knowledge of the heme coordination chemistry in biological systems.
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Volkov AN, van Nuland NAJ. Solution NMR study of the yeast cytochrome c peroxidase: cytochrome c interaction. JOURNAL OF BIOMOLECULAR NMR 2013; 56:255-263. [PMID: 23708935 DOI: 10.1007/s10858-013-9744-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 05/13/2013] [Indexed: 06/02/2023]
Abstract
Here we present a solution NMR study of the complex between yeast cytochrome c (Cc) and cytochrome c peroxidase (CcP), a paradigm for understanding the biological electron transfer. Performed for the first time, the CcP-observed heteronuclear NMR experiments were used to probe the Cc binding in solution. Combining the Cc- and CcP-detected experiments, the binding interface on both proteins was mapped out, confirming that the X-ray structure of the complex is maintained in solution. Using NMR titrations and chemical shift perturbation analysis, we show that the interaction is independent of the CcP spin-state and is only weakly affected by the Cc redox state. Based on these findings, we argue that the complex of the ferrous Cc and the cyanide-bound CcP is a good mimic of the catalytically-active Cc-CcP compound I species. Finally, no chemical shift perturbations due to the Cc binding at the low-affinity CcP site were observed at low ionic strength. We discuss possible reasons for the absence of the effects and outline future research directions.
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Volkov AN, Wohlkonig A, Soror SH, van Nuland NAJ. Expression, Purification, Characterization, and Solution Nuclear Magnetic Resonance Study of Highly Deuterated Yeast Cytochrome c Peroxidase with Enhanced Solubility. Biochemistry 2013; 52:2165-75. [DOI: 10.1021/bi400220w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Volkov AN, van Nuland NAJ. Electron transfer interactome of cytochrome C. PLoS Comput Biol 2012; 8:e1002807. [PMID: 23236271 PMCID: PMC3516563 DOI: 10.1371/journal.pcbi.1002807] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 10/12/2012] [Indexed: 01/31/2023] Open
Abstract
Lying at the heart of many vital cellular processes such as photosynthesis and respiration, biological electron transfer (ET) is mediated by transient interactions among proteins that recognize multiple binding partners. Accurate description of the ET complexes – necessary for a comprehensive understanding of the cellular signaling and metabolism – is compounded by their short lifetimes and pronounced binding promiscuity. Here, we used a computational approach relying solely on the steric properties of the individual proteins to predict the ET properties of protein complexes constituting the functional interactome of the eukaryotic cytochrome c (Cc). Cc is a small, soluble, highly-conserved electron carrier protein that coordinates the electron flow among different redox partners. In eukaryotes, Cc is a key component of the mitochondrial respiratory chain, where it shuttles electrons between its reductase and oxidase, and an essential electron donor or acceptor in a number of other redox systems. Starting from the structures of individual proteins, we performed extensive conformational sampling of the ET-competent binding geometries, which allowed mapping out functional epitopes in the Cc complexes, estimating the upper limit of the ET rate in a given system, assessing ET properties of different binding stoichiometries, and gauging the effect of domain mobility on the intermolecular ET. The resulting picture of the Cc interactome 1) reveals that most ET-competent binding geometries are located in electrostatically favorable regions, 2) indicates that the ET can take place from more than one protein-protein orientation, and 3) suggests that protein dynamics within redox complexes, and not the electron tunneling event itself, is the rate-limiting step in the intermolecular ET. Further, we show that the functional epitope size correlates with the extent of dynamics in the Cc complexes and thus can be used as a diagnostic tool for protein mobility. A number of vital cellular processes such as respiration, photosynthesis, and multifarious metabolic conversions rely on a long-range electron transfer (ET) among protein molecules. Full understanding of the biological ET requires accurate description of the redox protein complexes, which is hampered by their pronounced mobility and short lifetimes. Here we used a simple computational approach to predict the ET properties of the physiological protein complexes of cytochrome c (Cc) – a small electron carrier that coordinates the electron flow among different redox partners. By performing extensive conformational sampling of the possible binding geometries, we mapped out functional epitopes in the Cc complexes and assessed their ET properties. Our study suggests that protein dynamics within redox complexes is the rate-limiting step in the intermolecular ET and indicates that the functional epitope size correlates with the extent of dynamics in the Cc complexes. We believe that the latter finding can be used as a diagnostic tool for protein mobility and expect that this work will engender future studies of the intermolecular ET in biological networks.
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Volkov AN, Vanwetswinkel S, Van de Water K, van Nuland NAJ. Redox-dependent conformational changes in eukaryotic cytochromes revealed by paramagnetic NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2012; 52:245-256. [PMID: 22318343 DOI: 10.1007/s10858-012-9607-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Accepted: 01/15/2012] [Indexed: 05/31/2023]
Abstract
Cytochrome c (Cc) is a soluble electron carrier protein, transferring reducing equivalents between Cc reductase and Cc oxidase in eukaryotes. In this work, we assessed the structural differences between reduced and oxidized Cc in solution by paramagnetic NMR spectroscopy. First, we have obtained nearly-complete backbone NMR resonance assignments for iso-1-yeast Cc and horse Cc in both oxidation states. These were further used to derive pseudocontact shifts (PCSs) arising from the paramagnetic haem group. Then, an extensive dataset comprising over 450 measured PCSs and high-resolution X-ray and solution NMR structures of both proteins were used to define the anisotropic magnetic susceptibility tensor, Δχ. For most nuclei, the PCSs back-calculated from the Δχ tensor are in excellent agreement with the experimental PCS values. However, several contiguous stretches-clustered around G41, N52, and A81-exhibit large deviations both in yeast and horse Cc. This behaviour is indicative of redox-dependent structural changes, the extent of which is likely conserved in the protein family. We propose that the observed discrepancies arise from the changes in protein dynamics and discuss possible functional implications.
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