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Rudge MVC, Souza FP, Abbade JF, Hallur RLS, Marcondes JPC, Piculo F, Marini G, Vesentini G, Thabane L, Witkin SS, Calderon IMP, Barbosa AMP, Rudge MV, Barbosa AMP, Calderon IMP, Souza FP, Abbade JF, Hallur LSR, Piculo F, Marini G, Vesentini G, Thabane L, Palma MS, Graeff CFO, Arni RK, Herculano RD, Salvadori DF, Mateus S, Dal Pai Silva M, Magalhães CG, Costa RA, Lima SAM, Felisbino SL, Barbosa W, Atallah A, Girão MJB, Di Bella Z, Uchoa SM, Payão S, Hijas A, Berghman B, De Bie R, Sobrevia L, Junginger B, Alves FCB, Rossignoli PS, Prudencio CB, Orlandi MIG, Gonçalves MI, Nunes SK, Catinelli BB, Quiroz S, Sarmento BV, Pinheiro FA, Sartorão CI, Lucas RR, Reyes DRA, Quiroz SBCV, Enriquez EMA, Oliveira RG, Floriano JF, Marcondes JPC, Barneze S, Dangió TD, Pascon T, Rossignoli P, Freitas JV, Takano L, Reis F, Caldeirão TD, Fernandes JN, Carr AM, Gaitero MVC, Corrente JE, Nunes HRC, Candido AF, Costa SMB, Dangió TD, Pascon T, Melo JVF, Takano L, Reis FVDS, Caldeirão TD, Carr AM, Garcia GA, Rabadan GB, Bassin HCM, Suyama KS, Damasceno LN, Takemoto MLS, Menezes MD, Bussaneli DG, Nogueira VKC, Lima PR, Lourenço IO, Marostica de Sá J, Megid RA, Caruso IP, Rasmussen LT, Prata GM, Piculo F, Vesentini G, Arantes MA, Ferraz GAR, Camargo LP, Kron MR, Corrente JE, Nunes HRC. Study protocol to investigate biomolecular muscle profile as predictors of long-term urinary incontinence in women with gestational diabetes mellitus. BMC Pregnancy Childbirth 2020; 20:117. [PMID: 32075598 PMCID: PMC7031907 DOI: 10.1186/s12884-020-2749-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 01/17/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pelvic floor muscles (PFM) and rectus abdominis muscles (RAM) of pregnant diabetic rats exhibit atrophy, co-localization of fast and slow fibers and an increased collagen type I/III ratio. However, the role of similar PFM or RAM hyperglycemic-related myopathy in women with gestational diabetes mellitus (GDM) remains poorly investigated. This study aims to assess the frequency of pelvic floor muscle disorders and pregnancy-specific urinary incontinence (PS-UI) 12 months after the Cesarean (C) section in women with GDM. Specifically, differences in PFM/RAM hyperglycemic myopathy will be evaluated. METHODS The Diamater is an ongoing cohort study of four groups of 59 pregnant women each from the Perinatal Diabetes Research Centre (PDRC), Botucatu Medical School (FMB)-UNESP (São Paulo State University), Brazil. Diagnosis of GDM and PS-UI will be made at 24-26 weeks, with a follow-up at 34-38 weeks of gestation. Inclusion in the study will occur at the time of C-section, and patients will be followed at 24-48 h, 6 weeks and 6 and 12 months postpartum. Study groups will be classified as (1) GDM plus PS-UI; (2) GDM without PS-UI; (3) Non-GDM plus PS-UI; and (4) Non-GDM without PS-UI. We will analyze relationships between GDM, PS-UI and hyperglycemic myopathy at 12 months after C-section. The mediator variables to be evaluated include digital palpation, vaginal squeeze pressure, 3D pelvic floor ultrasound, and 3D RAM ultrasound. RAM samples obtained during C-section will be analyzed for ex-vivo contractility, morphological, molecular and OMICS profiles to further characterize the hyperglycemic myopathy. Additional variables to be evaluated include maternal age, socioeconomic status, educational level, ethnicity, body mass index, weight gain during pregnancy, quality of glycemic control and insulin therapy. DISCUSSION To our knowledge, this will be the first study to provide data on the prevalence of PS-UI and RAM and PFM physical and biomolecular muscle profiles after C-section in mothers with GDM. The longitudinal design allows for the assessment of cause-effect relationships between GDM, PS-UI, and PFMs and RAMs myopathy. The findings may reveal previously undetermined consequences of GDM.
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Affiliation(s)
- Marilza V C Rudge
- Department of Gynecology and Obstetrics, Botucatu Medical School (FMB), São Paulo State University (UNESP), CEP18618-687, Sao Paulo, Brazil.
| | - Fátima P Souza
- Physics Department, Institute of Biosciences, Letters and Exact Sciences, Multiuser Center for Biomolecular Innovation, UNESP-São Paulo State University, Sao Paulo, Brazil
| | - Joelcio F Abbade
- Department of Gynecology and Obstetrics, Botucatu Medical School (FMB), São Paulo State University (UNESP), CEP18618-687, Sao Paulo, Brazil
| | - Raghavendra L S Hallur
- Department of Gynecology and Obstetrics, Botucatu Medical School (FMB), São Paulo State University (UNESP), CEP18618-687, Sao Paulo, Brazil
| | - João Paulo C Marcondes
- Department of Gynecology and Obstetrics, Botucatu Medical School (FMB), São Paulo State University (UNESP), CEP18618-687, Sao Paulo, Brazil
| | - Fernanda Piculo
- Department of Gynecology and Obstetrics, Botucatu Medical School (FMB), São Paulo State University (UNESP), CEP18618-687, Sao Paulo, Brazil.,Physiotherapy Department, Faculdades Integradas de Bauru, FIB, Sao Paulo, Brazil
| | - Gabriela Marini
- Department of Gynecology and Obstetrics, Botucatu Medical School (FMB), São Paulo State University (UNESP), CEP18618-687, Sao Paulo, Brazil.,Universidade do Sagrado Coração (USC), Jardim Brasil, Bauru, Sao Paulo, Brazil
| | - Giovana Vesentini
- Department of Gynecology and Obstetrics, Botucatu Medical School (FMB), São Paulo State University (UNESP), CEP18618-687, Sao Paulo, Brazil
| | - Lehana Thabane
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada.,Biostatistics Unit, Father Sean O'Sullivan Research Centre, St Joseph's Healthcare-Hamilton, Hamilton, ON, Canada
| | - Steven S Witkin
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA.,Institute of Tropical Medicine, University of Sao Paulo Medical School, Sao Paulo, Brazil
| | - Iracema M P Calderon
- Department of Gynecology and Obstetrics, Botucatu Medical School (FMB), São Paulo State University (UNESP), CEP18618-687, Sao Paulo, Brazil
| | - Angélica M P Barbosa
- Department of Gynecology and Obstetrics, Botucatu Medical School (FMB), São Paulo State University (UNESP), CEP18618-687, Sao Paulo, Brazil.,School of Philosophy and Sciences, Department of Physiotherapy and Occupational Therapy, UNESP-São Paulo State University, Marília, Sao Paulo, Brazil
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Ullah A, Souza TACB, Zanphorlin LM, Mariutti RB, Santana VS, Murakami MT, Arni RK. Crystal structure of Jararacussin-I: the highly negatively charged catalytic interface contributes to macromolecular selectivity in snake venom thrombin-like enzymes. Protein Sci 2014; 22:128-32. [PMID: 23139169 DOI: 10.1002/pro.2189] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/27/2012] [Accepted: 10/29/2012] [Indexed: 11/07/2022]
Abstract
Snake venom serine proteinases (SVSPs) are hemostatically active toxins that perturb the maintenance and regulation of both the blood coagulation cascade and fibrinolytic feedback system at specific points, and hence, are widely used as tools in pharmacological and clinical diagnosis. The crystal structure of a thrombin-like enzyme (TLE) from Bothrops jararacussu venom (Jararacussin-I) was determined at 2.48 Å resolution. This is the first crystal structure of a TLE and allows structural comparisons with both the Agkistrodon contortrix contortrix Protein C Activator and the Trimeresurus stejnegeri plasminogen activator. Despite the highly conserved overall fold, significant differences in the amino acid compositions and three-dimensional conformations of the loops surrounding the active site significantly alter the molecular topography and charge distribution profile of the catalytic interface. In contrast to other SVSPs, the catalytic interface of Jararacussin-I is highly negatively charged, which contributes to its unique macromolecular selectivity.
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Affiliation(s)
- A Ullah
- Multi User Center for Biomolecular Innovation, Department of Physics, IBILCE/UNESP, São Jose do Rio Preto, SP, Brazil
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3
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Ullah A, Souza TACB, Abrego JRB, Betzel C, Murakami MT, Arni RK. Structural insights into selectivity and cofactor binding in snake venom L-amino acid oxidases. Biochem Biophys Res Commun 2012; 421:124-8. [PMID: 22490662 DOI: 10.1016/j.bbrc.2012.03.129] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 03/26/2012] [Indexed: 11/17/2022]
Abstract
L-Amino acid oxidases (LAAOs) are flavoenzymes that catalytically deaminate L-amino acids to corresponding α-keto acids with the concomitant production of ammonia (NH(3)) and hydrogen peroxide (H(2)O(2)). Particularly, snake venom LAAOs have been attracted much attention due to their diverse clinical and biological effects, interfering on human coagulation factors and being cytotoxic against some pathogenic bacteria and Leishmania ssp. In this work, a new LAAO from Bothrops jararacussu venom (BjsuLAAO) was purified, functionally characterized and its structure determined by X-ray crystallography at 3.1 Å resolution. BjsuLAAO showed high catalytic specificity for aromatic and aliphatic large side-chain amino acids. Comparative structural analysis with prokaryotic LAAOs, which exhibit low specificity, indicates the importance of the active-site volume in modulating enzyme selectivity. Surprisingly, the flavin adenine dinucleotide (FAD) cofactor was found in a different orientation canonically described for both prokaryotic and eukaryotic LAAOs. In this new conformational state, the adenosyl group is flipped towards the 62-71 loop, being stabilized by several hydrogen-bond interactions, which is equally stable to the classical binding mode.
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Affiliation(s)
- A Ullah
- Centro Multiusuário de Inovação Biomolecular, Departamento de Física, Universidade Estadual Paulista (UNESP), 15054-000 São José do Rio Preto, SP, Brazil
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Georgieva D, Greunke K, Arni RK, Betzel C. Three-Dimensional Modelling of Honeybee Venom Allergenic Proteases: Relation to Allergenicity. Z NATURFORSCH C 2011. [DOI: 10.5560/znc.2011.66c0305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Murakami MT, Kini RM, Arni RK. Crystal structure of bucain, a three-fingered toxin from the venom of the Malayan krait (Bungarus candidus). Protein Pept Lett 2010; 16:1473-7. [PMID: 20001910 DOI: 10.2174/092986609789839304] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bucain, a potent neurotoxin isolated from the venom of the Malayan krait (Bungarus candidus), induces paralysis and death. Its crystal structure has been determined at 2.10 A resolution and based on the molecular topology and hydrophobicity profile is structurally classified as a three-fingered alpha-neurotoxin possessing a positively charged AChR-binding site.
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Affiliation(s)
- M T Murakami
- Center of Structural & Molecular Biology, Department of Physics, IBILCE/UNESP, São Josë do Rio Preto, SP, Brazil
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Langer K, Tillmanns E, Kersten M, Almen H, Arni RK. The crystal chemistry of Mn3+ in the clino- and orthozoisite structure types, Ca2M3
3+[OH|O|SiO4|Si2O7]: A structural and spectroscopic study of some natural piemontites and “thulites” and their synthetic equivalents. ACTA ACUST UNITED AC 2009. [DOI: 10.1524/zkri.217.11.563.20780] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
Six new structure refinements and eleven sets of polarised, single-crystal electronic absorption spectra, E‖X, Y and Z, in the energy range 35000–5000 cm–1 were obtained on natural and synthetic orthozoisite-type “thulites” and clinozoisite-type piemontites: Ca2(Al3–pMp
3+) [OH|O|SiO4|Si2O7] where M3+ = Mn3+ or (Mn1–n
3+Fen
3+) for the synthetic or natural minerals, respectively. Electron microprobe analyses of the single crystals studied revealed substitutional degrees pM3+ = 0.13 or 0.51 in natural and synthetic “thulite”, respectively, and 0.57 ≤ pM3+ ≤ 1.17 or 0.83 ≤ pM3+ ≤ 1.47 in the natural or synthetic piemontites, respectively.
Manganese in “thulite” is trivalent, as it is in piemontite. In both structure types, M3+ fractionates strongly into the axially compressed [M(3)O6] polyhedra, and does not enter the M(2) sites. Mean M(3)—O and M(1)—O distances increase in both structures, compared to the M3+-free Al end members. Such distance changes in piemontite are +0.47% and +0.53% per 0.1x
M3+, respectively, (x = site fraction). The bending angle of the Si2O7-group in cis-configuration, ∢Si(1)—O(9)—Si(2), decreases from 164.4° in clinozoisite to 147.4° in the most Mn3+-rich synthetic piemontite with p
Mn³⁺ = 1.47 (emp) or x
Mn³⁺(M3) = 0.931 and x
Mn³⁺(M1) = 0.460 (from structure refinement).
The detailed evaluation of the changes, due to Al→M3+ substitution, of individual bond lengths, as well as the quantitative evaluation of the intensities of the strong spinallowed dd bands of Mn3+ in M(3), prove that in natural piemontite the preference of Mn3+ for M(3) over M(1) is more pronounced than that of Fe3+. This is in accord with the Jahn-Teller effect of 3d4-configurated Mn3+. In addition, evaluation of the individual M(3)–O(i) distances with increasing x
Mn³⁺(M3) in piemontite indicates that the axial compression of the [M(3)O6] polyhedra increases. This contrasts with the behaviour of Fe3+-bearing epidotes and is again in accord with the Jahn-Teller effect of Mn3+.
The polarisation behaviour of the three strong spin-allowed dd-bands of Mn3+ in M(3), v
I at 13000–12000 cm–1 (E‖Y), v
II at 19000–18000 cm–1 (E‖Y and Z, Z > Y) and v
III at 24000–22000 cm–1 (E‖X) is best interpreted by assuming a C
2
v
(C
2″) pseudo-symmetry of the M(3) sites, a super-group of their site symmetry Cs
. Evaluation of the energies of v
I, v
II and v
III on the basis of the energy level diagram obtained for Mn3+ with the above pseudo-symmetry yields the crystal field parameter 10 Dq = 13540 cm–1 for x
Mn³⁺(M3) = 0:931. 10 Dq increases slightly by 30 cm–1 per -0.1x
Mn³⁺(M3). Such values and the Jahn-Teller splitting of the octahedral crystalfield ground-state of Mn3+, δ = v
I, yield a crystal field stabilisation energy of Mn3+(M3) of 14080 cm–1 for x
Mn³⁺(M3) = 0:931. CFSEMn
3+ increases slightly by 28 cm–1 per -0.1x
Mn³⁺(M3). Such values are appreciably smaller than those typical of Mn3+ substituting for Al in the axially elongated [M(1)O6] octahedra in the andalusite structure type. This different behaviour of Mn3+ in the two structure types is likely due to the smaller deviation of (c=a)oct in piemontite M(3) compared to andalusite M(1) for the same site fractions of Mn3+. In addition, the axial inversion effect — compressed [M(3)O6] in the clinozoisite-type or elongated [M(1)O6] in the andalusite-type, involving the electron hole of 3d4 in d
z
2 or d(
x
²-
y
²), respectively — may play a role.
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Akao PK, Tonoli CCC, Navarro MS, Cintra ACO, Neto JR, Arni RK, Murakami MT. Structural studies of BmooMPalpha-I, a non-hemorrhagic metalloproteinase from Bothrops moojeni venom. Toxicon 2009; 55:361-8. [PMID: 19706302 DOI: 10.1016/j.toxicon.2009.08.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 08/13/2009] [Accepted: 08/17/2009] [Indexed: 10/20/2022]
Abstract
Hemostatically active snake venom metalloproteinases (SVMPs) perturb the blood coagulation cascade at specific points and due to their potential application as thrombolytic agents, the fibrin(ogen)olytic non-hemorrhagic SVMPs have been employed as biochemical tools in coagulation research and diagnosis. Structural studies complemented by the design of metalloproteinase inhibitors have been instrumental in understanding their stereo specificity and action mechanism. We present here, details of the crystal structure of BmooMPalpha-I, a 22.6 kDa non-hemorrhagic P-I class SVMP isolated from Bothrops moojeni venom, determined at 1.76 A resolution. In this structure, the catalytic zinc ion displays an unusual octahedral coordination formed by the three canonical histidines (His(142), His(146) and His(152)) and additionally, by three solvent molecules. Comparative sequence and structural studies indicate that the motif comprising amino acid segments 153-164 and 167-176 adjacent to the methionine-turn is a salient feature that differentiates both non and hemorrhagic P-I class SVMPs and could directly be involved in the development of the hemorrhagic activity.
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Affiliation(s)
- P K Akao
- Center for Structural Molecular Biology, Brazilian Synchrotron Light Laboratory, Campinas, SP 13083-970, Brazil
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8
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Santos KF, Murakami MT, Cintra ACO, Toyama MH, Marangoni S, Forrer VP, Brandão Neto JR, Polikarpov I, Arni RK. Crystallization and preliminary X-ray crystallographic analysis of the heterodimeric crotoxin complex and the isolated subunits crotapotin and phospholipase A2. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:287-90. [PMID: 17401196 PMCID: PMC2330203 DOI: 10.1107/s1744309107006719] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2006] [Accepted: 02/08/2007] [Indexed: 11/10/2022]
Abstract
Crotoxin, a potent neurotoxin from the venom of the South American rattlesnake Crotalus durissus terrificus, exists as a heterodimer formed between a phospholipase A(2) and a catalytically inactive acidic phospholipase A(2) analogue (crotapotin). Large single crystals of the crotoxin complex and of the isolated subunits have been obtained. The crotoxin complex crystal belongs to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 38.2, b = 68.7, c = 84.2 A, and diffracted to 1.75 A resolution. The crystal of the phospholipase A(2) domain belongs to the hexagonal space group P6(1)22 (or its enantiomorph P6(5)22), with unit-cell parameters a = b = 38.7, c = 286.7 A, and diffracted to 2.6 A resolution. The crotapotin crystal diffracted to 2.3 A resolution; however, the highly diffuse diffraction pattern did not permit unambiguous assignment of the unit-cell parameters.
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Affiliation(s)
- K. F. Santos
- Department of Physics, IBILCE/UNESP, Cristóvão Colombo 2265, CEP 15054-000, São José do Rio Preto, SP, Brazil
| | - M. T. Murakami
- Department of Physics, IBILCE/UNESP, Cristóvão Colombo 2265, CEP 15054-000, São José do Rio Preto, SP, Brazil
| | - A. C. O. Cintra
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - M. H. Toyama
- Departamento de Bioquímica, Universidade de Campinas, Campinas, SP, Brazil
| | - S. Marangoni
- Departamento de Bioquímica, Universidade de Campinas, Campinas, SP, Brazil
| | - V. P. Forrer
- Laboratório Nacional de Luz Síncrotron, Campinas, SP, Brazil
| | | | - I. Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - R. K. Arni
- Department of Physics, IBILCE/UNESP, Cristóvão Colombo 2265, CEP 15054-000, São José do Rio Preto, SP, Brazil
- Center for Applied Toxinology, CEPID, Brazil
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Murakami MT, Rios-Steiner J, Weaver SE, Tulinsky A, Geiger JH, Arni RK. Intermolecular interactions and characterization of the novel factor Xa exosite involved in macromolecular recognition and inhibition: crystal structure of human Gla-domainless factor Xa complexed with the anticoagulant protein NAPc2 from the hematophagous nematode Ancylostoma caninum. J Mol Biol 2006; 366:602-10. [PMID: 17173931 DOI: 10.1016/j.jmb.2006.11.040] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Revised: 11/04/2006] [Accepted: 11/09/2006] [Indexed: 11/22/2022]
Abstract
NAPc2, an anticoagulant protein from the hematophagous nematode Ancylostoma caninum evaluated in phase-II/IIa clinical trials, inhibits the extrinsic blood coagulation pathway by a two step mechanism, initially interacting with the hitherto uncharacterized factor Xa exosite involved in macromolecular recognition and subsequently inhibiting factor VIIa (K(i)=8.4 pM) of the factor VIIa/tissue factor complex. NAPc2 is highly flexible, becoming partially ordered and undergoing significant structural changes in the C terminus upon binding to the factor Xa exosite. In the crystal structure of the ternary factor Xa/NAPc2/selectide complex, the binding interface consists of an intermolecular antiparallel beta-sheet formed by the segment of the polypeptide chain consisting of residues 74-80 of NAPc2 with the residues 86-93 of factor Xa that is additional maintained by contacts between the short helical segment (residues 67-73) and a turn (residues 26-29) of NAPc2 with the short C-terminal helix of factor Xa (residues 233-243). This exosite is physiologically highly relevant for the recognition and inhibition of factor X/Xa by macromolecular substrates and provides a structural motif for the development of a new class of inhibitors for the treatment of deep vein thrombosis and angioplasty.
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Affiliation(s)
- M T Murakami
- Department of Physics, IBILCE/UNESP, São José do Rio Preto, SP 15054-000, Brazil
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Murakami MT, Gabdoulkhakov A, Genov N, Cintra ACO, Betzel C, Arni RK. Insights into metal ion binding in phospholipases A2: ultra high-resolution crystal structures of an acidic phospholipase A2 in the Ca2+ free and bound states. Biochimie 2006; 88:543-9. [PMID: 16376474 DOI: 10.1016/j.biochi.2005.10.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2005] [Revised: 07/25/2005] [Accepted: 10/28/2005] [Indexed: 10/25/2022]
Abstract
The electrophile Ca(2+) is an essential multifunctional co-factor in the phospholipase A(2) mediated hydrolysis of phospholipids. Crystal structures of an acidic phospholipase A(2) from the venom of Bothrops jararacussu have been determined both in the Ca(2+) free and bound states at 0.97 and 1.60 A resolutions, respectively. In the Ca(2+) bound state, the Ca(2+) ion is penta-coordinated by a distorted pyramidal cage of oxygen and nitrogen atoms that is significantly different to that observed in structures of other Group I/II phospholipases A(2). In the absence of Ca(2+), a water molecule occupies the position of the Ca(2+) ion and the side chain of Asp49 and the calcium-binding loop adopts a different conformation.
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Affiliation(s)
- M T Murakami
- Department of Physics, IBILCE/UNESP, Cristovão Colombo 2265, São José do Rio Preto, SP 15054-000, Brazil
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Arni RK, Ward RJ, Gutierrez JM, Tulinsky A. Structure of a calcium-independent phospholipase-like myotoxic protein from Bothrops asper venom. Acta Crystallogr D Biol Crystallogr 2005; 51:311-7. [PMID: 15299297 DOI: 10.1107/s0907444994011455] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Myotoxin II, a myotoxic calcium-independent phospholipase-like protein isolated from the venom of Bothrops asper, possesses no detectable phospholipase activity. The crystal structure has been determined and refined at 2.8 A to an R-factor of 16.5% (F > 3sigma) with excellent stereochemistry. Amino-acid differences between catalytically active phospholipases and myotoxin II in the Ca(2+)-binding region, specifically the substitutions Tyr28-->Asn, Gly32-->Leu and Asp49-->Lys, result in an altered local conformation. The key difference is that the epsilon-amino group of Lys49 fills the site normally occupied by the calcium ion in catalytically active phospholipases. In contrast to the homologous monomeric Lys49 variant from Agkistrodon piscivorus piscivorus, myotoxin II is present as a dimer both in solution and in the crystalline state. The two molecules in the asymmetric unit are related by a nearly perfect twofold axis, yet the dimer is radically different from the dimer formed by the phospholipase from Crotalus atrox. Whereas in C. atrox the dimer interface occludes the active sites, in myotoxin II they are exposed to solvent.
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Affiliation(s)
- R K Arni
- Department of Physics, UNEXSP-IBILCE, São José do Rio Preto-SP, Brazil
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Murakami MT, Ruller R, Ward RJ, Arni RK. Crystallization and preliminary X-ray crystallographic studies of the mesophilic xylanase A from Bacillus subtilis 1A1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:219-20. [PMID: 16510999 PMCID: PMC1952261 DOI: 10.1107/s1744309105000904] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2004] [Accepted: 01/10/2005] [Indexed: 11/10/2022]
Abstract
Xylanases have been the focus of research owing to their industrial potential in animal feed production, food processing and pulp and paper processes. In order to obtain insight into the structural stability of family 11 xylanases, the mesophilic family 11 xylanase (beta-1,4-xylan xylanohydrolase; EC 3.2.1.8) from Bacillus subtilis 1A1 has been crystallized and diffraction data have been collected to 1.7 A. The crystals belong to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 50.93, b = 70.50, c = 40.05 A. The structure has been determined by molecular replacement, resulting in a crystallographic residual of 36.4% after rigid-body refinement.
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Affiliation(s)
- M. T. Murakami
- Department of Physics, IBILCE/UNESP, Cristovao Colombo 2265, 15054-000 Sao Jose do Rio Preto, Sao Paulo, Brazil
| | - R. Ruller
- Department of Chemistry, Avenida do Cafe 1544, USP, Ribeirao Preto, Sao Paulo, Brazil
| | - R. J. Ward
- Department of Chemistry, Avenida do Cafe 1544, USP, Ribeirao Preto, Sao Paulo, Brazil
| | - R. K. Arni
- Department of Physics, IBILCE/UNESP, Cristovao Colombo 2265, 15054-000 Sao Jose do Rio Preto, Sao Paulo, Brazil
- Correspondence e-mail:
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Watanabe L, Fontes MRM, Soares AM, Giglio JR, Arni RK. Initiating structural studies of Lys49-PLA2 homologues complexed with an anionic detergent, a fatty acid and a natural lipid. Protein Pept Lett 2004; 10:525-30. [PMID: 14561144 DOI: 10.2174/0929866033478726] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Lys49-Phospholipase A2 (Lys49-PLA(2) - EC 3.1.1.4) homologues damage membranes by a Ca2+-independent mechanism which does not involve catalytic activity. Both MjTX-II from Bothrops moojeni and BthTX-I from Bothrops jararacussu are dimeric in solution and in the crystalline states, and a model for the Ca2+-independent membrane damaging mechanism has been suggested in which flexibility at the dimer interface region permits quaternary structural transitions between "open" and "closed" membrane bound dimer conformations which results in the perturbation of membrane phospholipids and disruption of the bilayer structure. With the aim of gaining insights into the structural determinants involved in protein/lipid association, we report here the crystallization and preliminary X-ray analysis of the (i) MjTX-II/SDS complex at a resolution of 2.78A, (ii) MjTX-II/STE complex at a resolution of 1.8 A and (iii) BthTX-I/DMPC complex at 2.72A. These complexes were crystallized by the hanging drop vapour-diffusion technique in (i) HEPES buffer (pH 7.5) 1.8M ammonium sulfate with 2% (w/v) polyethyleneglycol 400, in (ii) 0.6-0.8 M sodium citrate as the precipitant (pH 6.0-6.5) and in (iii) sodium citrate buffer (pH 5.8) and PEG 4000 and 20% isopropanol, respectively. Single crystals of these complexes have been obtained and X-ray diffraction data have been collected at room temperature using a R-AXIS IV imaging plate system and graphite monochromated Cu Kalpha X-ray radiation generated by a Rigaku RU300 rotating anode generator for (i) and (iii) and using using a Synchrotron Radiation Source (Laboratório Nacional de Luz Sincrotron, LNLS, Campinas, Brazil) for (ii).
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Affiliation(s)
- L Watanabe
- Department of Physics, IBILCE/UNESP, São José do Rio Preto, SP, CEP 15054-000, Brasil
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Zela SP, Fernandes Pedrosa MF, Murakami MT, De Andrade SA, Arni RK, Tambourgi DV. Crystallization and preliminary crystallographic analysis of SMase I, a sphingomyelinase from Loxosceles laeta spider venom. Acta Crystallogr D Biol Crystallogr 2004; 60:1112-4. [PMID: 15159572 DOI: 10.1107/s090744490400678x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2004] [Accepted: 03/22/2004] [Indexed: 11/10/2022]
Abstract
SMase I, a 32 kDa sphingomyelinase found in Loxosceles laeta venom, is responsible for the major pathological effects of spider envenomation. This toxin has been cloned and functionally expressed as a fusion protein containing a 6 x His tag at its N-terminus to yield a 33 kDa protein [Fernandes-Pedrosa et al. (2002), Biochem. Biophys. Res. Commun. 298, 638-645]. The recombinant protein possesses all the biological properties ascribed to the whole L. laeta venom, including dermonecrotic and complement-dependent haemolytic activities. Dynamic light-scattering experiments conducted at 291 K demonstrate that the sample possesses a monomodal distribution, with a hydrodynamic radius of 3.57 nm. L. laeta SMase I was crystallized by the hanging-drop vapour-diffusion technique using the sparse-matrix method. Single crystals were obtained using a buffer solution consisting of 0.08 M HEPES and 0.9 M trisodium citrate, which was titrated to pH 7.5 using 0.25 M sodium hydroxide. Complete three-dimensional diffraction data were collected to 1.8 angstroms at the Laboratório Nacional de Luz Síncrotron (LNLS, Campinas, Brazil). The crystals belong to the hexagonal system (space group P6(1) or P6(5)), with unit-cell parameters a = b = 140.6, c = 113.6 angstroms. A search for heavy-atom derivatives has been initiated and elucidation of the crystal structure is currently in progress.
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Affiliation(s)
- S P Zela
- Department of Physics, IBILCE/UNESP, CP 136, São José do Rio Preto, SP, CEP 15054-000, Brazil
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Abstract
Venom phospholipase A2s (PLA2s) display a wide spectrum of pharmacological activities and, based on the wealth of biochemical and structural data currently available for PLA2s, mechanistic models can now be inferred to account for some of these activities. A structural model is presented for the role played by the distribution of surface electrostatic potential in the ability of myotoxic D49/K49 PLA2s to disrupt multilamellar vesicles containing negatively charged natural and non-hydrolyzable phospholipids. Structural evidence is provided for the ability of K49 PLA2s to bind phospholipid analogues and for the existence of catalytic activity in K49 PLA2s. The importance of the existence of catalytic activity of D49 and K49 PLA2s in myotoxicity is presented.
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Affiliation(s)
- M T Murakami
- Department of Biophysics, IBILCE/UNESP, R. Cristovão Colombo 2265, CEP 15054-000, São José do Rio Preto-SP, Brazil
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Ketelhut DFJ, de Mello MH, Veronese ELG, Esmeraldino LE, Murakami MT, Arni RK, Giglio JR, Cintra ACO, Sampaio SV. Isolation, characterization and biological activity of acidic phospholipase A2 isoforms from Bothrops jararacussu snake venom. Biochimie 2003; 85:983-91. [PMID: 14644553 DOI: 10.1016/j.biochi.2003.09.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acidic phospholipase A(2) (PLA(2)) isoforms in snake venoms, particularly those from Bothrops jararacussu, have not been characterized. This article reports the isolation and partial biochemical, functional and structural characterization of four acidic PLA(2)s (designated SIIISPIIA, SIIISPIIB, SIIISPIIIA and SIIISPIIIB) from this venom. The single chain purified proteins contained 122 amino acid residues and seven disulfide bonds with approximate molecular masses of 15 kDa and isoelectric points of 5.3. The respective N-terminal sequences were: SIIISPIIA-SLWQFGKMIDYVMGEEGAKS; SIIISPIIB-SLWQFGKMIFYTGKNEPVLS; SIIISPIIIA-SLWQFGKMILYVMGGEGVKQ and SIIISPIIIB-SLWQFGKMIFYEMTGEGVL. Crystals of the acidic protein SIIISPIIB diffracted beyond 1.8 A resolution. These crystals are monoclinic with unit cell dimensions of a = 40.1 A, b = 54.2 A and c = 90.7 A. The crystal structure has been refined to a crystallographic residual of 16.1% (R(free) = 22.9%). Specific catalytic activity (U/mg) of the isolated acidic PLA(2)s were SIIISPIIA = 290.3 U/mg; SIIISPIIB = 279.0 U/mg; SIIISPIIIA = 270.7 U/mg and SIIISPIIIB = 96.5 U/mg. Although their myotoxic activity was low, SIIISPIIA, SIIISPIIB and SIIISPIIIA showed significant anticoagulant activity. However, there was no indirect hemolytic activity. SIIISPIIIB revealed no anticoagulant, but presented indirect hemolytic activity. With the exception of SIIISPIIB, which inhibited platelet aggregation, all the others were capable of inducing time-independent edema. Chemical modification with 4-bromophenacyl bromide did not inhibit the induction of edema, but did suppress other activities.
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Affiliation(s)
- D F J Ketelhut
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Avenida do Café, s/n, Bairro Monte Alegre, 14040-903, SP Ribeirão Preto, Brazil
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Murakami MT, Zela SP, Gava LM, Michelan-Duarte S, Cintra ACO, Arni RK. Crystal structure of the platelet activator convulxin, a disulfide-linked α4β4 cyclic tetramer from the venom of Crotalus durissus terrificus. Biochem Biophys Res Commun 2003; 310:478-82. [PMID: 14521935 DOI: 10.1016/j.bbrc.2003.09.032] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Convulxin (CVX), a C-type lectin, isolated from the venom of the South American rattlesnake Crotalus durissus terrificus, causes cardiovascular and respiratory disturbances and is a potent platelet activator which binds to platelet glycoprotein GPVI. The structure of CVX has been solved at 2.4A resolution to a crystallographic residual of 18.6% (R(free)=26.4%). CVX is a disulfide linked heterodimer consisting of homologous alpha and beta chains. The heterodimers are additionally linked by disulfide bridges to form cyclic alpha(4)beta(4)heterotetramers. These domains exhibit significant homology to the carbohydrate-binding domains of C-type lectins, to the factor IX-binding protein (IX-bp), and to flavocetin-A (Fl-A) but sequence and structural differences are observed in both the domains in the putative Ca(2+)and carbohydrate binding regions.
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Affiliation(s)
- M T Murakami
- Department of Physics, IBILCE/UNESP, R. Cristovão Colombo 2265, CEP 15054-000, São Josédo Rio Preto-SP, Brazil
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Murakami MT, Watanabe L, Gava LM, Zela SP, Cintra ACO, Arni RK. Initial structural analysis of an α4β4C-type lectin from the venom ofCrotalus durissus terrificus. Acta Crystallogr D Biol Crystallogr 2003; 59:1813-5. [PMID: 14501123 DOI: 10.1107/s0907444903016202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2003] [Accepted: 07/22/2003] [Indexed: 11/10/2022]
Abstract
Convulxin, an alphabeta C-type lectin, is a potent platelet activator isolated from the venom of the South American rattlesnake Crotalus durissus terrificus. It is a 26.5 kDa alphabeta heterodimer consisting of two homologous disulfide-linked chains. The crystals belong to space group I4, with unit-cell parameters a = b = 131.61, c = 121.85 A, and diffraction data were collected to 2.7 A. The structure was solved by molecular replacement and the asymmetric unit contains two alphabeta heterodimers, each of which forms a disulfide-linked cyclic alpha(4)beta(4) tetramer in the unit cell. These alpha(4)beta(4) tetramers are stacked to form a large solvent channel.
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Affiliation(s)
- M T Murakami
- Department of Physics, IBILCE/UNESP, R. Cristovão Colombo 2265, CEP 150054-000, São Jose do Rio Preto-SP, Brazil
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Bell BJ, Watanabe L, Rios-Steiner JL, Tulinsky A, Lebioda L, Arni RK. Structure of 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase from Pseudomonas putida. Acta Crystallogr D Biol Crystallogr 2003; 59:1454-8. [PMID: 12876349 DOI: 10.1107/s0907444903013192] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2003] [Accepted: 06/12/2003] [Indexed: 11/10/2022]
Abstract
2-Keto-3-deoxy-6-phosphogluconate (KDPG) aldolase from Pseudomonas putida is a key enzyme in the Entner-Doudoroff pathway which catalyses the cleavage of KDPG via a class I Schiff-base mechanism. The crystal structure of this enzyme has been refined to a crystallographic residual R = 17.1% (R(free) = 21.4%). The N-terminal helix caps one side of the torus of the (betaalpha)(8)-barrel and the active site is located on the opposite, carboxylic side of the barrel. The Schiff-base-forming Lys145 is coordinated by a sulfate (or phosphate) ion and two solvent water molecules. The interactions that stabilize the trimer are predominantly hydrophobic, with the exception of the cyclically permuted bonds formed between Glu132 OE1 of one molecule and Thr129 OG1 of a symmetry-equivalent molecule. Except for the N-terminal helix, the structure of KDPG aldolase from P. putida closely resembles the structure of the homologous enzyme from Escherichia coli.
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Affiliation(s)
- B J Bell
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
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Watanabe L, Nirthanan S, Rajaseger G, Polikarpov I, Kini RM, Arni RK. Crystallization and preliminary X-ray analysis of bucain, a novel toxin from the Malayan krait Bungarus candidus. Acta Crystallogr D Biol Crystallogr 2002; 58:1879-81. [PMID: 12351845 DOI: 10.1107/s0907444902011022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2002] [Accepted: 06/19/2002] [Indexed: 11/10/2022]
Abstract
Bucain is a three-finger toxin, structurally homologous to snake-venom muscarinic toxins, from the venom of the Malayan krait Bungarus candidus. These proteins have molecular masses of approximately 6000-8000 Da and encompass the potent curaremimetic neurotoxins which confer lethality to Elapidae and Hydrophidae venoms. Bucain was crystallized in two crystal forms by the hanging-drop vapour-diffusion technique in 0.1 M sodium citrate pH 5.6, 15% PEG 4000 and 0.15 M ammonium acetate. Form I crystals belong to the monoclinic system space group C2, with unit-cell parameters a = 93.73, b = 49.02, c = 74.09 A, beta = 111.32 degrees, and diffract to a nominal resolution of 1.61 A. Form II crystals also belong to the space group C2, with unit-cell parameters a = 165.04, b = 49.44, c = 127.60 A, beta = 125.55 degrees, and diffract to a nominal resolution of 2.78 A. The self-rotation function indicates the presence of four and eight molecules in the crystallographic asymmetric unit of the form I and form II crystals, respectively. Attempts to solve these structures by molecular-replacement methods have not been successful and a heavy-atom derivative search has been initiated.
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Affiliation(s)
- L Watanabe
- Department of Physics, IBILCE/UNESP, CP 136, CEP 15054-000, São José do Rio Preto SP, Brazil
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21
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Watanabe L, Vieira DF, Bortoleto RK, Arni RK. Crystallization of bothrombin, a fibrinogen-converting serine protease isolated from the venom of Bothrops jararaca. Acta Crystallogr D Biol Crystallogr 2002; 58:1036-8. [PMID: 12037309 DOI: 10.1107/s0907444902003645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2001] [Accepted: 02/25/2002] [Indexed: 11/10/2022]
Abstract
Bothrombin, a snake-venom serine protease, specifically cleaves fibrinogen, releasing fibrinopeptide A to form non-crosslinked soft clots, aggregates platelets in the presence of exogenous fibrinogen and activates blood coagulation factor VIII. Bothrombin shares high sequence homology with other snake-venom proteases such as batroxobin (94% identity), but only 30 and 34% identity with human alpha-thrombin and trypsin, respectively. Single crystals of bothrombin have been obtained and X-ray diffraction data have been collected at the Laboratorio Nacional de Luz Sincrotron to a resolution of 2.8 A. The crystals belong to the space group P2(1)2(1)2(1), with unit-cell parameters a = 94.81, b = 115.68, c = 155.97 A.
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Affiliation(s)
- L Watanabe
- Department of Physics, IBILCE/UNESP, CP 136, Sao José do Rio Preto, CEP 15054-000, Brazil
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Watanabe L, Rucavado A, Kamiguti A, Theakston RDG, Gutiérrez JM, Arni RK. Crystallization and preliminary diffraction data of BaP1, a haemorrhagic metalloproteinase from Bothrops asper snake venom. Acta Crystallogr D Biol Crystallogr 2002; 58:1034-5. [PMID: 12037308 DOI: 10.1107/s0907444902003633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2001] [Accepted: 02/25/2002] [Indexed: 11/10/2022]
Abstract
BaP1 is a metalloproteinase isolated from the venom of the Central American snake Bothrops asper (terciopelo). It is a 24 kDa protein consisting of a single chain which includes the metalloproteinase domain only, therefore being classified as a class P-I snake-venom metalloproteinase. BaP1 induces prominent local tissue damage, such as haemorrhage, myonecrosis, blistering, dermonecrosis and oedema. In order to elucidate its structure, BaP1 was crystallized by the hanging-drop vapour-diffusion technique in 0.1 M bicine pH 9.0, 10% PEG 20 000 and 2%(v/v) dioxane. Diffraction data were observed to a resolution of 2.7 A. Crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 38.22, b = 60.17, c = 86.09 A.
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Affiliation(s)
- L Watanabe
- Department of Physics, IBILCE/UNESP, CP 136, Sao José do Rio Preto, CEP 15054-000, Brazil
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Abstract
Angiogenesis inhibitors have gained much public attention recently as anti-cancer agents and several are currently in clinical trials, including angiostatin (Phase I, Thomas Jefferson University Hospital, Philadelphia, PA). We report here the bowl-shaped structure of angiostatin kringles 1-3, the first multi-kringle structure to be determined. All three kringle lysine-binding sites contain a bound bicine molecule of crystallization while the former of kringle 2 and kringle 3 are cofacial. Moreover, the separation of the kringle 2 and kringle 3 lysiner binding sites is sufficient to accommodate the alpha-helix of the 30 residue peptide VEK-30 found in the kringle 2/VEK-30 complex. Together the three kringles produce a central cavity suggestive of a unique domain where they may function in concert.
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Affiliation(s)
- Marta C Abad
- Department of Chemistry, Michigan State University, East Lansing 48824, USA
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Soares AM, Andrião-Escarso SH, Bortoleto RK, Rodrigues-Simioni L, Arni RK, Ward RJ, Gutiérrez JM, Giglio JR. Dissociation of Enzymatic and Pharmacological Properties of Piratoxins-I and -III, Two Myotoxic Phospholipases A2 from Bothrops pirajai Snake Venom. Arch Biochem Biophys 2001; 387:188-96. [PMID: 11370840 DOI: 10.1006/abbi.2000.2244] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Piratoxins (PrTX) I and III are phospholipases A2 (PLA2s) or PLA2 homologue myotoxins isolated from Bothrops pirajai snake venom, which also induce myonecrosis, bactericidal activity against Escherichia coli, disruption of artificial membranes, and edema. PrTX-III is a catalytically active hemolytic and anticoagulant Asp49 PLA2, while PrTX-I is a Lys49 PLA2 homologue, which is catalytically inactive on artificial substrates, but promotes blockade of neuromuscular transmission. Chemical modifications of His, Lys, Tyr, and Trp residues of PrTX-I and PrTX-III were performed, together with cleavage of the N-terminal octapeptide by CNBr and inhibition by heparin and EDTA. The lethality, bactericidal activity, myotoxicity, neuromuscular effect, edema inducing effect, catalytic and anticoagulant activities, and the liposome-disruptive activity of the modified toxins were evaluated. A complex pattern of functional differences between the modified and native toxins was observed. However, in general, chemical modifications that significantly affected the diverse pharmacological effects of the toxins did not influence catalytic or membrane disrupting activities. Analysis of structural changes by circular dichroism spectroscopy demonstrated significant changes in the secondary structure only in the case of N-terminal octapeptide cleavage. These data indicate that PrTX-I and PrTX-III possess regions other than the catalytic site, which determine their toxic and pharmacological activities.
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Affiliation(s)
- A M Soares
- Departamento de Bioquímica e Immunologia, Faculdade de Medicina, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
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Binderup K, Watanabe L, Polikarpov I, Preiss J, Arni RK. Crystallization and preliminary X-ray diffraction analysis of the catalytic subunit of ADP-glucose pyrophosphorylase from potato tuber. Acta Crystallogr D Biol Crystallogr 2000; 56:192-4. [PMID: 10666602 DOI: 10.1107/s0907444999015012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
ADP-glucose pyrophosphorylase is the key regulatory enzyme in the biosynthesis of starch in plants and glycogen in bacteria. The enzyme from potato tuber is comprised of a regulatory subunit and a catalytic subunit and is present as a heterotetramer (alpha(2)beta(2)). The catalytic subunit from potato tuber (50 kDa) was crystallized in four different forms, two of which are suitable for structural studies. A tetragonal crystal form obtained in the presence of the substrate analog Cr-ATP diffracted to 2.2 A and belongs to space group P4(1) (or its enantiomorph), with unit-cell parameters a = b = 110.57, c = 190.14 A. A second crystal form obtained diffracted to 2.8 A and belongs to space group P2, with unit-cell parameters a = 80.06, b = 138.84, c = 92.20 A, beta = 112. 40 degrees. As this protein displays no significant homology to any currently known protein structure, a search for heavy-atom derivatives has been initiated.
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Affiliation(s)
- K Binderup
- Department of Biochemistry, Michigan State University, East Lansing, MI 48824, USA
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Soares AM, Andrião-Escarso SH, Angulo Y, Lomonte B, Gutiérrez JM, Marangoni S, Toyama MH, Arni RK, Giglio JR. Structural and functional characterization of myotoxin I, a Lys49 phospholipase A(2) homologue from Bothrops moojeni (Caissaca) snake venom. Arch Biochem Biophys 2000; 373:7-15. [PMID: 10620318 DOI: 10.1006/abbi.1999.1492] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Myotoxin-I (MjTX-I) was purified to homogeneity from the venom of Bothrops moojeni by ion-exchange chromatography on CM-Sepharose. Its molecular weight, estimated by SDS-PAGE, was 13,400 (reduced) or 26, 000 (unreduced). The extinction coefficient (E(1.0 mg/ml)(1.0 cm)) of MjTX-I was 1.145 at lambda = 278 nm, pH 7.0, and its isoelectric point was 8.2 at ionic strength mu = 0.1. When lyophilized and stored at 4 degrees C, dimeric, trimeric, and pentameric forms of the protein were identified by SDS-PAGE. This "heterogeneous" sample could be separated into three fractions by gel filtration on Sephadex G-50. The fractions were analyzed by isoelectric focusing, immunoelectrophoresis, and amino acid composition, which indicated that heterogeneity was the result of different levels of self-association. Protein sequencing indicated that MjTX-I is a Lys49 myotoxin and consists of 121 amino acids (M(r) = 13,669), containing a high proportion of basic and hydrophobic residues. It shares a high degree of sequence identity with other Lys49 PLA(2)-like myotoxins, but shows a significantly lower identity with catalytically active Asp49 PLA(2)s. The three-dimensional structure of MjTX-I was modeled based on the crystal structures of three highly homologous Lys49 PLA(2)-like myotoxins. This model showed that the amino acid substitutions are conservative, and mainly limited to three structural regions: the N-terminal helix, the beta-wing region, and the C-terminal extended random coil. MjTX-I displays local myotoxic and edema-inducing activities in mice, and is lethal by intraperitoneal injection, with an LD(50) value of 8.5 +/- 0.8 mg/kg. In addition, it is cytotoxic to myoblasts/myotubes in culture, and disrupts negatively charged liposomes. In comparison with the freshly prepared dimeric sample, the more aggregated forms showed significantly reduced myotoxic activity. However, the edema-inducing activity of MjTX-I was independent of molecular association. Phospholipase A(2) activity on egg yolk, as well as anticoagulant activity, were undetectable both in the native and in the more associated forms. His, Tyr, and Trp residues of the toxin were chemically modified by specific reagents. Although the myotoxic and lethal activities of the modified toxins were reduced by these treatments, neither its edema-inducing or liposome-disrupting activities were significantly altered. Rabbit antibodies to native MjTX-I cross-reacted with the chemically modified forms, and both the native and modified MjTX-I preparations were recognized by antibodies against the C-terminal region 115-129 of myotoxin II from B. asper, a highly Lys49 PLA(2)-homologue with high sequencial similarity.
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Affiliation(s)
- A M Soares
- Faculdade de Medicina, Universidade de São Paulo, Ribeirão Preto-SP, 14049-900, Brazil
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27
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Arni RK, Padmanabhan KP, Tulinsky A. Crystallization and preliminary diffraction data of a platelet-aggregation inhibitor from the venom of Agkistrodon piscivorus piscivorus (North American water moccasin). Acta Crystallogr D Biol Crystallogr 1999; 55:1468-70. [PMID: 10417418 DOI: 10.1107/s0907444999006332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Applaggin (Agkistrodon piscivorus piscivorus platelet-aggregation inhibitor) is a potent inhibitor of blood platelet aggregation derived from the venom of the North American water moccasin. The protein consists of 71 amino acids, is rich in cysteines, contains the sequence-recognition site of adhesion proteins at positions 50-52 (Arg-Gly-Asp) and shares high sequence homology with other snake-venom disintegrins such as echistatin, kistrin and trigramin. Single crystals of applaggin have been grown and X-ray diffraction data have been collected to a resolution of 3.2 A. The crystals belong to space group P4(1)2(1)2 (or its enantiomorph), with unit-cell dimensions a = b = 63.35, c = 74.18 A and two molecules per asymmetric unit. Molecular replacement using models constructed from the NMR structures of echistatin and kistrin has not been successful in producing a trial structure for applaggin.
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Affiliation(s)
- R K Arni
- Department of Physics, IBILCE/UNESP, CP 136, São Jose do Rio Preto-SP, CEP 15054-000, Brazil
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28
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Arni RK, Fontes MR, Barberato C, Gutiérrez JM, Díaz C, Ward RJ. Crystal structure of myotoxin II, a monomeric Lys49-phospholipase A2 homologue isolated from the venom of Cerrophidion (Bothrops) godmani. Arch Biochem Biophys 1999; 366:177-82. [PMID: 10356281 DOI: 10.1006/abbi.1999.1210] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Lys49-Phospholipase A2 (Lys49-PLA2) homologues damage membranes by a Ca2+-independent mechanism which does not involve catalytic activity. With the aim of determining the structural basis for this novel activity, we have solved the crystal structure of myotoxin-II, a Lys49-PLA2 isolated from the venom of Cerrophidion (Bothrops) godmani (godMT-II) at 2.8 A resolution by molecular replacement. The final model has been refined to a final crystallografic residual (Rfactor) of 18.8% (Rfree = 28.2%), with excellent stereochemistry. godMT-II is also monomeric in the crystalline state, and small-angle X-ray scattering results demonstrate that the protein is monomeric in solution under fisicochemical conditions similar to those used in the crystallographic studies.
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Affiliation(s)
- R K Arni
- Department of Physics, IBILCE/UNESP, São José do Rio Preto-SP, Brazil.
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29
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Arni RK, Watanabe L, Ward RJ, Kreitman RJ, Kumar K, Walz FG. Three-dimensional structure of ribonuclease T1 complexed with an isosteric phosphonate substrate analogue of GpU: alternate substrate binding modes and catalysis. Biochemistry 1999; 38:2452-61. [PMID: 10029539 DOI: 10.1021/bi982612q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The X-ray crystal structure of a complex between ribonuclease T1 and guanylyl(3'-6')-6'-deoxyhomouridine (GpcU) has been determined at 2. 0 A resolution. This ligand is an isosteric analogue of the minimal RNA substrate, guanylyl(3'-5')uridine (GpU), where a methylene is substituted for the uridine 5'-oxygen atom. Two protein molecules are part of the asymmetric unit and both have a GpcU bound at the active site in the same manner. The protein-protein interface reveals an extended aromatic stack involving both guanines and three enzyme phenolic groups. A third GpcU has its guanine moiety stacked on His92 at the active site on enzyme molecule A and interacts with GpcU on molecule B in a neighboring unit via hydrogen bonding between uridine ribose 2'- and 3'-OH groups. None of the uridine moieties of the three GpcU molecules in the asymmetric unit interacts directly with the protein. GpcU-active-site interactions involve extensive hydrogen bonding of the guanine moiety at the primary recognition site and of the guanosine 2'-hydroxyl group with His40 and Glu58. On the other hand, the phosphonate group is weakly bound only by a single hydrogen bond with Tyr38, unlike ligand phosphate groups of other substrate analogues and 3'-GMP, which hydrogen-bonded with three additional active-site residues. Hydrogen bonding of the guanylyl 2'-OH group and the phosphonate moiety is essentially the same as that recently observed for a novel structure of a RNase T1-3'-GMP complex obtained immediately after in situ hydrolysis of exo-(Sp)-guanosine 2',3'-cyclophosphorothioate [Zegers et al. (1998) Nature Struct. Biol. 5, 280-283]. It is likely that GpcU at the active site represents a nonproductive binding mode for GpU [Steyaert, J., and Engleborghs (1995) Eur. J. Biochem. 233, 140-144]. The results suggest that the active site of ribonuclease T1 is adapted for optimal tight binding of both the guanylyl 2'-OH and phosphate groups (of GpU) only in the transition state for catalytic transesterification, which is stabilized by adjacent binding of the leaving nucleoside (U) group.
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Affiliation(s)
- R K Arni
- Department of Physics, UNESP/IBILCE, S. J. do Rio Preto-SP, Brazil
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30
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Abstract
Lys49-Phospholipase A2 (Lys49-PLA2) homologues damage membranes by a Ca2+-independent mechanism which does not involve catalytic activity. We have solved the structure of myotoxin-I, a Lys49-PLA2 homologue isolated from the venom of Bothrops nummifer (jumping viper) at 2.4 A resolution using molecular replacement techniques. The final model has been refined to a final R-factor of 18.4% (R-free = 23.2%), and shows excellent geometry. The myotoxin-I from Bothrops nummifer is dimeric in the crystalline state as has been observed for other Lys49-PLA2 homologues. In addition, a continuous electron density in the active site and substrate binding channel could be successfully modeled as a fatty-acid molecule.
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Affiliation(s)
- W F de Azevedo
- Department of Physics, IBILCE/UNESP, São José do Rio Preto, SP, Brazil
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31
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Abstract
The protein content of many snake venoms often includes one or more phospholipases A2 (PLA2). In recent years a growing number of venoms from snakes of Agkistrodon, Bothrops and Trimeresurus species have been shown to contain a catalytically inactive PLA2-homologue in which the highly conserved aspartic acid at position 49 (Asp49) is substituted by lysine (Lys49). Although demonstrating little or no catalytic activity, these Lys49-PLA2s disrupt membranes by a Ca2+-independent mechanism of action. In addition, this family of PLA2s demonstrates myotoxic and cytolytic pharmacological activities, however the structural bases underlying these functional properties are poorly understood. Through the application of X-ray crystallography in combination with biophysical and bioinformatics techniques, we are studying structure/function relationships of Lys49-PLA2s. We here present results of a systematic X-ray crystallographic and amino acid sequence analysis study of Lys49 PLA2s and propose a model to explain the Ca2+-independent membrane damaging activity.
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Affiliation(s)
- R J Ward
- Department of Physics, IBILCE-UNESP, Sao Jose do Rio Preto SP, Brazil
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32
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Canduri F, Teodoro LG, Lorenzi CC, Gomes RA, Fontes MR, Arni RK, de Azevedo Júnior WF. Crystallization, preliminary X-ray analysis and Patterson search of a new aspartic protease isolated from human urine. Biochem Mol Biol Int 1998; 46:355-63. [PMID: 9801803 DOI: 10.1080/15216549800203862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Aspartic protease (EC 3.4.23) make up a widely distributed class of enzymes in animals, plants, microbes and, viruses. In animals these enzymes perform diverse functions, which range from digestion of food proteins to very specific regulatory roles. In contrast the information about the well-characterized aspartic proteases, very little is known about the corresponding enzyme in urine. A new aspartic protease isolated from human urine has been crystallized and X-ray diffraction data collected to 2.45 A resolution using a synchrotron radiation source. Crystals belong to the space group P2(1)2(1)2(1). The cell parameters obtained were a = 50.99, b = 75.56 and c = 89.90 A. Preliminary analysis revealed the presence of one molecule in the asymmetric unit. The structure was determined using the molecular replacement technique and is currently being refined using simulated annealing and conjugate gradient protocols.
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Affiliation(s)
- F Canduri
- Departamento de Física, UNESP, São José do Rio Preto
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33
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de Azevedo WF, Ward RJ, Canduri F, Soares A, Giglio JR, Arni RK. Crystal structure of piratoxin-I: a calcium-independent, myotoxic phospholipase A2-homologue from Bothrops pirajai venom. Toxicon 1998; 36:1395-406. [PMID: 9723838 DOI: 10.1016/s0041-0101(98)00017-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The crystal structure of Piratoxin-I (PrTX-I) a Lys49 homologue isolated from the venom of Bothrops pirajai has been determined and refined at 2.8 A to a crystallographic residual of 19.7% (Rfree = 29.7%). Amino-acid sequence differences between catalytically active phospholipases and PrTX-I in the putative Ca2+-binding loop, specifically the substitutions Tyr28 --> Asn, Gly32 --> Leu and Asp49 --> Lys, result in an altered conformation of this loop. The analysis of the position of the epsilon-amino group of Lys49 in the PrTX-I structure indicates that it fills the site normally occupied by the calcium ion in the catalytically active phospholipases. In contrast to the homologous monomeric Lys49 variant from Agkistrodon piscivorus piscivorus (App), PrTX-I is present as a dimer in the crystalline state, as observed in the structures of myotoxin II from Bothrops asper and Bothropstoxin I from Bothrops jararacussu. The two molecules in the asymmetric unit in the crystal structure of PrTX-I are related by a nearly perfect two-fold symmetry axis, yet the dimeric structure is radically different from the dimeric structure of the phospholipase from Crotalus atrox. In the C. atrox structure the dimer interface occludes the active sites, whereas in the PrTX-I structure they are exposed to solvent.
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Affiliation(s)
- W F de Azevedo
- Department of Physics, IBILCE/UNESP, São José do Rio Preto - SP, Brazil
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34
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Krishnan R, Zhang E, Hakansson K, Arni RK, Tulinsky A, Lim-Wilby MS, Levy OE, Semple JE, Brunck TK. Highly selective mechanism-based thrombin inhibitors: structures of thrombin and trypsin inhibited with rigid peptidyl aldehydes. Biochemistry 1998; 37:12094-103. [PMID: 9724521 DOI: 10.1021/bi980840e] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The crystal structures of three highly potent and selective low-molecular weight rigid peptidyl aldehyde inhibitors complexed with thrombin have been determined and refined to R values 0.152-0. 170 at 1.8-2.1 A resolution. Since the selectivity of two of the inhibitors was >1600 with respect to trypsin, the structures of trypsin-inhibited complexes of these inhibitors were also determined (R = 0.142-0.157 at 1.9-2.1 A resolution). The selectivity appears to reside in the inability of a benzenesulfonamide group to bind at the equivalent of the D-enantiomorphic S3 site of thrombin, which may be related to the lack of a 60-insertion loop in trypsin. All the inhibitors have a novel lactam moiety at the P3 position, while the two with greatest trypsin selectivity have a guanidinopiperidyl group at the P1 position that binds in the S1 specificity site. Differences in the binding constants of these inhibitors are correlated with their interactions with thrombin and trypsin. The kinetics of inhibition vary from slow to fast with thrombin and are fast in all cases with trypsin. The kinetics are examined in terms of the slow formation of a stable transition-state complex in a two-step mechanism. The structures of both thrombin and trypsin complexes show similar well-defined transition states in the S1 site and at the electrophilic carbon atom and Ser195OG. The trypsin structures, however, suggest that the first step in a two-step kinetic mechanism may involve formation of a weak transition-state complex, rather than binding dominated by the P2-P4 positions.
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Affiliation(s)
- R Krishnan
- Corvas International Inc., San Diego, California 92121, USA
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35
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Canduri F, Ward RJ, de Azevedo Júnior WF, Gomes RA, Arni RK. Purification and partial characterization of cathepsin D from porcine (Sus scrofa) liver using affinity chromatography. Biochem Mol Biol Int 1998; 45:797-803. [PMID: 9713704 DOI: 10.1080/15216549800203222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cathepsin D, a lysosomal aspartic protease, has been purified from porcine liver using a combination of pepstatin-A agarose and Affi-Gel Blue affinity chromatography, followed by size-exclusion chromatography. The purified protein consists of two polypeptide chains of 15 and 30 kDa, and has an isoelectric point of 6.8. Porcine liver cathepsin D has maximum activity at pH 2.5-3.0 as determined by its activity against hemoglobin, with a Kcat of 14.3 s-1 and a kcat/KM of 2.70 x 10(6) s-1M-1 as determined by the hydrolysis of a fluorogenic peptide substrate.
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Affiliation(s)
- F Canduri
- Departamento de Física, IBILCE/UNESP, São José do Rio Preto, Brazil
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36
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de Sousa MV, Morhy L, Arni RK, Ward RJ, Díaz C, Gutiérrez JM. Amino acid sequence of a myotoxic Lys49-phospholipase A2 homologue from the venom of Cerrophidion (Bothrops) godmani. Biochim Biophys Acta 1998; 1384:204-8. [PMID: 9659381 DOI: 10.1016/s0167-4838(98)00023-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The complete amino acid sequence of myotoxin II (godMT-II), a myotoxic phospholipase A2 (PLA2) homologue from the venom of the Central American crotaline snake Cerrophidion (Bothrops) godmani, was determined by direct protein sequencing methods. GodMT-II is a class II PLA2 showing a Lys instead of Asp at position 49. An additional substitution in the calcium binding loop region (Asn instead of Tyr at position 28) suggests the lack of enzymatic activity observed in this toxin is due to loss of its ability to bind the co-factor Ca2+, since the residues involved in forming the catalytic network of PLA2s (His-48, Tyr-52 and Asp-99) are conserved in godMT-II. This myotoxin shows highest sequence homology with other Lys-49 PLA2 s from Bothrops, Agkistrodon and Trimeresurus species, suggesting that they constitute a conserved family of proteins, yet in contrast presents lower homology with Bothrops asper myotoxin III, a catalytically-active PLA2. The C-terminal region of godMT-II, which is rich in cationic and hydrophobic residues, shares high sequence homology to the corresponding region in the myotoxin II from B. asper, which has been proposed to play an important role in the Ca(2+)-independent membrane damaging activity.
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Affiliation(s)
- M V de Sousa
- Departamento da Biologia Celular, Universidade de Brasília, Brazil
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37
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Ward RJ, Alves AR, Ruggiero Neto J, Arni RK, Casari G. A SequenceSpace analysis of Lys49 phopholipases A2: clues towards identification of residues involved in a novel mechanism of membrane damage and in myotoxicity. Protein Eng 1998; 11:285-94. [PMID: 9680190 DOI: 10.1093/protein/11.4.285] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
'SequenceSpace' analysis is a novel approach which has been used to identify unique amino acids within a sub-family of phospholipases A2 (PLA2) in which the highly conserved active site residue Asp49 is substituted by Lys (Lys49-PLA2s). Although Lys49-PLA2s do not bind the catalytic co-factor Ca2+ and possess extremely low catalytic activity, they demonstrate a Ca2+-independent membrane damaging activity through a poorly understood mechanism, which does not involve lipid hydrolysis. Additionally, Lys49-PLA2s possess combined myotoxic, oedema forming and cardiotoxic pharmacological activities, however the structural basis of these varied functions is largely unknown. Using the 'SequenceSpace' analysis we have identified nine residues highly unique to the Lys49-PLA2 sub-family, which are grouped in three amino acid clusters in the active site, hydrophobic substrate binding channel and homodimer interface regions. These three highly specific residue clusters may have relevance for the Ca2+-independent membrane damaging activity. Of a further 15 less stringently conserved residues, nine are located in two additional clusters which are well isolated from the active site region. The less strictly conserved clusters have been used in predictive sequence searches to correlate amino acid patterns in other venom PLA2s with their pharmacological activities, and motifs for presynaptic and combined toxicities are proposed.
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Affiliation(s)
- R J Ward
- Department of Physics, IBILCE/UNESP, São José do Rio Preto-SP, Brazil
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38
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Canduri F, Mancuso LC, Soares AM, Giglio JR, Ward RJ, Arni RK. Crystallization of piratoxin I, a myotoxic Lys49-phospholipase A2 homologue isolated from the venom of Bothrops pirajai. Toxicon 1998; 36:547-51. [PMID: 9637374 DOI: 10.1016/s0041-0101(97)00120-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Large single crystals of piratoxin I. a Lys49-PLA2 homologue with low enzymatic activity, have been obtained. The crystals belong to the orthorhombic system space group P2(1)2(1)2(1), and diffract X-rays to a resolution of 2.8 A. Preliminary analysis reveals the presence of two molecules in the crystallographic asymmetric unit.
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Affiliation(s)
- F Canduri
- Departamento de Física, IBILCE/UNESP, São José do Rio Preto, SP, Brazil
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39
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Soares AM, Rodrigues VM, Homsi-Brandeburgo MI, Toyama MH, Lombardi FR, Arni RK, Giglio JR. A rapid procedure for the isolation of the Lys-49 myotoxin II from Bothrops moojeni (caissaca) venom: biochemical characterization, crystallization, myotoxic and edematogenic activity. Toxicon 1998; 36:503-14. [PMID: 9637370 DOI: 10.1016/s0041-0101(97)00133-5] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bothtrops moojeni snake venom was fractionated on a CM-Sepharose column which was previously equilibrated with 0.05 M ammonium bicarbonate buffer at pH 8.0 and subsequently eluted with an ammonium bicarbonate concentration gradient from 0.05 to 0.5 M at constant pH (8.0) and temperature (25 degrees C). The fraction which eluted last (M-VI) showed, after direct lyophilization, a single band by polyacrylamide gel electrophoresis (PAGE) and SDS-PAGE, indicating an approximate Mr of 14000 and 27000, in the presence and absence of dithiothreitol, respectively. Its amino acid composition revealed a high level of hydrophobic and basic amino acids as well as 14 half-cystine residues. Its isoelectric point and extinction coefficient (E(1.0 mg/ml) (1.0 cm) at 278 nm and pH 7.0) were 8.2 and 1.170, respectively. M-VI was devoid of phospholipase A2 (PLA2) activity on egg yolk, as well as of hemorrhagic, anticoagulant and coagulant activities, but could induce drastic necrosis on skeletal muscle fibres as well as rapid and transient edema on the rat paw. Its N-terminal sequence: SLFELGKMILQETGKNPAKSYGVYGCNCGVGGRGKPKDATDRCCYVHKCCYK... revealed high homology with other Lys 49 PLA2-like myotoxins from other bothropic venoms. Orthorhombic crystals of M-VI, which diffracted to a maximal resolution of 1.6 A, were obtained and indicated the presence of a dimer in the asymmetrical unit.
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Affiliation(s)
- A M Soares
- Departamento de Bioquímica, Faculdade de Medicina, Universidade de São Paulo, Ribeirao Preto, SP, Brazil
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40
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Bortoleto RK, de Oliveira AH, Ruller R, Arni RK, Ward RJ. Tertiary structural changes of the alpha-hemolysin from Staphylococcus aureus on association with liposome membranes. Arch Biochem Biophys 1998; 351:47-52. [PMID: 9500849 DOI: 10.1006/abbi.1997.0550] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The interaction of alpha-hemolysin (also called alpha-toxin) from Staphylococcus aureus with mixed egg-yolk phosphatidylcholine/cholesterol liposomes has been investigated using the intrinsic tryptophan fluorescence emission (ITFE) signal. The ITFE intensity of alpha-hemolysin, which was obtained using a novel purification protocol, showed a triphasic increase on incubation with liposomes at low protein/lipid ratios. The first, rapid phase results in an increase in ITFE of 10%, which reflects rapid conformation changes in the alpha-hemolysin on association with the liposome membrane. The second phase of the ITFE increase is associated with a red shift from 334 to 339 nm in the maximum emission wavelength, suggesting the transition to a partially unfolded intermediate in the oligomerization process. The third phase of the ITFE intensity change demonstrates a temporal correlation with the appearance of SDS-stable oligomers. The results demonstrate the feasibility of identification of intermediate protein conformations in complex membrane-associated processes by manipulation of the liposomal membrane composition.
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Affiliation(s)
- R K Bortoleto
- Department of Physics, IBILCE/UNESP, São José do Rio Preto, SP, Brazil
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41
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da Silva Giotto MT, Garratt RC, Oliva G, Mascarenhas YP, Giglio JR, Cintra AC, de Azevedo WF, Arni RK, Ward RJ. Crystallographic and spectroscopic characterization of a molecular hinge: conformational changes in bothropstoxin I, a dimeric Lys49-phospholipase A2 homologue. Proteins 1998; 30:442-54. [PMID: 9533628 DOI: 10.1002/(sici)1097-0134(19980301)30:4<442::aid-prot11>3.0.co;2-i] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Bothropstoxin I (BthTX-I) from the venom of Bothrops jararacussu is a myotoxic phospholipase A2 (PLA2) homologue which, although catalytically inactive due to an Asp49-->Lys substitution, disrupts the integrity of lipid membranes by a Ca2+-independent mechanism. The crystal structures of two dimeric forms of BthTX-I which diffract X-rays to resolutions of 3.1 and 2.1 angstroms have been determined. The monomers in both structures are related by an almost perfect twofold axis of rotation and the dimer interfaces are defined by contacts between the N-terminal alpha-helical regions and the tips of the beta-wings of partner monomers. Significant differences in the relative orientation of the monomers in the two crystal forms results in "open" and "closed" dimer conformations. Spectroscopic investigations of BthTX-I in solution have correlated these conformational differences with changes in the intrinsic fluorescence emission of the single tryptophan residues located at the dimer interface. The possible relevance of this structural transition in the Ca2+-independent membrane damaging activity is discussed.
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42
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Zhang E, Arni RK, Levy OE, Tulinsky A. Stereochemical considerations in drug design: the crystal structures of human α-thrombin complexed with two tripeptidyl aldehyde inhibitors at 2.1 Å resolution. Acta Crystallogr A 1996. [DOI: 10.1107/s0108767396091015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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43
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Abstract
Phospholipases A2 (PLA2) are widely distributed in nature and are well characterized proteins with respect to their catalytic and pharmacological activities. A wealth of structural information has recently become available both from X-ray diffraction and NMR studies, and although a detailed model of the catalytic mechanism of PLA2 has been proposed, the structural bases of other aspects of PLA2 function, such as interfacial activation and venom PLA2 pharmacological activities, are still under debate. An appreciation of the PLA2 protein structure will yield new insights with regard to these activities. The salient structural features of the class I, II and III PLA2 are discussed with respect to their functional roles.
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Affiliation(s)
- R K Arni
- Department of Physics, IBILCE/UNESP, São Jose do Rio Preto, Brazil
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44
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Abstract
A myotoxic phospholipase A2, bothropstoxin II, which exhibits low hydrolytic activity, was crystallized and X-ray diffraction data were collected to a resolution of 2.2 A. Preliminary analysis reveals the presence of three molecules in the asymmetric unit.
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Affiliation(s)
- R K Bortoleto
- Departamento de Fisica, Universidade Estadual Paulista, São Jose do Rio Preto, SP, Brazil
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45
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Abstract
With the aim of further understanding the structure/function relationships in the membrane-damaging activity of the Lys49 phospholipase A2 (Lys49-PLA2) sub-family, we used PCR (polymerase chain reaction) on total venom gland cDNAs from Bothrops jararacussu with degenerate oligodeoxyribonucleotides encoding the N- and C-termini of myotoxin II, a Lys49-PLA2 from Bothrops asper. A 350-bp cDNA coding for bothropstoxin I (BtxtxI) was amplified. Sequencing of the amplified fragment shows that BtxtxI has a Lys49, and comparison with the known structure of myotoxin II showed that the amino acids involved in the formation of a novel dimeric structure in this protein were also conserved.
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Affiliation(s)
- R J Ward
- Departamento de Fisica, IBILCE-UNESP, São José do Rio Preto-SP, Brasil
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46
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Arni RK, Ward RJ, Cintra AC, Giglio JR. Crystallization and preliminary diffraction data of bothropstoxin I isolated from the venom of Bothrops jararacussu. Toxicon 1995; 33:383-6. [PMID: 7638878 DOI: 10.1016/0041-0101(94)00156-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The myotoxic Lys-49 phospholipase bothropstoxin I was crystallized, and X-ray diffraction data were collected to 3.5 A resolution. Preliminary analysis reveals the presence of four molecules in the asymmetric unit.
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Affiliation(s)
- R K Arni
- Departamento de Física, Universidade Estadual Paulista, São José do Rio, Preto-SP, Brazil
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47
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Abstract
Prothrombin fragment 2 (the second kringle) has been co-crystallized with PPACK (D-Phe-Pro-Arg)-thrombin and the structure of the non-covalent complex has been determined and refined (R = 0.16) at 3.2 A resolution using X-ray crystallographic methods. The kringles interact with thrombin at a site that has previously been proposed to be the heparin binding region. The latter is a highly electropositive surface near the C-terminal helix of thrombin abundant in arginine and lysine residues. These form salt bridges with acidic side chains of kringle 2. Somewhat unexpectedly, the negative groups of the kringle correspond to an enlarged anionic center of the lysine binding site of lysine binding kringles such as plasminogen K1 and K4 and TPA K2. The anionic motif is DGDEE in prothrombin kringle 2. The corresponding cationic center of the lysine binding site region has an unfavorable Arg71Phe substitution but Lys35 is conserved. However, the folding of fragment 2 is different from that of prothrombin kringle 1 and other kringles: the second outer loop possesses a distorted two-turn helix and the hairpin beta-turn of the second inner loop pivots at V64 and D70 by 60 degrees. The Lys35 is located on a turn of the helix, which causes it to project into solvent space in the fragment 2-thrombin complex, thereby devastating the cationic center of the lysine binding site.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- R K Arni
- Department of Chemistry, Michigan State University, East Lansing 48824-1322
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48
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Arni RK, Ward R, Gutierrez JM. Crystal structures of LYS49 phospholipases A2 from Bothrops asperand Bothrops godmanivenoms. Acta Crystallogr A 1993. [DOI: 10.1107/s0108767378097007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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49
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Arni RK, Gutiérrez JM. Crystallization and preliminary diffraction data of two myotoxins isolated from the venoms of Bothrops asper (Terciopelo) and Bothrops nummifer (jumping viper). Toxicon 1993; 31:1061-4. [PMID: 8212044 DOI: 10.1016/0041-0101(93)90264-j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Two myotoxins isolated from B. asper (myotoxin II) and B. nummifer (myotoxin I) snake venoms have been crystallized and their diffraction properties are described. These myotoxins are phospholipase A2 variants which lack enzymatic activity; B. asper myotoxin II is a lysine-49 phospholipase. Crystals were obtained at room temperature by standard hanging-drop vapour diffusion methods. Crystals diffracted to a resolution of 2.8 and 2.3 A, respectively.
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Affiliation(s)
- R K Arni
- Departamento de Fisica, Universidade Estadual Paulista, S.J. Do Rico preto-sp, Brazil
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50
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Arni RK, Padmanabhan K, Padmanabhan KP, Wu TP, Tulinsky A. Structures of the noncovalent complexes of human and bovine prothrombin fragment 2 with human PPACK-thrombin. Biochemistry 1993; 32:4727-37. [PMID: 8387813 DOI: 10.1021/bi00069a006] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Both human and bovine prothrombin fragment 2 (the second kringle) have been cocrystallized separately with human PPACK (D-Phe-Pro-Arg)-thrombin, and the structures of these noncovalent complexes have been determined and refined (R = 0.155 and 0.157, respectively) at 3.3-A resolution using X-ray crystallographic methods. The kringles interact with thrombin at a site that has previously been proposed to be the heparin binding region. The latter is a highly electropositive surface near the C-terminal helix of thrombin abundant in arginine and lysine residues. These form salt bridges with acidic side chains of kringle 2. Somewhat unexpectedly, the negative groups of the kringle correspond to an enlarged anionic center of the lysine binding site of lysine binding kringles such as plasminogens K1 and K4 and TPA K2. The anionic motif is DGDEE in prothrombin kringle 2. The corresponding cationic center of the lysine binding site region has an unfavorable Arg70Asp substitution, but Lys35 is conserved. However, the folding of fragment 2 is different from that of prothrombin kringle 1 and other kringles: the second outer loop possesses a distorted two-turn helix, and the hairpin beta-turn of the second inner loop pivots at Val64 and Asp70 by 60 degrees. Lys35 is located on a turn of the helix, which causes it to project into solvent space in the fragment 2-thrombin complex, thereby devastating any vestige of the cationic center of the lysine binding site. Since fragment 2 has not been reported to bind lysine, it most likely has a different inherent folding conformation for the second outer loop, as has also been observed to be the case with TPA K2 and the urokinase kringle. The movement of the Val64-Asp70 beta-turn is most likely a conformational change accompanying complexation, which reveals a new heretofore unsuspected flexibility in kringles. The fragment 2-thrombin complex is only the second cassette module-catalytic domain structure to be determined for a multidomain blood protein and only the third domain-domain interaction to be described among such proteins, the others being factor Xa without a Gla domain and Ca2+ prothrombin fragment 1 with a Gla domain and a kringle.
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Affiliation(s)
- R K Arni
- Department of Chemistry, Michigan State University, East Lansing 48824-1322
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