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1.
Phytochem Anal ; 29(3): 242-249, 2018 May.
Artigo em Inglês | MEDLINE | ID: mdl-29148164

RESUMO

INTRODUCTION: Cumin (Cuminum cyminum), a popular spice has been widely used in traditional medicine to cure various ailments. Despite the existence of scientific literature about its pharmacological properties, no successful proteome profiling has yet been attempted. OBJECTIVE: To optimise extraction of cumin proteins and analyse its profile by shotgun proteomics, using one-dimensional electrophoresis coupled with nano-ESI-LC-MS/MS. METHODOLOGY: As a first step, we have compared three extraction protocols for total proteins extraction from cumin. Extracted proteins were separated on one-dimensional gel and analysed by state-of-the-art linear ion trap (LTQ)-Orbitrap Velose and Q Exactive HF mass spectrometer. RESULTS: Evaluation of extraction method revealed significant differences in protein yield and proteome composition between the three extracts. LC-MS/MS allowed identification of several proteins with functional significance in various biological processes. CONCLUSION: This study provides identification of a large number of proteins and offers a molecular basis for future research on potential pharmacologically active cumin proteins. Copyright © 2017 John Wiley & Sons, Ltd.


Assuntos
Cuminum/metabolismo , Proteínas de Plantas/metabolismo , Proteômica , Cromatografia Líquida/métodos , Bases de Dados de Proteínas , Eletroforese em Gel de Poliacrilamida/métodos , Nanotecnologia , Espectrometria de Massas por Ionização por Electrospray/métodos , Espectrometria de Massas em Tandem/métodos
2.
Microb Pathog ; 105: 298-306, 2017 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-28258002

RESUMO

Enterococci, no more regarded as GRAS (Generally Recognized As Safe) organism, are emerging as an important source of nosocomial infections worldwide. The main contributors in pathogenesis of enterococci are the presence of various virulent factors and antibiotic resistance genes. We aimed to examine the prevalence, dissemination, antibiotic resistance and virulent factors associated with enterococci from bulk soil (BS). A total of 372 enterococci were isolated from 500 soil samples. PCR was used to identify the isolates up to species level and for carriage of 16 virulence genes including hospital associated marker (i.e. IS16). E. faecium (77%), E. faecalis (10%), E. hirae (4%) and E. casseliflavus (1%) were the major species isolated. The efaAfs was the most dominant gene (100%), followed by gelE (78.9%), sprE (76.3%) and esp (13%) in E. faecalis isolates. The E. faecium carried largely efaAfm (86.8%) and acm (50.3%) genes. Presence of entP (10%), entA (8.3%) and entB (6.9%) genes was detected mostly in E. faecium, while enlA (18%) and ef1097 (2.6%) was only detected in E. faecalis isolates. 50% E. faecalis and 2% E. faecium isolates harbored IS16, while five E. faecalis harbored both IS16 and espTIM genes providing strong evidence about the presence of espTIM gene on 64 Kb pathogenicity island. BOX and RAPD PCR analysis revealed high degree of genetic variation within the species. Degree of resistance against 12 major antibiotics showed chloramphenicol as the most effective and meropenom as the least effective antibiotic. Presence of multiple antibiotic resistant, virulent and hospital associated enterococci in bulk soil represents a potential source for further dissemination to humans and animals and poses potential impact on public health.


Assuntos
Proteínas de Bactérias/genética , Enterococcus/classificação , Enterococcus/efeitos dos fármacos , Microbiologia do Solo , Fatores de Virulência/genética , Adesinas Bacterianas/genética , Antibacterianos/farmacologia , Farmacorresistência Bacteriana , Enterococcus/genética , Enterococcus/patogenicidade , Enterococcus faecalis/efeitos dos fármacos , Enterococcus faecalis/genética , Enterococcus faecalis/isolamento & purificação , Enterococcus faecalis/patogenicidade , Enterococcus faecium/efeitos dos fármacos , Enterococcus faecium/genética , Enterococcus faecium/isolamento & purificação , Enterococcus faecium/patogenicidade , Hospitais , Proteínas de Membrana/genética , Testes de Sensibilidade Microbiana , Paquistão , Filogenia , Prevalência , Solo , Fatores de Virulência/classificação
3.
Toxins (Basel) ; 8(2): 36, 2016 Feb 02.
Artigo em Inglês | MEDLINE | ID: mdl-26848686

RESUMO

Animal venom (e.g., scorpion) is a rich source of various protein and peptide toxins with diverse physio-/pharmaco-logical activities, which generally exert their action via target-specific modulation of different ion channel functions. Scorpion venoms are among the most widely-known source of peptidyl neurotoxins used for callipering different ion channels, such as; Na⁺, K⁺, Ca⁺, Cl(-), etc. A new peptide of the chlorotoxin family (i.e., Bs-Tx7) has been isolated, sequenced and synthesized from scorpion Buthus sindicus (family Buthidae) venom. This peptide demonstrates 66% with chlorotoxin (ClTx) and 82% with CFTR channel inhibitor (GaTx1) sequence identities reported from Leiurus quinquestriatus hebraeus venom. The toxin has a molecular mass of 3821 Da and possesses four intra-chain disulphide bonds. Amino acid sequence analysis of Bs-Tx7 revealed the presence of a scissile peptide bond (i.e., Gly-Ile) for human MMP2, whose activity is increased in the case of tumour malignancy. The effect of hMMP2 on Bs-Tx7, or vice versa, observed using the FRET peptide substrate with methoxycoumarin (Mca)/dinitrophenyl (Dnp) as fluorophore/quencher, designed and synthesized to obtain the lowest Km value for this substrate, showed approximately a 60% increase in the activity of hMMP2 upon incubation of Bs-Tx7 with the enzyme at a micromolar concentration (4 µM), indicating the importance of this toxin in diseases associated with decreased MMP2 activity.


Assuntos
Proteínas de Artrópodes , Metaloproteinase 2 da Matriz/metabolismo , Peptídeos , Venenos de Escorpião/química , Sequência de Aminoácidos , Animais , Proteínas de Artrópodes/química , Proteínas de Artrópodes/isolamento & purificação , Proteínas de Artrópodes/farmacologia , Humanos , Peptídeos/química , Peptídeos/isolamento & purificação , Peptídeos/farmacologia , Conformação Proteica , Relação Estrutura-Atividade
4.
Toxicon ; 80: 47-57, 2014 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-24462660

RESUMO

Echis carinatus (saw-scaled viper) has been the major culprit responsible for serious envenomation casualties throughout the subcontinent. The present study describes the electrophoretic and zymographic characterization of E. carinatus venom and its effect on mammalian smooth muscle. Crude venom showed the presence of disintegrin, PLA2, C-type lectin/lectin-like components, CRISP, Serine protease, l-amino acid oxidase and very high concentrations of SVMPs. E. carinatus venom (1, 10, 30, 50, 100 µg/ml) inhibited the active tension/force of muscle contraction in a time and concentration dependent manner. The observed effects abolished when the venom was heated at 100 °C for 5 min. However, a decrease in bath temperature from 37 °C to 26 °C or an increase in CaCl2 concentration to 5 mM did not prevent the inhibition of contractile activity. The contractile response elicited by exogenous application of 50 mM KCl and 1 µM acetylcholine (ACh) was also significantly inhibited by all venom concentrations. Prior administration of commercially available polyvalent anti-venom partially neutralized and prevented the effect of E. carinatus venom whereas addition of anti-venom at t50 failed to reverse the inhibitory effect. Studies on isolated intestinal muscle indicate involvement of myotoxic and apoptotic components in E. carinatus venom for irreversible damage to muscle tissue.


Assuntos
Venenos de Víboras/química , Venenos de Víboras/farmacologia , Viperidae , Animais , Antivenenos/farmacologia , Relação Dose-Resposta a Droga , Técnicas In Vitro , Intestinos/efeitos dos fármacos , L-Aminoácido Oxidase , Lectinas Tipo C , Contração Muscular/efeitos dos fármacos , Músculo Liso/efeitos dos fármacos , Paquistão , Coelhos , Mordeduras de Serpentes/tratamento farmacológico
5.
Cell Stress Chaperones ; 16(6): 585-605, 2011 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-21660646

RESUMO

Recent work was conducted to predict the structure of functionally distinct regions of Avicennia marina peroxidase (AP) by using the structural coordinates of barley grains peroxidase as the template. This enzyme is utilized by all living organisms in many biosynthetic or degradable processes and in defense against oxidative stress. The homology model showed some distinct structural changes in the heme, calcium, and substrate-binding regions. Val53 was found to be an important coordinating residue between distal calcium ion and the distal heme site while Ser176 is coordinated to the proximal histidine through Ala174 and Leu172. Different ionic and hydrogen-bonded interactions were also observed in AP. Analyses of various substrate-enzyme interactions revealed that the substrate-binding pocket is provided by the residues, His41, Phe70, Gly71, Asp138, His139, and Lys176; the later three residues are not conserved in the peroxidase family. We have also performed structural comparison of the A. marina peroxidase with that of two class III salt-sensitive species, peanut and soybean. Four loop regions were found to have largest structural deviation. The overall protein sequence was also analyzed for the presence of probable post-translational modification sites and the functional significance of these sites were outlined.


Assuntos
Avicennia/enzimologia , Peroxidases/química , Peroxidases/metabolismo , Sequência de Aminoácidos , Avicennia/química , Avicennia/genética , Sítios de Ligação , Heme/química , Heme/metabolismo , Modelos Moleculares , Dados de Sequência Molecular , Peroxidases/genética , Filogenia , Alinhamento de Sequência , Homologia Estrutural de Proteína , Especificidade por Substrato
6.
Artigo em Inglês | MEDLINE | ID: mdl-21584193

RESUMO

Chemotherapeutic agents for cancer are highly toxic to healthy tissues and hence alternative medicine avenues are widely researched. Majority of the recent studies on alternative medicine suggested that Amoora rohituka possesses considerable antitumor and antibacterial properties. In this work, rohituka and chittagonga, fractionated with petroleum ether, dichloromethane, and ethanol, were explored for their anticancer potential against two breast cancer (MCF-7 and HTB-126) and three pancreatic cancer (Panc-1, Mia-Paca2, and Capan1). The human foreskin fibroblast, Hs68, was also included. Cytotoxicity of each extract was analyzed using the MTT assay and label-free photonic crystal biosensor assay. A concentration series of each extract was performed on the six cell lines. For MCF-7 cancer cells, the chittagonga (Pet-Ether and CH(2)Cl(2)) and rohituka (Pet-Ether) extracts induced cytotoxicity; the chittagonga (EtoAC) and rohituka (MeOH) extracts did not induce cytotoxicity. For HTB126, Panc-1, Mia-Paca2, and Capan-1 cancer cells, only the chittagonga CH(2)Cl(2) extract showed a significant cytotoxic effect. The extracts were not cytotoxic to normal fibroblast Hs68 cells, which may be correlated to the specificity of Amoora extracts in targeting cancerous cells. Based on these results, further examination of the potential anticancer properties Amoora species and the identification of the active ingredients of these extracts is warranted.

7.
BMC Complement Altern Med ; 10: 52, 2010 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-20849608

RESUMO

BACKGROUND: There has been a long standing interest in the identification of medicinal plants and derived natural products for developing cancer therapeutics. Our study focuses upon pancreatic cancer, due to its high mortality rate, that is attributed in part to the lack of an effective chemotherapeutic agent. Previous reports on the use of medicinal plant extracts either alone or alongside conventional anticancer agents in the treatment of this cancer have shown promising results. This work aims to investigate the therapeutic properties of a library of medicinal plants from Bangladesh. METHODS: 56 extracts of 44 unique medicinal plants were studied. The extracts were screened for cytotoxicity against the pancreatic adenocarcinoma cell line Panc-1, using a label-free biosensor assay. The top cytotoxic extracts identified in this screen were tested on two additional pancreatic cancer cell lines (Mia-Paca2 and Capan-1) and a fibroblast cell line (Hs68) using an MTT proliferation assay. Finally, one of the most promising extracts was studied using a caspase-3 colorimetric assay to identify induction of apoptosis. RESULTS: Crude extracts of Petunia punctata, Alternanthera sessilis, and Amoora chittagonga showed cytotoxicity to three cancer cell lines with IC50 values ranging between 20.3 - 31.4 µg/mL, 13.08 - 34.9 µg/mL, and 42.8 - 49.8 µg/mL, respectively. Furthermore, treatment of Panc-1 cells with Petunia punctata was shown to increase caspase-3 activity, indicating that the observed cytotoxicity was mediated via apoptosis. Only Amoora chittagonga showed low cytotoxicity to fibroblast cells with an IC50 value > 100 µg/mL. CONCLUSION: Based upon the initial screening work reported here, further studies aimed at the identification of active components of these three extracts and the elucidation of their mechanisms as cancer therapeutics are warranted.


Assuntos
Adenocarcinoma/tratamento farmacológico , Antineoplásicos Fitogênicos/uso terapêutico , Apoptose/efeitos dos fármacos , Neoplasias Pancreáticas/tratamento farmacológico , Fitoterapia , Extratos Vegetais/uso terapêutico , Plantas Medicinais , Adenocarcinoma/metabolismo , Antineoplásicos Fitogênicos/farmacologia , Bangladesh , Caspase 3/metabolismo , Linhagem Celular Tumoral , Fibroblastos/efeitos dos fármacos , Humanos , Concentração Inibidora 50 , Magnoliopsida , Neoplasias Pancreáticas/metabolismo , Extratos Vegetais/farmacologia
8.
Nat Prod Commun ; 5(6): 931-4, 2010 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-20614828

RESUMO

A high molecular weight serine protease has been purified to electrophoretic homogeneity from the seeds of Caesalpinia bonducella Flem. (Caesalpiniaceae) by the combination of size exclusion and ion exchange chromatography. About 524 fold purification was achieved with an overall recovery of 6.8%. The specific activity was found to be 86 U/mg/min at pH 8.0. The calculated K(m) and V(max) were 1.66 mg/mL and 496.68 units/min per mg of protein, respectively. The molecular mass was estimated to be about 63 kDa by sodium dodecyl sulfate PAGE. The enzyme showed optimum activity at pH 8.0 and exhibited its highest activity at 40 degrees C. The enzyme was strongly inhibited by 2mM phenylmethylsulfonyl fluoride (PMSF), suggesting the presence of a serine residue at the active site. PMSF showed a pure competitive type of inhibition with the serine protease enzyme. It was observed that enzyme activity was enhanced in the presence of dications and was active against a variety of modified substrates and natural proteins.


Assuntos
Caesalpinia/enzimologia , Proteínas de Plantas/metabolismo , Serina Endopeptidases/metabolismo , Inibidores Enzimáticos , Concentração de Íons de Hidrogênio , Metais , Proteínas de Plantas/química , Serina Endopeptidases/química , Temperatura
9.
Phytochemistry ; 70(8): 979-87, 2009 May.
Artigo em Inglês | MEDLINE | ID: mdl-19473681

RESUMO

Cuminum cyminum, an aromatic plant from the family Umbelliferae, is used as a flavoring and seasoning agent in foods. This communication reports the characterization of a nonspecific lipid transfer protein nsLTP1 from its seeds. Plant nsLTPs are small basic proteins involved in transport of lipids between membranes. These proteins are known to participate in plant defense; however, the exact mechanism of their antimicrobial action against fungi or bacteria is still unclear. The cumin nsLTP1 has been purified using a combination of chromatographic procedures and further characterized using mass spectrometry, circular dichroism spectroscopy and Edman degradation. Amino acid sequence has been used to predict homology model of cumin nsLTP1 in complex with myristic acid, and lyso-myristoyl phosphatidyl choline (LMPC). Cumin nsLTP1 is a monomeric protein with a molecular weight of 9.7 kDa as estimated by SDS-PAGE and ESIMS. The protein shows an isoelectric point of 7.8 on 6% PAGE. The primary structure consists of 92 amino acids with eight conserved cysteine residues. The global fold of cumin nsLTP1 includes four alpha-helices stabilized by four disulfide bonds and a C-terminal tail. The role of internal hydrophobic cavity of the protein in lipid transfer is discussed.


Assuntos
Proteínas de Transporte/isolamento & purificação , Cuminum/química , Proteínas de Plantas/isolamento & purificação , Sequência de Aminoácidos , Proteínas de Transporte/química , Eletroforese em Gel de Poliacrilamida , Modelos Moleculares , Dados de Sequência Molecular , Proteínas de Plantas/química , Conformação Proteica , Sementes/química , Análise de Sequência de Proteína
10.
Protein Pept Lett ; 14(5): 481-8, 2007.
Artigo em Inglês | MEDLINE | ID: mdl-17584175

RESUMO

Blue oxygen binding protein hemocyanin from scorpion Buthus sindicus has been investigated using low resolution techniques. The native protein is a polymer of eight different types of subunits arranged in four cubic hexameric form (4x6-mers) as previously annotated using a combination of various types of chromatographic and electrophoretic techniques. In addition, both "top face" as well as the "side view" of the native assembly has also been identified from the negatively stained specimens using transmission electron microscopy confirming the overall structural features of arthropodan hemocyanins. These results are also supported from data obtained from another low resolution technique i.e. Small Angle X-ray scattering (SAXS). SAXS results under oxygenated and deoxygenated states represent a validation case for this technique with key conformational changes of Rg 88.0 --> 86.0 A; +/- 1% (Dmax 280.0 --> 290.0 A; +/- 2%), respectively suggesting that the oxygenated hemocyanin is longer then the deoxygenated hemocyanin by almost 2 A;. Likewise, active conformations of the purified structural and functional subunit Bsin1 under oxygenated and deoxygenated states also determined by SAXS measurements revealed a Rg value of 25.2 --> 25.7 A; +/- 1% (Dmax 75.0 --> 75.5 A; +/- 2%), respectively suggesting very little or no contribution of the individual subunit in the overall conformational change in the native assembly during molecular breathing. Preliminary molecular shapes for the oxy-molecules, calculated directly from the scattering profile-alone in a model-independent procedure, superimpose well on other closely related known three-dimensional structures of the same size. Structural and functional aspects of the native as well as purified subunit and the application of these low resolution techniques like transmission electron microscopy and Small Angle X-ray scattering have been discussed.


Assuntos
Hemocianinas/química , Escorpiões/química , Animais , Microscopia Eletrônica de Transmissão , Modelos Moleculares , Oxigênio/metabolismo , Conformação Proteica , Estrutura Quaternária de Proteína , Espalhamento a Baixo Ângulo , Difração de Raios X
11.
Arch Biochem Biophys ; 445(1): 81-94, 2006 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-16309623

RESUMO

Scorpion venoms are among the most widely known source of peptidyl neurotoxins used for callipering different ion channels, e.g., for Na(+), K(+), Ca(+) or Cl(-). An alpha-toxin (Bs-Tx28) has been purified from the venom of scorpion Buthus sindicus, a common yellow scorpion of Sindh, Pakistan. The primary structure of Bs-Tx28 was established using a combination of MALDI-TOF-MS, LC-ESI-MS, and automated Edman degradation analysis. Bs-Tx28 consists of 65 amino acid residues (7274.3+/-2Da), including eight cysteine residues, and shows very high sequence identity (82-94%) with other long-chain alpha-neurotoxins, active against receptor site-3 of mammalian (e.g., Lqq-IV and Lqh-IV from scorpions Leiurus sp.) and insect (e.g., BJalpha-IT and Od-1 from Buthotus judaicus and Odonthobuthus doriae, respectively) voltage-gated Na(+) channels. Multiple sequence alignment and phylogenetic analysis of Bs-Tx28 with other known alpha- and alpha-like toxins suggests the presence of a new and separate subfamily of scorpion alpha-toxins. Bs-Tx28 which is weakly active in both, mammals and insects (LD(50) 0.088 and 14.3microg/g, respectively), shows strong induction of the rat afferent nerve discharge in a dose-dependent fashion (EC(50)=0.01microg/mL) which was completely abolished in the presence of tetrodotoxin suggesting the binding of Bs-Tx28 to the TTX-sensitive Na(+)-channel. Three-dimensional structural features of Bs-Tx28, established by homology modeling, were compared with other known classical alpha-mammal (AaH-II), alpha-insect (Lqh-alphaIT), and alpha-like (BmK-M4) toxins and revealed subtle variations in the Nt-, Core-, and RT-CT-domains (functional domains) which constitute a "necklace-like" structure differing significantly in all alpha-toxin subfamilies. On the other hand, a high level of conservation has been observed in the conserved hydrophobic surface with the only substitution of W43 (Y43/42) and an additional hydrophobic character at position F40 (L40/A/V/G39), as compared to the other mentioned alpha-toxins. Despite major differences within the primary structure and activities of Bs-Tx28, it shares a common structural and functional motif (e.g., transRT-farCT) within the RT-CT domain which is characteristic of scorpion alpha-mammal toxins.


Assuntos
Neurotoxinas/química , Venenos de Escorpião/química , Potenciais de Ação , Sequência de Aminoácidos , Animais , Blattellidae , Dicroísmo Circular , Motilidade Gastrointestinal , Técnicas In Vitro , Jejuno/efeitos dos fármacos , Jejuno/inervação , Jejuno/fisiologia , Dose Letal Mediana , Artérias Mesentéricas/inervação , Camundongos , Modelos Moleculares , Dados de Sequência Molecular , Neurotoxinas/toxicidade , Filogenia , Conformação Proteica , Ratos , Ratos Sprague-Dawley , Venenos de Escorpião/toxicidade , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Bloqueadores dos Canais de Sódio/química , Bloqueadores dos Canais de Sódio/toxicidade , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Relação Estrutura-Atividade , Tetrodotoxina/química , Tetrodotoxina/metabolismo
12.
Biochem Biophys Res Commun ; 326(1): 123-30, 2005 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-15567161

RESUMO

Avian hemoglobins have attracted much attention in view of the unique oxygen transport characteristics. The present study describes the primary structure of minor hemoglobin component HbD from Tufted duck (Aythya fuligula), a migratory bird seen in Pakistan during the winter season. Separation of the polypeptide subunits was achieved by ion exchange chromatography in the presence of 8M urea. Molecular masses of the intact protein as well as peptides obtained from chemical and enzymatic cleavages were determined by electrospray ionization mass spectrometry. The sequence was studied by automatic Edman degradation of the native chains and their tryptic/hydrolytic fragments in a gas-phase sequencer. Comparison of the hemoglobin sequence with the corresponding sequences of Anseriform representatives and other avian species shows residues like alpha(D)23 Asp, alpha(D)120 Asp as being specific to Tufted duck. The three-dimensional structure analyzed with the protein structure modeling package, WHAT IF, using the crystal structure coordinates of chicken hemoglobin (PDB code=1hbr) shows alpha(D)34 Val, alpha(D)38 Gln, and alpha(D)94 Asp as possible mediators offering alternate pathway for oxygen uptake and release thereby leading to distinct hypoxia tolerance in the Tufted ducks. Results are discussed with reference to function and evolution in the Anseriform representatives.


Assuntos
Patos/metabolismo , Hemoglobinas/química , Modelos Químicos , Modelos Moleculares , Respiração , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Adaptação Fisiológica/fisiologia , Altitude , Sequência de Aminoácidos , Animais , Simulação por Computador , Sequência Conservada , Patos/classificação , Evolução Molecular , Hemoglobinas/análise , Dados de Sequência Molecular , Peso Molecular , Conformação Proteica , Especificidade da Espécie , Relação Estrutura-Atividade
13.
Biochem Biophys Res Commun ; 326(4): 711-7, 2005 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-15607727

RESUMO

BAP1 is an apurinic/apyrimidinic lyase (AP lyase) that plays an important role in the repair of DNA damage. The present study deals with the prediction of the 3D structure of bovine AP lyase based on its sequence homology with human AP lyase. The predicted 3D model of bovine AP1 shows remarkable similarity with human endonuclease in the overall 3D fold. However, significant differences in the model and the X-ray structure were located at some of the important sites. We have analyzed the active center of the enzyme and other sites that are involved in DNA repair. A number of amino acids bind the bases located in the major/minor grooves of DNA. An insertion of Arg176 in the major groove and Met270 in the minor groove caps the DNA bound enzyme's active site, stabilizing the extra helical AP site conformation and effectively locking the protein onto the AP-DNA. Three BAP1 mutants were also modeled and analyzed as regards the changes in the structure. Substitution of Arg176-->Ala leads to the loss of DNA binding whereas mutation of Asp282-->Ala and His308-->Asn leads to a decrease in the enzymatic activity.


Assuntos
DNA Liase (Sítios Apurínicos ou Apirimidínicos)/química , DNA/química , Modelos Químicos , Análise de Sequência de Proteína/métodos , Substituição de Aminoácidos , Animais , Sítios de Ligação , Bovinos , Ativação Enzimática , Modelos Moleculares , Mutagênese Sítio-Dirigida , Ligação Proteica , Conformação Proteica , Dobramento de Proteína , Estrutura Secundária de Proteína , Relação Estrutura-Atividade , Especificidade por Substrato
14.
Biochem Biophys Res Commun ; 314(3): 755-65, 2004 Feb 13.
Artigo em Inglês | MEDLINE | ID: mdl-14741700

RESUMO

Serine proteinase inhibitors are widely distributed in nature and inhibit the activity of enzymes like trypsin and chymotrypsin. These proteins interfere with the physiological processes such as germination, maturation and form the first line of defense against the attack of seed predator. The most thoroughly examined plant serine proteinase inhibitors are found in the species of the families Leguminosae, Graminae, and Solanaceae. Leucaena leucocephala belongs to the family Leguminosae. It is widely used both as an ornamental tree as well as cattle food. We have constructed a three-dimensional model of a serine proteinase inhibitor from L. leucocephala seeds (LTI) complexed with trypsin. The model was built based on its comparative homology with soybean trypsin inhibitor (STI) using the program, MODELLER6. The quality of the model was assessed stereochemically by PROCHECK. LTI shows structural features characteristic of the Kunitz type trypsin inhibitor and shows 39% residue identity with STI. LTI consists of 172 amino acid residues and is characterized by two disulfide bridges. The protein is a dimer with the two chains being linked by a disulfide bridge. Despite the high similarity in the overall tertiary structure, significant differences exist at the active site between STI and LTI. The present study aims at analyzing these interactions based on the available amino acid sequences and structural data. We have also studied some functional sites such as phosphorylation, myristoylation, which can influence the inhibitory activity or complexation with other molecules. Some of the differences observed at the active site and functional sites can explain the unique features of LTI.


Assuntos
Fabaceae/química , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Inibidores da Tripsina/química , Inibidores da Tripsina/metabolismo , Sequência de Aminoácidos , Sítios de Ligação , Dimerização , Dissulfetos/química , Modelos Moleculares , Dados de Sequência Molecular , Filogenia , Proteínas de Plantas/genética , Estrutura Secundária de Proteína , Sementes/química , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Homologia Estrutural de Proteína , Tripsina/química , Tripsina/metabolismo , Inibidores da Tripsina/genética
15.
Biochem Biophys Res Commun ; 308(4): 726-35, 2003 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-12927779

RESUMO

Cytotoxic lymphocytes (CTLs), the key players of cell mediated immunity, induce apoptosis by engaging death receptors or through exocytosis of cytolytic granules containing granzyme (proteases) and pore-forming protein (perforin). The crystal structure of granzyme B from human (B(h)) and rat (B(r)), as well as that of pro-granzyme K (K(h)) has been reported recently. In the present communication, we describe the homology modeling of granzyme family (in particular Gzm A(h), M(h), B(m), and C(m) from human and mouse) based on the crystal structural coordinates of trypsin, granzyme K (K(h)), and granzyme B (B(h)). These models have been used for establishing phylogenetic relationship as well as identifying characteristic features for designing specific inhibitors. The paper also highlights key residues at the S1, S2, and S2(') binding subsites in all granzyme, which may be involved in the structure-function relationship of this enzyme family. The predicted 3D homology models show a conserved two similar domain structure, i.e., an N-terminal domain and a C-terminal domain comprising predominantly of beta-sheet structure with a little alpha-helical content. Micro-heterogeneities have been observed in the vicinity of the active site in all granzymes as compared to granzyme B(h). For example, in granzyme M(h), valine is present at the S1 subsite instead of arginine. Similarly differences at S2 (Leu-->Phe), S3 (Ser-->Gly), and S4 (Arg-->Asn) subsites are quite apparent and appear to hold the potential for selective designing of inhibitors for possible therapeutic applications. Furthermore, analysis of the electrostatic surface potential on the shape of granzyme-inhibitor binding groove reveals clear differences at the reactive site. Additionally the different posttranslational modification sites such as phosphorylation (e.g., in granzyme M Thr101, Ser109), myristoylation (Gly22, 117, and 131), and glycosylation (Ser160) have been identified, as very little is known about the functional significance of these modifications in the granzyme family. Thus, glycosylation at Ser160 in granzyme M may influence the net charge of the enzyme, resulting in altered substrate binding as compared to granzyme B. Also this modification may influence the rate of complexation and binding affinity with proteoglycans. These studies are expected to contribute towards the basic understanding of functional associations of the granzymes with other molecules and their possible role in apoptosis.


Assuntos
Serina Endopeptidases/química , Sequência de Aminoácidos , Animais , Apoptose , Sítios de Ligação , Biologia Computacional , Granzimas , Humanos , Camundongos , Modelos Moleculares , Dados de Sequência Molecular , Filogenia , Ligação Proteica , Estrutura Terciária de Proteína , Ratos , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos , Relação Estrutura-Atividade , Especificidade por Substrato , Linfócitos T Citotóxicos/metabolismo , Tripsina/química , Triptases
16.
Biochem Biophys Res Commun ; 308(3): 497-504, 2003 Aug 29.
Artigo em Inglês | MEDLINE | ID: mdl-12914778

RESUMO

Caspases, the intracellular cysteine proteinases, play a central role in the process of programmed cell death. Caspases induce apoptosis through a highly integrated and regulated biological, biochemical, and genetic mechanism. Although proper execution of apoptosis is fundamental for cell growth artificial caspase inhibition can be considered in certain degenerative diseases. This realization has attracted attention towards caspases as likely targets for pharmaceutical intervention. Here we analyze the structure of caspase-6 and also predict the possible glycosylation, phosphorylation, and myristoylation sites as very little is known about the functional role of these post translational modifications in the caspase family. These studies are expected to improve our understanding of associations of caspases with other molecules and the possible role played in apoptosis. The predicted tertiary structure of caspase-6 as well as the enzyme complexed with its inhibitor (tetra-peptide aldehyde Ac-IETD-CHO) shows similar binding feature as seen in other caspases. Cys/His catalytic dyad for caspase-6 and -8 show possible involvement of a third component, i.e., Pro29 and Arg258 in caspase-6 and caspase-8, respectively. Changes in the length and nature of loop between alpha5 and beta9, involved in defining the S4 subsite, result in modification of P4 (Ile) site. These interactions provide detail of inhibitor binding on structural level and also help in designing mutants for structure-function studies of these enzymes.


Assuntos
Caspases/química , Modelos Moleculares , Sequência de Aminoácidos , Apoptose , Ácido Aspártico/química , Sítios de Ligação , Caspase 6 , Caspase 8 , Caspase 9 , Caspases/metabolismo , Domínio Catalítico , Inibidores Enzimáticos/química , Inibidores Enzimáticos/metabolismo , Isoleucina/química , Dados de Sequência Molecular , Ácidos Mirísticos/metabolismo , Fosforilação , Alinhamento de Sequência , Homologia Estrutural de Proteína
17.
Biochem Biophys Res Commun ; 291(1): 176-84, 2002 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-11829480

RESUMO

The primary structure of the major hemoglobin component, HbA (alpha(A)- and beta-chain), from Tufted duck (Aythya fuligula) is presented. The separation of the globin subunits was achieved by ion exchange chromatography on CM-cellulose in 8 M urea. The amino acid sequence was determined by automatic Edman degradation of native chains as well as tryptic and hydrolytic peptides in a gas-phase sequencer. The automated homology model was generated by the protein structure modeling package WHAT IF using the crystal structure coordinates of Bar-headed goose hemoglobin. The 3D structure prediction enables alpha99Arg and beta101Glu to emerge as a new intersubunit contact site not found in the hemoglobin structure of any other species. alpha99Arg forms a complex salt bridge network involving alpha99Arg-beta101Glu-beta104Arg-beta108Asp. Also the substitution at alpha34 --> Ile, alpha38 --> Gln and beta55 --> Leu serves to stabilize the oxy-structure, leading to higher oxygen affinity.


Assuntos
Hemoglobina A/química , Hemoglobina A/metabolismo , Subunidades Proteicas , Respiração , Sais/química , Aminoácidos/análise , Animais , Sítios de Ligação/fisiologia , Cromatografia Líquida de Alta Pressão , Simulação por Computador , Patos , Eletroforese em Gel de Poliacrilamida , Gansos , Substâncias Macromoleculares , Modelos Moleculares , Dados de Sequência Molecular , Filogenia , Estrutura Terciária de Proteína , Análise de Sequência de Proteína , Homologia de Sequência de Aminoácidos , Especificidade da Espécie , Espectrometria de Massas por Ionização por Electrospray , Relação Estrutura-Atividade
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