1
|
Siddiqui U, Khan AB, Ahmad T, Rehman AA, Jairajpuri MA. A common protein C inhibitor exosite partially controls the heparin induced activation and inhibition of serine proteases. Int J Biol Macromol 2024; 266:131065. [PMID: 38521329 DOI: 10.1016/j.ijbiomac.2024.131065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 01/06/2024] [Revised: 03/04/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
Protein C inhibitor (PCI) maintains hemostasis by inhibiting both procoagulant and anticoagulant serine proteases, and plays important roles in coagulation, fibrinolysis, reproduction, and anti-angiogenesis. The reactive site loop of PCI traps and irreversibly inhibits the proteases like APC (activating protein C), thrombin (FIIa) and factor Xa (FXa). Previous studies on antithrombin (ATIII) had identified Tyr253 and Glu255 as functional exosites that interact and aid in the inhibition of factor IXa and FXa. Presence of exosite in PCI is not known, however a sequence comparison with the PCI from different vertebrate species and ATIII identified Glu239 to be absolutely conserved. PCI residues analogous to ATIII exosite residues were mutated to R238A and E239A. Purified variant PCI in the presence of heparin (10 μg/ml) showed a 2-4 fold decrease in the rate of inhibition of the proteases. However, the stoichiometry of inhibition of FIIa, APC, and FXa by native PCI, R238A and E239A variants were found to be close to 1.0, which also indicated the formation of stable complexes based on SDS-PAGE and western blot analysis with thrombin and APC. Our findings revealed the possible presence of an exosite in PCI that influences the protease inhibition rates.
Collapse
Affiliation(s)
- Urfi Siddiqui
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Abdul Burhan Khan
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Tahif Ahmad
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ahmed Abdur Rehman
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | | |
Collapse
|
2
|
Khan AB, Siddiqui U, Fatima S, Rehman AA, Jairajpuri MA. Protein disulfide isomerase uses thrombin-antithrombin complex as a template to bind its target protein and alter the blood coagulation rates. Biosci Rep 2024:BSR20231540. [PMID: 38660763 DOI: 10.1042/bsr20231540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
During inflammation and situations of cellular stress Protein Disulfide Isomerase (PDI) is released in the blood plasma from the platelet and endothelial cells to influence thrombosis. The addition of exogenous PDI makes the environment pro-thrombotic by inducing disulfide bond formation in specific plasma protein targets like vitronectin, factor V, and factor XI. However, the mechanistic details of PDI interaction with its target remain largely unknown. A decrease in the coagulation time was detected in activated partial thromboplastin time (APTT), prothrombin time (PT), and thrombin time (TT) in addition to the purified recombinant PDI (175nM). The coagulation time can be controlled using an activator (quercetin penta sulfate, QPS) or an inhibitor (Quercetin 3-rutinoside, Q3R) of PDI activity. Likewise, the PDI variants that increase the PDI activity (H399R) decrease, and the variant with low activity (C53A) increases the blood coagulation time. An SDS-PAGE and western blot analysis showed that the PDI does not form a stable complex with either thrombin or Antithrombin (ATIII) but it uses the ATIII-thrombin complex as a template to bind and maintain its activity. A complete inhibition of thrombin activity on the formation of ATIII-thrombin-PDI complex, and the complex-bound PDI-catalyzed disulfide bond formation of the target proteins may control the pro- and anti-thrombotic role of PDI.
Collapse
|
3
|
Khan AB, Siddiqui U, Fatima S, Rehman AA, Jairajpuri MA. Naringin binds to protein disulfide isomerase to inhibit its activity and modulate the blood coagulation rates: Implications in controlling thrombosis. Int J Biol Macromol 2023; 252:126241. [PMID: 37567521 DOI: 10.1016/j.ijbiomac.2023.126241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/23/2023] [Revised: 07/25/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023]
Abstract
Currently used antithrombotic drugs are beset with several drawbacks which necessitates the need for new and cheaper alternatives. Protein disulfide isomerase (PDI) is secreted in the blood plasma in cellular stress conditions and initiates the thrombus formation. A screening of library of natural compounds revealed that naringin had a high binding affinity for the PDI (-8.2 kcal/mol). Recombinant PDI was purified using the affinity chromatography. Incubation of purified PDI (3 μM) with naringin (0-100 μM, pH 7.4, 25 °C) partially modulated its conformation. Consequently, the fluorescence emission spectra of the PDI binding to naringin were assessed using the Stern-Volmer equation, which indicated an association constant of 2.78 × 104 M-1 suggesting an appreciable affinity for the naringin, with a unique binding site. An insulin turbidity assay showed that PDI activity is decreased in the presence of naringin indicating inhibition. Molecular dynamic simulation studies showed the changes in the PDI structure on binding to the naringin. Incubation of naringin (80 μM) in fresh human plasma along with exogenous PDI (175 nM) showed a significant delay in the intrinsic and extrinsic coagulation pathways. We show that naringin is able to modulate the PDI conformation and activity resulting in altered blood coagulation rates.
Collapse
Affiliation(s)
- Abdul Burhan Khan
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Urfi Siddiqui
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Sana Fatima
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ahmed Abdur Rehman
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | | |
Collapse
|
4
|
Bano S, Khan AB, Fatima S, Rashid Q, Prakash A, Gupta N, Ahmad I, Ansari S, Lynn AM, Abid M, Jairajpuri MA. Mannose 2, 3, 4, 5, 6- O-pentasulfate (MPS): a partial activator of human heparin cofactor II with anticoagulation potential. J Biomol Struct Dyn 2023; 41:3717-3727. [PMID: 35343865 DOI: 10.1080/07391102.2022.2053749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/22/2021] [Accepted: 03/09/2022] [Indexed: 10/18/2022]
Abstract
Thromboembolic diseases are a major cause of mortality in human and the currently available anticoagulants are associated with various drawbacks, therefore the search for anticoagulants that have better safety profile is highly desirable. Compounds that are part of the dietary routine can be modified to possibly increase their anticoagulant potential. We show mannose 2,3,4,5,6-O-pentasulfate (MPS) as a synthetically modified form of mannose that has appreciable anticoagulation properties. An in silico study identified that mannose in sulfated form can bind effectively to the heparin-binding site of antithrombin (ATIII) and heparin cofactor II (HCII). Mannose was sulfated using a simple sulfation strategy-involving triethylamine-sulfur trioxide adduct. HCII and ATIII were purified from human plasma and the binding analysis using fluorometer and isothermal calorimetry showed that MPS binds at a unique site. A thrombin inhibition analysis using the chromogenic substrate showed that MPS partially enhances the activity of HCII. Further an assessment of in vitro blood coagulation assays using human plasma showed that the activated partial thromboplastin time (APTT) and prothrombin time (PT) were prolonged in the presence of MPS. A molecular dynamics simulation analysis of the HCII-MPS complex showed fluctuations in a N-terminal loop and the cofactor binding site of HCII. The results indicate that MPS is a promising lead due to its effect on the in vitro coagulation rate.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shadabi Bano
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Abdul Burhan Khan
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Sana Fatima
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Qudsia Rashid
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Amresh Prakash
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Neha Gupta
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Irshad Ahmad
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Shoyab Ansari
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Andrew M Lynn
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mohammad Abid
- Medicinal Chemistry Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Mohamad Aman Jairajpuri
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| |
Collapse
|
5
|
Fatima S, Gupta S, Khan AB, Rehman SU, Jairajpuri MA. Identification and validation of two alternatively spliced novel isoforms of human alpha-1-antichymotrypsin. Biochem Biophys Res Commun 2022; 628:25-31. [DOI: 10.1016/j.bbrc.2022.08.061] [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] [Received: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/02/2022]
|
6
|
Fatima S, Ansari S, Bano S, Ahamad S, Ishqi HM, Tabish M, Gupta D, Rehman SU, Jairajpuri MA. Detection of truncated isoforms of human neuroserpin lacking the reactive center loop: Implications in noninhibitory role. IUBMB Life 2021; 73:941-952. [PMID: 33893722 DOI: 10.1002/iub.2475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 02/11/2021] [Revised: 03/23/2021] [Accepted: 04/13/2021] [Indexed: 12/27/2022]
Abstract
Neuroserpin is a serine protease inhibitor expressed mainly in the brain and at low levels in other tissues like the kidney, testis, heart, and spinal cord. It is involved in the inhibition of tissue plasminogen activator (tPA), plasmin, and to a lesser extent, urokinase-type plasminogen (uPA). Neuroserpin has also been shown to plays noninhibitory roles in the regulation of N-cadherin-mediated cell adhesion. It is involved in neuroprotection from seizure and stroke through tPA-mediated inhibition and also through its other protease targets. Mutations in critical domains of neuroserpin lead to its polymerization and neuronal death. In this study, a novel truncated isoform of human neuroserpin was identified in the brain and liver, which was confirmed by reverse transcriptase-PCR and DNA sequencing using exon-specific primers. Structural characterization of novel isoform using MD simulations studies indicated that it lacks the reactive center loop (RCL) but largely maintains its secondary structure fold. The novel truncated variant was cloned, expressed, and purified. A comparative intrinsic fluorescence and 4,4'-bis-1-anilino naphthalene 8-sulfonate studies revealed a decrease in fluorescence emission intensity and a more exposed hydrophobic surface as compared to the reported isoform. However, the novel isoform has lost its ability for tPA inhibition and complex formation. The absence of RCL indicates a noninhibitory role for the truncated isoform, prompting a detailed search and identification of two smaller isoforms in the human brain. With indications of the noninhibitory role of neuroserpin, identifying novel isoforms that appear to be without the tPA recognition domain is significant.
Collapse
Affiliation(s)
- Sana Fatima
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Shoyab Ansari
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Shadabi Bano
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Shahzaib Ahamad
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Hassan Mubarak Ishqi
- Molecular Genetics Laboratory, National Institute of Immunology, New Delhi, India
- Department of Biochemistry, Faculty of Life Sciences, Aligarh M. University, Aligarh, Uttar Pradesh, India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Sciences, Aligarh M. University, Aligarh, Uttar Pradesh, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sayeed Ur Rehman
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | | |
Collapse
|
7
|
Ansari S, Ray A, Ali MF, Bano S, Jairajpuri MA. Contrasting conformational dynamics of β-sheet A and helix F with implications in neuroserpin inhibition and aggregation. Int J Biol Macromol 2021; 176:117-125. [PMID: 33516851 DOI: 10.1016/j.ijbiomac.2021.01.171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 12/23/2020] [Revised: 01/18/2021] [Accepted: 01/26/2021] [Indexed: 11/25/2022]
Abstract
Neuroserpin (NS) is an inhibitory protein of serpin super family, its shutter region variants have high propensity to aggregate leading to pathological disorders like familial encephalopathy with NS inclusion bodies (FENIB). Helix F and β-sheet A of NS participate in the tissue plasminogen activator (tPA) inhibition but the mechanism is not yet completely understood. A microsecond (μs) molecular dynamics simulation of the helix F and strand 3A variants showed predominant fluctuations in the loop connecting the strands of β-sheet A. Therefore to understand the role of helix F and strand 3A of β-sheet A, cysteine was incorporated at the position N182 in stand 3A (N182C) and position W154 (W154C) in the helix F using site-directed mutagenesis. Purified variants were further labeled with Alexa Fluor488 C5 maleimide dye. Temperature dependent study using non-denaturing PAGE showed the formation of large aggregates of helix F variant W154C but not the strand 3A N182C variant. Interestingly tPA inhibition was found to be decreased in the labeled N182C with decreased tPA-complex formation as compared to labeled W154C NS variant. The fluorescence emission intensity of the labeled helix F variant W154C decreased in the presence of an increasing concentration of tPA, whereas an increase in emission intensity was observed in labeled strand 3A variant N182C, indicating more exposure of strand 3A and shielding of helix F. Taken together the data shows that helix F has a predominant role in the aggregation but a minor role in the inhibition mechanism.
Collapse
Affiliation(s)
- Shoyab Ansari
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Arjun Ray
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi 110020, India
| | - Mohammad Farhan Ali
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Shadabi Bano
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Mohamad Aman Jairajpuri
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India.
| |
Collapse
|
8
|
Bano S, Fatima S, Ahamad S, Ansari S, Gupta D, Tabish M, Rehman SU, Jairajpuri MA. Identification and characterization of a novel isoform of heparin cofactor II in human liver. IUBMB Life 2020; 72:2180-2193. [PMID: 32827448 DOI: 10.1002/iub.2361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/05/2020] [Accepted: 07/07/2020] [Indexed: 11/07/2022]
Abstract
Heparin cofactor II (HCII) is predominantly expressed in the liver and inhibits thrombin in blood plasma to influence the blood coagulation cascade. Its deficiency is associated with arterial thrombosis. Its cleavage by neutrophil elastase produces fragment that helps in neutrophil chemotaxis in the acute inflammatory response in human. In the present study, we have identified a novel alternatively spliced transcript of the HCII gene in human liver. This novel transcript includes an additional novel region in continuation with exon 3 called exon 3b. Exon 3b acts like an alternate last exon, and hence its inclusion in the transcript due to alternative splicing removes exon 4 and encodes for a different C-terminal region to give a novel protein, HCII-N. MD simulations of HCII-N and three-dimensional structure showed a unique 51 amino acid sequence at the C-terminal having unique RCL-like structure. The HCII-N protein purified from bacterial culture showed a protein migrating at lower molecular weight (MW 55 kDa) as compared to native HCII (MW 66 kDa). A fluorescence-based analysis revealed a more compact structure of HCII-N that was in a more hydrophilic environment. The HCII-N protein, however, showed no inhibitory activity against thrombin. Due to large conformational variation observed in comparison with native HCII, HCII-N may have alternate protease specificity or a non-inhibitory role. Western blot of HCII purified from large plasma volume showed the presence of a low MW 59 kDa band with no thrombin activity. This study provides the first evidence of alternatively spliced novel isoform of the HCII gene.
Collapse
Affiliation(s)
- Shadabi Bano
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Sana Fatima
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Shahzaib Ahamad
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Shoyab Ansari
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Sciences, Aligarh M. University, Aligarh, India
| | - Sayeed Ur Rehman
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | | |
Collapse
|
9
|
Khan AB, Gupta N, Rashid Q, Ahmad I, Bano S, Siddiqui U, Abid M, Jairajpuri MA. Quercetin 3, 3′, 4′, 5, 7-O- pentasulfate (QPS): A novel activator of protein disulfide isomerase. Medicine in Drug Discovery 2020. [DOI: 10.1016/j.medidd.2020.100029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
|
10
|
Kalam SURA, Jairajpuri MA. Identification and molecular characterization of a novel non‐inhibitory isoform of human neuroserpin gene. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.05742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
11
|
Ali MF, Kaushik A, Gupta D, Ansari S, Jairajpuri MA. Changes in strand 6B and helix B during neuroserpin inhibition: Implication in severity of clinical phenotype. Biochim Biophys Acta Proteins Proteom 2020; 1868:140363. [PMID: 31954927 DOI: 10.1016/j.bbapap.2020.140363] [Citation(s) in RCA: 2] [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] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 12/19/2019] [Accepted: 01/15/2020] [Indexed: 12/13/2022]
Abstract
Neuroserpin (NS) is predominantly expressed in brain and inhibits tissue-type plasminogen activator (tPA) with implications in brain development and memory. Nature of conformational change in pathological variants in strand 6B and helix B of NS that cause a relatively mild to severe epilepsy (and/or dementia) remains largely elusive. MD simulation with wild type (WT) NS, strand 6B and helix B variants indicated that substitution in this region affects the conformation of the strands 5B, 5A and reactive centre loop. Therefore, we designed variants of NS in strand 6B (I46D and F48S) and helix B (A54F, L55A and L55P) to investigate their role in tPA inhibition mechanism and propensity to aggregate. An interaction analysis showed disturbance of a hydrophobic patch centered at strands 5B, 6B and helix B in I46D and F48S but not in A54F, L55A, L55P and WT NS. Purified I46D, F48S and L55P variants showed decrease in fluorescence emission intensity but have similar α-helical content, however results of A54F and L55A were comparable to WT NS. Analysis of tPA inhibition showed marginal effect on A54F and L55A variant with tPA-NS complex formation. In contrast, I46D, F48S and L55P variants showed massive decrease in tPA inhibition, with no tPA-NS complex formation. Analysis of native PAGE under under polymerization condition showed prompt conversion of I46D, F48S and L55P to latent conformation but not A54F and L55A variants. Identification of these novel conformational changes will aid in the understanding of variable clinical phenotype of shutter region NS variants and other serpins.
Collapse
Affiliation(s)
- Mohammad Farhan Ali
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Abhinav Kaushik
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shoyab Ansari
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Mohamad Aman Jairajpuri
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India.
| |
Collapse
|
12
|
Ahmad P, Tantry IQ, Ali A, Siddiqui SA, Rehman SU, Waris S, Jairajpuri MA. Structural alteration in hypochlorous acid modified antithrombin indicates generation of neo-epitopes. Arch Biochem Biophys 2020; 685:108332. [PMID: 32194043 DOI: 10.1016/j.abb.2020.108332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 03/03/2020] [Accepted: 03/10/2020] [Indexed: 01/25/2023]
Abstract
Increased tendency of cancer patients to develop venous thromboembolism (VTE) is associated with high rates of mortality. Elevation of procoagulant proteins and down regulation of naturally occurring coagulation inhibitors appears to form the basis of high risk of VTE in malignancy. A reduced level of anticoagulant protein like antithrombin (AT) will influence both coagulation and angiogenesis, as its cleaved and latent conformations show potent antiangiogenic activity. We show a concentration dependent perturbation in the secondary and tertiary structures of AT conformers exposed to hypochlorous acid (HOCl). Modulated under a very narrow concentration range of HOCl, native AT undergoes oligomerization, aggregation and fragmentation based on spectroscopic, SDS and native-PAGE studies. Factor Xa inhibition assay demonstrated a progressive decrease in inhibition activity of AT on modification by HOCl. Bis-ANS result showed that hydrophobic patches were more exposed in the case of HOCl-modified AT when assessed fluorometrically. Dosage of HOCl-modified AT in experimental animals induced high titer antibodies showing more specificity towards modified forms in comparison to unmodified forms. Auto-antibodies isolated from cancer patients also showed enhanced binding with HOCl-modified AT in comparison to native counterpart. Compared to normal AT, structurally and functionally altered conformation of HOCl-modified AT showed increased immunogenic sensitivity. HOCl modified AT can contribute to prothrombotic and angiogenic environment during cancer progression/development.
Collapse
Affiliation(s)
- Parvez Ahmad
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi, 110025, India.
| | - Irfan Qadir Tantry
- Department of Biochemistry, Faculty of Medicine, Aligarh Muslim University, Aligarh, 202002, India.
| | - Asif Ali
- Department of Biochemistry, Faculty of Medicine, Aligarh Muslim University, Aligarh, 202002, India.
| | - Shahid Ali Siddiqui
- Department of Radiotherapy, Faculty of Medicine, Aligarh Muslim University, Aligarh, 202002, India.
| | - Sayeed Ur Rehman
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110062, India.
| | - Sana Waris
- Department of Biochemistry, Faculty of Medicine, Aligarh Muslim University, Aligarh, 202002, India.
| | - Mohamad Aman Jairajpuri
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi, 110025, India.
| |
Collapse
|
13
|
Rehman SU, Ashraf S, Ahamad S, Sarwar T, Husain MA, Ahmad P, Tabish M, Jairajpuri MA. Identification of a novel alternatively spliced isoform of antithrombin containing an additional RCL-like loop. Biochem Biophys Res Commun 2019; 517:421-426. [PMID: 31378371 DOI: 10.1016/j.bbrc.2019.07.113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 07/16/2019] [Accepted: 07/28/2019] [Indexed: 11/22/2022]
Abstract
Antithrombin (AT3) is one of the most important inhibitors of blood coagulation proteases that belong to the serpin family of protease inhibitors. In this study, a novel alternatively spliced isoform of AT3 was identified, both at transcript and protein level. This novel transcript contains an additional region in the continuation of exon 3b that was included in the transcript due to use of an alternate 5' splice site. The existence of the novel transcript was confirmed in human brain and liver through RT-PCR. An analysis of the complete transcript indicated that the native reactive centre loop (RCL) of AT3 is maintained; however the novel amino acid sequence projects out as an additional loop as evident from MD simulation studies. A unique amino acid sequence present in the novel isoform was used for the development of polyclonal antibody. The expression of novel isoform was confirmed in human brain and liver tissue using Western blot analysis. Interestingly an alignment of RCL like domain with other inhibitory serpins showed significant similarity with the neuroserpin RCL. To the best of our knowledge, this is the first evidence of alternatively spliced AT3 sequence containing an additional loop and could have physiological relevance.
Collapse
Affiliation(s)
- Sayeed Ur Rehman
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India; Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi, India
| | - Shazia Ashraf
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India; Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shahzaib Ahamad
- Department of Biotechnology, School of Engineering & Technology, IFTM University, Lodhipur-Rajput, Delhi Road, Moradabad, India
| | - Tarique Sarwar
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | | | - Parvez Ahmad
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Sciences, A.M.U, Aligarh, U.P, India
| | | |
Collapse
|
14
|
Soleja N, Jairajpuri MA, Queen A, Mohsin M. Genetically encoded FRET-based optical sensor for Hg 2+ detection and intracellular imaging in living cells. J Ind Microbiol Biotechnol 2019; 46:1669-1683. [PMID: 31531745 DOI: 10.1007/s10295-019-02235-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 05/03/2019] [Accepted: 09/05/2019] [Indexed: 12/31/2022]
Abstract
Due to the potential toxicity of mercury, there is an immediate need to understand its uptake, transport and flux within living cells. Conventional techniques used to analyze Hg2+ are invasive, involve high cost and are less sensitive. In the present study, a highly efficient genetically encoded mercury FRET sensor (MerFS) was developed to measure the cellular dynamics of Hg2+ at trace level in real time. To construct MerFS, the periplasmic mercury-binding protein MerP was sandwiched between enhanced cyan fluorescent protein (ECFP) and venus. MerFS is pH stable, offers a measurable fluorescent signal and binds to Hg2+ with high sensitivity and selectivity. Mutant MerFS-51 binds with an apparent affinity (Kd) of 5.09 × 10-7 M, thus providing a detection range for Hg2+ quantification between 0.210 µM and 1.196 µM. Furthermore, MerFS-51 was targeted to Escherichia coli (E. coli), yeast and human embryonic kidney (HEK)-293T cells that allowed dynamic measurement of intracellular Hg2+ concentration with a highly responsive saturation curve, proving its potential application in cellular systems.
Collapse
Affiliation(s)
- Neha Soleja
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | | | - Aarfa Queen
- Department of Chemistry, Jamia Millia Islamia, New Delhi, 110025, India
| | - Mohd Mohsin
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India.
| |
Collapse
|
15
|
Ahmad I, Sharma S, Gupta N, Rashid Q, Abid M, Ashraf MZ, Jairajpuri MA. Antithrombotic potential of esculin 7, 3', 4', 5', 6'-O-pentasulfate (EPS) for its role in thrombus reduction using rat thrombosis model. Int J Biol Macromol 2018; 119:360-368. [PMID: 30009901 DOI: 10.1016/j.ijbiomac.2018.07.048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 12/16/2022]
Abstract
Currently available anticoagulants for prevention and treatment of thrombosis have several limitations, thus, small organic scaffolds that can dissolve clots in vivo in a dose dependent manner with lesser side effects are highly desirable. Here we report the synthesis of esculin pentasulfate (EPS) and assessment of its in vitro, in vivo and ex vivo anticoagulant and antithrombotic potential. Assessment of in vitro clotting times showed prolonged activated partial thromboplastin time (APTT), prothrombin time (PT) and thrombin time (TT) in the presence of EPS. EPS also showed remarkable reduction in thrombus formation when administered in occlusion induced thrombotic rats at a low dose (2.5 mg/kg). Further, assessment of clot rate with plasma isolated from EPS treated rats confirmed its anticoagulation potential. EPS at varying concentrations showed no significant cytotoxic effect on HEK293 cell line. Further, molecular docking analysis of EPS with known anticoagulant proteins [(antithrombin (ATIII) and heparin cofactor II (HCF II)] that require heparin revealed good binding affinity (-7.9 kcal/mol) with ATIII but not with HCF II. ATIII when incubated with EPS showed increased fluorescence intensity, with no change in secondary structure. Overall, our results clearly show the in vivo modulation of thrombus formation using a modified natural scaffold EPS.
Collapse
Affiliation(s)
- Irshad Ahmad
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Swati Sharma
- Defence Institute of Physiology & Allied Sciences, Timarpur, New Delhi 110 054, India
| | - Neha Gupta
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Qudsia Rashid
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Mohammad Abid
- Medicinal Chemistry Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi 110 025, India
| | - Mohammad Z Ashraf
- Defence Institute of Physiology & Allied Sciences, Timarpur, New Delhi 110 054, India
| | - Mohamad Aman Jairajpuri
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India.
| |
Collapse
|
16
|
Ali MF, Kaushik A, Kapil C, Gupta D, Jairajpuri MA. A hydrophobic patch surrounding Trp154 in human neuroserpin controls the helix F dynamics with implications in inhibition and aggregation. Sci Rep 2017; 7:42987. [PMID: 28230174 PMCID: PMC5322333 DOI: 10.1038/srep42987] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 01/17/2017] [Indexed: 01/23/2023] Open
Abstract
Neuroserpin (NS) mediated inhibition of tissue-type plasminogen activator (tPA) is important for brain development, synapse formation and memory. Aberrations in helix F and β-sheet A movement during inhibition can directly lead to epilepsy or dementia. Conserved W154 residue in a hydrophobic patch between helix F and β-sheet A is ideally placed to control their movement during inhibition. Molecular Dynamics (MD) simulation on wild type (WT) NS and its two variants (W154A and W154P) demonstrated partial deformation in helix F and conformational differences in strands 1A and 2A only in W154P. A fluorescence and Circular Dichroism (CD) analysis with purified W154 variants revealed a significant red-shift and an increase in α-helical content in W154P as compared to W154A and WT NS. Kinetics of tPA inhibition showed a decline in association rates (ka) for W154A as compared to WT NS with indication of complex formation. Appearance of cleaved without complex formation in W154P indicates that the variant acts as substrate due to conformational misfolding around helix F. Both the variants however showed increased rate of aggregation as compared to WT NS. The hydrophobic patch identified in this study may have importance in helix F dynamics of NS.
Collapse
Affiliation(s)
- Mohammad Farhan Ali
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi-110025, India
| | - Abhinav Kaushik
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Charu Kapil
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi-110025, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Mohamad Aman Jairajpuri
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi-110025, India
| |
Collapse
|
17
|
Aneja B, Irfan M, Kapil C, Jairajpuri MA, Maguire R, Kavanagh K, Rizvi MMA, Manzoor N, Azam A, Abid M. Effect of novel triazole-amino acid hybrids on growth and virulence of Candida species: in vitro and in vivo studies. Org Biomol Chem 2016; 14:10599-10619. [PMID: 27735963 DOI: 10.1039/c6ob01718e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The increasing incidence of human candidiasis and the tendency of Candida species to become resistant to existing chemotherapies are well-recognized health problems. The present study demonstrates the successful synthesis of novel triazole-amino acid hybrids with potent in vitro and in vivo inhibitory activity against Candida species. Particularly, compounds 68 and 70 showed potent in vitro activity against fluconazole (FLC) resistant as well as sensitive clinical isolates of Candida albicans. Time kill curve analysis of lead inhibitors 68 and 70 showed their fungistatic nature. Secretion of hydrolytic enzymes, mainly proteinases and phospholipases, decreased considerably in the presence of 68 and 70 indicating their interference in fungal virulence. TEM analysis of Candida cells exposed to compounds 68 and 70 clearly showed morphological changes and intracellular damage as their possible mode of action. A preliminary mechanistic study carried out on the two most effective inhibitors (68 and 70) revealed the inhibition of ergosterol biosynthesis thereby causing the cells to lose their integrity and viability. The selected compounds did not show significant cytotoxicity up to a concentration of 200 μg mL-1 in the HEK293 cell line. An in silico analysis of 68 and 70 binding to a modeled C. albicans CYP51 showed critical H-bonding as well as hydrophobic interactions with the important active site residues indicating the basis of their anti-Candida role. Studies on the larvae of Galleria mellonella showed that the selected inhibitors (68 and 70) were non-toxic, did not provoke an immune response and significantly reduced Candida proliferation in vivo.
Collapse
Affiliation(s)
- Babita Aneja
- Medicinal Chemistry Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), Jamia Nagar, New Delhi 110025, India.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Bhakuni T, Sharma A, Ali MF, Mahapatra M, Saxena R, Jairajpuri MA. Identification of 2 Novel Polymorphisms and rs3138521 in 5′ Untranslated Region of SERPINC1 Gene in North Indian Population With Deep Vein Thrombosis. Clin Appl Thromb Hemost 2016; 23:865-870. [DOI: 10.1177/1076029616652725] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Antithrombin III (AT) is the most important endogenous anticoagulant, and genetic variability in SERPINC1, gene encoding AT, is low. Mutations leading to AT deficiency and increased thrombotic risk are well known; however, only 2 studies have reported mutations in regulatory region of SERPINC1 gene till date. Aim of the present study was to identify genetic variations in SERPINC1 5′ untranslated region (UTR) in Indian patients with deep vein thrombosis (DVT) having AT deficiency. DNA sequencing was used to identify underlying genetic defects in SERPINC1 regulatory region. In silico tools TFBIND and PROMO were used to identify transcription factor binding sites in the promoter region. We have identified 2 novel polymorphisms, g.25G>A and g.−1A>T, and 2 known g.67G>A and rs3138521 5′ UTR polymorphisms in SERPINC1 regulatory region in Indian patients with DVT for the first time. In present study, allele frequencies of rs3138521 (S: 0.37 and F: 0.63) were similar to that reported in Western population and were not associated with low plasma AT levels ( P value .5). This is the first report of regulatory region polymorphisms in SERPINC1 gene in Indian population. Our results strongly suggest that similar studies should be included when ever no mutation is detected in protein-coding region of AT gene.
Collapse
Affiliation(s)
- Teena Bhakuni
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Amit Sharma
- Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
| | - Mohammad Farhan Ali
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Manoranjan Mahapatra
- Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
| | - Renu Saxena
- Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
| | - Mohamad Aman Jairajpuri
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| |
Collapse
|
19
|
Gupta P, Jairajpuri MA, Durani S. Correction: Redox Specificity of 2-Hydroxyacid-Coupled NAD+/NADH Dehydrogenases: A Study Exploiting "Reactive" Arginine as a Reporter of Protein Electrostatics. PLoS One 2016; 11:e0154163. [PMID: 27088861 PMCID: PMC4835086 DOI: 10.1371/journal.pone.0154163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
|
20
|
Azhar A, Khan MS, Swaminathan A, Naseem A, Chatterjee S, Jairajpuri MA. Oxidized antithrombin is a dual inhibitor of coagulation and angiogenesis: Importance of low heparin affinity. Int J Biol Macromol 2016; 82:541-50. [DOI: 10.1016/j.ijbiomac.2015.10.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/01/2015] [Accepted: 10/05/2015] [Indexed: 01/09/2023]
|
21
|
Abstract
This article provides a comprehensive review of inhibitors from natural, semisynthetic or synthetic sources against key targets ofPlasmodium falciparum.
Collapse
Affiliation(s)
- Babita Aneja
- Medicinal Chemistry Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| | - Bhumika Kumar
- Medicinal Chemistry Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| | - Mohamad Aman Jairajpuri
- Protein Conformation and Enzymology Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| | - Mohammad Abid
- Medicinal Chemistry Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| |
Collapse
|
22
|
Sharma A, Bhakuni T, Biswas A, Ranjan R, Kumar R, Kishore K, Mahapatra M, Jairajpuri MA, Saxena R. Prevalence of Factor V Genetic Variants Associated With Indian APCR Contributing to Thrombotic Risk. Clin Appl Thromb Hemost 2015; 23:596-600. [PMID: 26699866 DOI: 10.1177/1076029615623376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Phenotypic resistance to activated protein C (APC) is a complex mechanism associated with increased thrombosis risk. Activated protein C resistance (APCR) is mainly influenced by FVLeiden mutation, and various other single nucleotide polymorphisms (SNPs) in FV gene are known to be associated with APCR. The aim of present study was to investigate the incidence and assess possible mechanisms of APCR in Indian patients with deep vein thrombosis (DVT). Three hundred and ten Doppler-proven patients with DVT were screened for APCR, and 50 APCR positive patients and 50 controls were typed for FVLeiden, Hong Kong, Cambridge, HR2 haplotype, Glu666Asp, Ala485Lys, and Liverpool using either polymerase chain reaction (PCR)-restriction fragment length polymorphism or allele specific PCR. FVLeiden was commonest cause of APCR (50%) in Indian patients with DVT being statistically significant ( P = .001) compared to controls. FV Liverpool, FV Glu666Asp and FV Ala485Lys were studied for the first time in Indian population. FV Liverpool, FV Glu666Asp, Hong Kong, and Cambridge were found to be absent. High frequency of Ala485Lys in patients shows that it might be a risk factor contributing to APCR in Indian patients with DVT. HR2 haplotype was not associated with APCR; however, presence of homozygous HR2 haplotype in patients only indicates the role it might play in Indian APCR population. In conclusion, contribution of FVLeiden causing APCR in Indian population is not as strong as previously reported in Western countries. The presence of other SNPs observed in the present study requires such studies on larger sample size to understand the molecular basis of defect.
Collapse
Affiliation(s)
- Amit Sharma
- 1 Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
| | - Teena Bhakuni
- 2 Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Arijit Biswas
- 3 Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany
| | - Ravi Ranjan
- 1 Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
| | - Ravi Kumar
- 1 Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
| | - Kamal Kishore
- 1 Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
| | - Manoranjan Mahapatra
- 1 Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
| | - Mohamad Aman Jairajpuri
- 2 Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Renu Saxena
- 1 Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
23
|
Bhakuni T, Sharma A, Rashid Q, Kapil C, Saxena R, Mahapatra M, Jairajpuri MA. Antithrombin III deficiency in Indian patients with deep vein thrombosis: identification of first India based AT variants including a novel point mutation (T280A) that leads to aggregation. PLoS One 2015; 10:e0121889. [PMID: 25811371 PMCID: PMC4374914 DOI: 10.1371/journal.pone.0121889] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/04/2015] [Indexed: 12/13/2022] Open
Abstract
Antithrombin III (AT) is the main inhibitor of blood coagulation proteases like thrombin and factor Xa. In this study we report the identification and characterization of several variants of AT for the first time in Indian population. We screened 1950 deep vein thrombosis (DVT) patients for AT activity and antigen levels. DNA sequencing was further carried out in patients with low AT activity and/or antigen levels to identify variations in the AT gene. Two families, one with type I and the other with type II AT deficiency were identified. Three members of family I showed an increase in the coagulation rates and recurrent thrombosis in this family was solely attributed to the rs2227589 polymorphism. Four members of family II spanning two generations had normal antigen levels and decreased AT activity. A novel single nucleotide insertion, g.13362_13363insA in this family in addition to g.2603T>C (p.R47C) mutation were identified. AT purified from patient’s plasma on hi-trap heparin column showed a marked decrease in heparin affinity and thrombin inhibition rates. Western blot analysis showed the presence of aggregated AT. We also report a novel point mutation at position g.7549 A>G (p.T280A), that is highly conserved in serpin family. Variant protein isolated from patient plasma indicated loss of regulatory function due to in-vivo polymerization. In conclusion this is the first report of AT mutations in SERPINC1 gene in Indo-Aryan population where a novel point mutation p.T280A and a novel single nucleotide insertion g.13362_13363insA are reported in addition to known variants like p.R47C, p.C4-X and polymorphisms of rs2227598, PstI and DdeI.
Collapse
Affiliation(s)
- Teena Bhakuni
- Protein Conformation and Enzymology lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Amit Sharma
- Department of Haematology, All India Institute of Medical Sciences, New Delhi, India
| | - Qudsia Rashid
- Protein Conformation and Enzymology lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Charu Kapil
- Protein Conformation and Enzymology lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Renu Saxena
- Department of Haematology, All India Institute of Medical Sciences, New Delhi, India
| | - Manoranjan Mahapatra
- Department of Haematology, All India Institute of Medical Sciences, New Delhi, India
| | - Mohamad Aman Jairajpuri
- Protein Conformation and Enzymology lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| |
Collapse
|
24
|
Singh P, Jairajpuri MA. Structure function analysis of serpin super-family: "a computational approach". Protein Pept Lett 2015; 21:714-21. [PMID: 23855665 DOI: 10.2174/09298665113209990060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 12/20/2012] [Accepted: 01/01/2013] [Indexed: 11/22/2022]
Abstract
Serine Protease inhibitors (serpins) are a super-family of proteins that controls the proteinases involved in the inflammation, complementation, coagulation and fibrinolytic pathways. Serpins are prone to conformational diseases due to a complex inhibition mechanism that involves large scale conformational change, and their susceptibility to undergo point mutations might lead to functional defects. Serpins are associated with diseases like emphysema/cirrhosis, angioedema, familial dementia, chronic obstructive bronchitis and thrombosis. Serpin polymerization based pathologies are fairly widespread and devising a cure has been difficult due to lack of clarity regarding its mechanism. Serpin can exist in various conformational states and has a variable cofactor binding ability. It has a large genome and proteome database which can be utilized to gain critical insight into their structure, mechanism and defects. Comprehensive computational studies on the serpin family is lacking, most of the work done till date is limited and deals mostly with few individual serpins. We have tried to analyze few aspect of this family using diverse computational biology tools and have shown the following: a) the importance of residue burial linked shift in the conformational stability as a major factor in increasing the polymer propensity in serpins. b) Amino acids involved in the polymerization are in general completely buried in the native conformation. c) An isozyme specific antithrombin study showed the structural basis of improved heparin binding to beta antithrombin as compared to alpha-antithrombin. d) A comprehensive cavity analysis showed its importance in inhibition and polymerizaiton and finally e) an interface analysis of various serpin protease complexes identified critical evolutionary conserved residues in exosite that determines its protease specificity. This work introduces the problem and emphasizes on the need for in-depth computational studies of serpin superfamily.
Collapse
Affiliation(s)
| | - Mohamad Aman Jairajpuri
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia University, Jamia Nagar, New-Delhi 110025, India.
| |
Collapse
|
25
|
Masood MM, Pillalamarri VK, Irfan M, Aneja B, Jairajpuri MA, Zafaryab M, Rizvi MMA, Yadava U, Addlagatta A, Abid M. Diketo acids and their amino acid/dipeptidic analogues as promising scaffolds for the development of bacterial methionine aminopeptidase inhibitors. RSC Adv 2015. [DOI: 10.1039/c5ra03354c] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Diketo acids and their peptidic analogues were designed and synthesised as bacterial MetAP inhibitors. In the enzymatic assay, the representative compound 5e showed excellent inhibition of bacterial MetAPs with no cytotoxicity.
Collapse
|
26
|
Rashid Q, Kapil C, Singh P, Kumari V, Jairajpuri MA. Understanding the specificity of serpin-protease complexes through interface analysis. J Biomol Struct Dyn 2014; 33:1352-62. [PMID: 25052369 DOI: 10.1080/07391102.2014.947525] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Serpins such as antithrombin, heparin cofactor II, plasminogen activator inhibitor, antitrypsin, antichymotrypsin, and neuroserpin are involved in important biological processes by inhibiting specific serine proteases. Initially, the protease recognizes the mobile reactive loop of the serpin eliciting conformational changes, where the cleaved loop together with the protease inserts into β-sheet A, translocating the protease to the opposite side of inhibitor leading to its inactivation. Serpin interaction with proteases is governed mainly by the reactive center loop residues (RCL). However, in some inhibitory serpins, exosite residues apart from RCL have been shown to confer protease specificity. Further, this forms the basis of multi-specificity of some serpins, but the residues and their dimension at interface in serpin-protease complexes remain elusive. Here, we present a comprehensive structural analysis of the serpin-protease interfaces using bio COmplexes COntact MAPS (COCOMAPS), PRotein Interface Conservation and Energetics (PRICE), and ProFace programs. We have carried out interface, burial, and evolutionary analysis of different serpin-protease complexes. Among the studied complexes, non-inhibitory serpins exhibit larger interface region with greater number of residue involvement as compared to the inhibitory serpins. On comparing the multi-specific serpins (antithrombin and antitrypsin), a difference in the interface area and residue number was observed, suggestive of a differential mechanism of action of these serpins in regulating their different target proteases. Further, detailed study of these multi-specific serpins listed few essential residues (common in all the complexes) and certain specificity (unique to each complex) determining residues at their interfaces. Structural mapping of interface residues suggested that individual patches with evolutionary conserved residues in specific serpins determine their specificity towards a particular protease.
Collapse
Affiliation(s)
- Qudsia Rashid
- a Protein Conformation and Enzymology Lab, Department of Biosciences , Jamia Millia Islamia (A Central University) , New Delhi 110025 , India
| | | | | | | | | |
Collapse
|
27
|
Rashid Q, Abid M, Jairajpuri MA. Elucidating the specificity of non-heparin-based conformational activators of antithrombin for factor Xa inhibition. J Nat Sci Biol Med 2014; 5:36-42. [PMID: 24678194 PMCID: PMC3961949 DOI: 10.4103/0976-9668.127282] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [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] [Indexed: 11/20/2022] Open
Abstract
Introduction: Antithrombin, the principal inhibitor of coagulation proteases, requires allosteric activation by its physiological cofactor, heparin or heparin sulfate to achieve physiologically permissible rates. This forms the basis of heparin's use as a clinical anticoagulant. However, heparin therapy is beset with severe complications, giving rise to the need to search new non-heparin activators of antithrombin, devoid of these complications and with favorable safety profiles. Materials and Methods: We chose some representative organic compounds that have been shown to be involved in coagulation modulation by affecting antithrombin and applied a blind docking protocol to find the binding energy and interactions of the modified (sulfated) versus unmodified organic scaffolds. Results and Conclusion: Increased sulfation plays a key role in shifting the specificity of organic compounds like quercetin, diosmin, rutin, mangiferin, isomangostin, Trapezifolixanthone and benzofuran towards the heparin binding site (HBS). However, in hesperetin and tetrahydroisoquinoline, sulfation shifts the specificity away from HBS. We have further tried to elucidate changes in the binding affinity of quercetin on account of gradual increase in the number of hydroxyl groups being substituted by sulfate groups. The results show gradual increase in binding energy with increase in sulfation. A theoretical screening approach is an ideal mechanism to predict lead molecules as activators of antithrombin and in determining the specificity for antithrombin.
Collapse
Affiliation(s)
- Qudsia Rashid
- Department of Bio-Sciences, Protein Conformation and Enzymology Lab, New Delhi, India
| | - Mohammad Abid
- Department of Organic Synthesis Lab, Jamia Millia Islamia, New Delhi, India
| | | |
Collapse
|
28
|
Gupta P, Jairajpuri MA, Durani S. Redox specificity of 2-hydroxyacid-coupled NAD(+)/NADH dehydrogenases: a study exploiting "reactive" arginine as a reporter of protein electrostatics. PLoS One 2013; 8:e83505. [PMID: 24391777 PMCID: PMC3877072 DOI: 10.1371/journal.pone.0083505] [Citation(s) in RCA: 1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 11/03/2013] [Indexed: 11/19/2022] Open
Abstract
With "reactive" arginine as a kinetic reporter, 2-hydroxyacid dehydrogenases are assessed in basis of their specialization as NAD(+)-reducing or NADH-oxidizing enzymes. Specifically, M4 and H4 lactate dehydrogenases (LDHs) and cytoplasmic and mitochondrial malate dehydrogenases (MDHs) are compared to assess if their coenzyme specificity may involve electrostatics of cationic or neutral nicotinamide structure as the basis. The enzymes from diverse eukaryote and prokaryote sources thus are assessed in "reactivity" of functionally-critical arginine as a function of salt concentration and pH. Electrostatic calculations were performed on "reactive" arginines and found good correspondence with experiment. The reductive and oxidative LDHs and MDHs are assessed in their count over ionizable residues and in placement details of the residues in their structures as proteins. The variants found to be high or low in ΔpKa of "reactive" arginine are found to be also strong or weak cations that preferentially oxidize NADH (neutral nicotinamide structure) or reduce NAD(+) (cationic nicotinamide structure). The ionized groups of protein structure may thus be important to redox specificity of the enzyme on basis of electrostatic preference for the oxidized (cationic nicotinamide) or reduced (neutral nicotinamide) coenzyme. Detailed comparisons of isozymes establish that the residues contributing in their redox specificity are scrambled in structure of the reductive enzyme.
Collapse
Affiliation(s)
- Pooja Gupta
- Department of Chemistry, Indian Institute of Biotechnology Bombay, Mumbai, India
| | - Mohamad Aman Jairajpuri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Biotechnology Bombay, Mumbai, India
| |
Collapse
|
29
|
Kapil C, Hussain T, Jairajpuri MA, Yogavel M, Chatterjee S, Sharma A. Systematic analysis of proteomes with emphasis on insertions in malaria parasite Plasmodium falciparum. Protein Pept Lett 2013; 20:1088-97. [PMID: 23688187 DOI: 10.2174/0929866511320100002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 05/13/2013] [Accepted: 05/13/2013] [Indexed: 11/22/2022]
Abstract
Protein insertion sequences and their biological role in many organisms have been largely unknown. Here we study proteomes of 12 organisms of diverse genomes for insertion length and amino acid preferences. A total of 871 common proteins were catalogued amongst the 12 organisms for structure based sequence alignment. This underscores the key observations: (i) AT-richness seems to have no implication on the average protein length in an organism as only Dictyostelium discoideum and Plasmodium falciparum encode proteins of high average length (ii) all studied organisms possess insertion in their proteins, however > 40 residue length insertions and unique insertions were abundant in pathogen proteomes of Plasmodium falciparum followed by Toxoplasma gondii and Leishmania major, suggesting accessory structural and functional features that may favour evolutionary fitness. (iii) Glu and Asp residues are over-represented in most proteomes irrespective of AT/GC compositions or pathogenecity with an exception of Plasmodium falciparum where Asn dominates (iv) Abundance of Asn residues in Plasmodium falciparum is exceptional given that this feature is not common to other AT-rich genomes. In conclusion, this bioinformatics based study provides comprehensive knowledge of insertions and residue's preference among pathogen proteins, which can be exploited for further inhibitor studies.
Collapse
Affiliation(s)
- Charu Kapil
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India.
| | | | | | | | | | | |
Collapse
|
30
|
Azhar A, Singh P, Rashid Q, Naseem A, Khan MS, Jairajpuri MA. Antiangiogenic function of antithrombin is dependent on its conformational variation: implication for other serpins. Protein Pept Lett 2013; 20:403-411. [PMID: 23016581] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 06/02/2011] [Accepted: 06/20/2011] [Indexed: 06/01/2023]
Abstract
Endogenous angiogenesis inhibitor that specifically decreases tumor cell proliferation can be used to treat cancer since angiogenesis is required at every step of tumor progression and metastasis. Endothelial cells are the main target for the antiangiogenic therapy because they are non-transformed and easily accessible to angiogenic inhibitors. Antithrombin functions as a principal plasma protein inhibitor of blood coagulation proteinases and belongs to the family of serine protease inhibitors (serpins) which have common mechanism of inhibition. Antithrombin acquires a potent antiangiogenic activity upon conversion of the native molecule to cleaved or latent conformation. Cleaved and latent preparations of bovine and human plasma derived antithrombin inhibits capillary endothelial cell proliferation and the growth of human SK-NAS neuroblastoma and Lewis lung carcinoma tumors in mice but not the native antithrombin's. The native form of antithrombin binds with high affinity to vascular heparan sulfate proteoglycans containing a specific pentasaccharide sequence and it is this cofactor interaction that activates antithrombin to maximal rate of thrombin inhibition. Upon inhibitory complex formation with target proteinases the antithrombin undergoes stressed to relaxed transformation and lose their high affinity for pentasacchride. Low affinity relaxed conformation with reduced heparin binding like cleaved and latent are antiangiogenic but native high affinity heparin binding stressed conformation is not, indicating the critical importance of heparin affinity in antithrombin antiangiogenic function. Based on evidence of interactions of the endothelial cell growth factors bFGF (basic fibroblast growth factor) and VEGF (vascular endothelial cell growth factor) with heparin like molecule in matrix, the possibility of antiangiogenic antithrombin to interfere with endothelial cell growth and angiogenesis through heparin mediated mechanism deserves serious consideration and investigation. It is also possible that cleaved and latent conformations with reduced affinity for heparins can also induce conformational change in the antithrombin which can open an epitope on the antithrombin surface for appropriate interactions on the endothelial surface for better antiangiogenic activity. This review illustrates the potential of antithrombin and other serpin family members as endogenous antiangiogenic proteins.
Collapse
Affiliation(s)
- Asim Azhar
- Department of Biosciences, Jamia Millia Islamia University, New-Delhi, India
| | | | | | | | | | | |
Collapse
|
31
|
Azhar A, Singh P, Rashid Q, Naseem A, Sazzad Khan M, Aman Jairajpuri M. Antiangiogenic Function of Antithrombin is Dependent on its Conformational Variation: Implication for Other Serpins. Protein Pept Lett 2013. [DOI: 10.2174/0929866511320040004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
32
|
Azhar A, Singh P, Rashid Q, Naseem A, Sazzad Khan M, Aman Jairajpuri M. Antiangiogenic Function of Antithrombin is Dependent on its Conformational Variation: Implication for Other Serpins. Protein Pept Lett 2013. [DOI: 10.2174/092986613805290408] [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: 11/22/2022]
|
33
|
Rashid Q, Singh P, Abid M, Jairajpuri MA. Limitations of conventional anticoagulant therapy and the promises of non-heparin based conformational activators of antithrombin. J Thromb Thrombolysis 2012; 34:251-9. [DOI: 10.1007/s11239-012-0712-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
34
|
Singh P, Singh K, Jairajpuri MA. Energetics of Hydrogen Bond Switch, Residue Burial and Cavity Analysis Reveals Molecular Basis of Improved Heparin Binding to Antithrombin. J Biomol Struct Dyn 2011; 29:339-50. [DOI: 10.1080/07391102.2011.10507389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
35
|
Singh P, Khan MS, Naseem A, Jairajpuri MA. Analysis of surface cavity in serpin family reveals potential binding sites for chemical chaperone to reduce polymerization. J Mol Model 2011; 18:1143-51. [PMID: 21681443 DOI: 10.1007/s00894-011-1110-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 04/26/2011] [Indexed: 10/18/2022]
Abstract
Serpin constitute about 10% of blood protein and are associated with mutations that results in aberrant intermolecular linkages which leads to polymer formation. Studies with short peptides have shown promise in depolymerization of serpins however a reactive center loop based peptide also makes the serpin inactive. A chemical chaperone based approach is a better option in terms of maintaining activity and retarding polymerization but not much is known about its binding and mechanism. Specific target for chemical chaperones and its effectiveness across many serpin is not known. We did an analysis of serpin cavity using CASTp and show that cavities are distributed throughout the molecule where the largest cavities are generally present in areas of major conformational change like shutter region, helix D and helix F. An analysis of different conformational states of serpins showed that this large cavity undergoes increase in size in latent and cleaved states as compared to native state. We targeted serpins with a variety of carbohydrate, methylamine and amino acid based chemical chaperones and selected those that have highest binding energy across different serpins to assess their ability to bind large cavities. The results show that carbohydrate based chemical chaperone like sorbitol, sucrose, arabitol and trehalose and amino acid based chaperones like dopamine, phenylalanine, arginine and glutamic acid are the most effective in binding serpins. Most of these chemical chaperone interacted with residues in the shutter region and the helix D arm at the C-terminal which are part of the largest cavities. We selected the carbohydrate based chemical chaperone with best binding energies and did experimental study under the condition that induce polymerization and show that indeed they were able to retard polymer formation with moderate effect on inhibition rates. However a fluorometric study with native antithrombin showed that chemical chaperone may effect the conformation of the proteins. Our study shows that chemical chaperones have the best binding affinities for the cavities around shutter region and helix D and that a cavity targeting based approach seems to be a better option for retarding polymerization in serpins, but a thorough analysis of its effect on folding, inhibition and cofactor binding is required.
Collapse
Affiliation(s)
- Poonam Singh
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia University, New-Delhi 110025, India
| | | | | | | |
Collapse
|
36
|
Khan MS, Singh P, Azhar A, Naseem A, Rashid Q, Kabir MA, Jairajpuri MA. Serpin Inhibition Mechanism: A Delicate Balance between Native Metastable State and Polymerization. J Amino Acids 2011; 2011:606797. [PMID: 22312466 PMCID: PMC3268027 DOI: 10.4061/2011/606797] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 03/07/2011] [Indexed: 12/02/2022]
Abstract
The serpins (serine proteinase inhibitors) are structurally similar but functionally diverse proteins that fold into a conserved structure and employ a unique suicide substrate-like inhibitory mechanism. Serpins play absolutely critical role in the control of proteases involved in the inflammatory, complement, coagulation and fibrinolytic pathways and are associated with many conformational diseases. Serpin's native state is a metastable state which transforms to a more stable state during its inhibitory mechanism. Serpin in the native form is in the stressed (S) conformation that undergoes a transition to a relaxed (R) conformation for the protease inhibition. During this transition the region called as reactive center loop which interacts with target proteases, inserts itself into the center of β-sheet A to form an extra strand. Serpin is delicately balanced to perform its function with many critical residues involved in maintaining metastability. However due to its typical mechanism of inhibition, naturally occurring serpin variants produces conformational instability that allows insertion of RCL of one molecule into the β-sheet A of another to form a loop-sheet linkage leading to its polymerization and aggregation. Thus understanding the molecular basis and amino acid involved in serpin polymerization mechanism is critical to devising strategies for its cure.
Collapse
Affiliation(s)
- Mohammad Sazzad Khan
- Department of Biosciences, Jamia Millia Islamia University, Jamia Nagar, New Delhi 110025, India
| | | | | | | | | | | | | |
Collapse
|
37
|
Singh P, Jairajpuri MA. Strand 6B deformation and residues exposure towards N-terminal end of helix B during proteinase inhibition by Serpins. Bioinformation 2011; 5:315-9. [PMID: 21383917 PMCID: PMC3046034 DOI: 10.6026/97320630005315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [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: 09/13/2010] [Accepted: 10/26/2010] [Indexed: 11/30/2022] Open
Abstract
Serine Protease inhibitors (Serpins) like antithrombin, antitrypsin, neuroserpin, antichymotrypsin, protein C-inhibitor and plasminogen activator inhibitor
is involved in important biological functions like blood coagulation, fibrinolysis, inflammation, cell migration and complement activation. Serpins native
state is metastable, which undergoes transformation to a more stable state during the process of protease inhibition. Serpins are prone to conformation
defects, however little is known about the factors and mechanisms which promote its conformational change and misfolding. Helix B region in serpins is
with several point mutations which result in pathological conditions due to polymerization. Helix B analysis for residue burial and cavity was undertaken
to understand its role in serpin structure function. A structural overlap and an accessible surface area analysis showed the deformation of strand 6B and
exposure of helix B at N-terminal end in cleaved conformation but not in the native and latent conformation of various inhibitory serpins. A cleaved
polymer like conformation of antitrypsin also showed deformation of s6B and helix B exposure. Cavity analysis showed that helix B residues were part of
the largest cavity in most of the serpins in the native state which increase in size during the transformation to cleaved and latent states. These data for the
first time show the importance of strand 6B deformation and exposure of helix B in smooth insertion of the reactive center loop during serpin inhibition
and indicate that helix B exposure due to variants may increase its polymer propensity.
Collapse
Affiliation(s)
- Poonam Singh
- Department of Biosciences, Jamia Millia Islamia University, Jamia Nagar, New Delhi-110025, India; Mohamad Aman Jairajpuri-
| | | |
Collapse
|
38
|
Bhatt TK, Kapil C, Khan S, Jairajpuri MA, Sharma V, Santoni D, Silvestrini F, Pizzi E, Sharma A. A genomic glimpse of aminoacyl-tRNA synthetases in malaria parasite Plasmodium falciparum. BMC Genomics 2009; 10:644. [PMID: 20042123 PMCID: PMC2813244 DOI: 10.1186/1471-2164-10-644] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 12/31/2009] [Indexed: 12/14/2022] Open
Abstract
Background Plasmodium parasites are causative agents of malaria which affects >500 million people and claims ~2 million lives annually. The completion of Plasmodium genome sequencing and availability of PlasmoDB database has provided a platform for systematic study of parasite genome. Aminoacyl-tRNA synthetases (aaRSs) are pivotal enzymes for protein translation and other vital cellular processes. We report an extensive analysis of the Plasmodium falciparum genome to identify and classify aaRSs in this organism. Results Using various computational and bioinformatics tools, we have identified 37 aaRSs in P. falciparum. Our key observations are: (i) fraction of proteome dedicated to aaRSs in P. falciparum is very high compared to many other organisms; (ii) 23 out of 37 Pf-aaRS sequences contain signal peptides possibly directing them to different cellular organelles; (iii) expression profiles of Pf-aaRSs vary considerably at various life cycle stages of the parasite; (iv) several PfaaRSs posses very unusual domain architectures; (v) phylogenetic analyses reveal evolutionary relatedness of several parasite aaRSs to bacterial and plants aaRSs; (vi) three dimensional structural modelling has provided insights which could be exploited in inhibitor discovery against parasite aaRSs. Conclusion We have identified 37 Pf-aaRSs based on our bioinformatics analysis. Our data reveal several unique attributes in this protein family. We have annotated all 37 Pf-aaRSs based on predicted localization, phylogenetics, domain architectures and their overall protein expression profiles. The sets of distinct features elaborated in this work will provide a platform for experimental dissection of this family of enzymes, possibly for the discovery of novel drugs against malaria.
Collapse
Affiliation(s)
- Tarun Kumar Bhatt
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Cruz RGCD, Jairajpuri MA, Bock SC. Disruption of a Tight Cluster Surrounding Tyrosine 131 in the Native Conformation of Antithrombin III Activates It for Factor Xa Inhibition. J Biol Chem 2006. [DOI: 10.1016/s0021-9258(19)84080-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
40
|
dela Cruz RGC, Jairajpuri MA, Bock SC. Disruption of a tight cluster surrounding tyrosine 131 in the native conformation of antithrombin III activates it for factor Xa inhibition. J Biol Chem 2006; 281:31668-76. [PMID: 16940049 DOI: 10.1074/jbc.m604826200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [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: 11/06/2022] Open
Abstract
The native conformation of antithrombin III (ATIII) is a poor inhibitor of its coagulation pathway target enzymes because of the partial insertion of its reactive center loop (RCL) in its central A beta-sheet. This study focused on tyrosine 131, which is located at the helix D-sheet A interface, adjacent to the ATIII pentasaccharide and heparin cofactor-binding sites and some 17A away from the RCL insertion. Crystallographic structures show that the Tyr(131) ring is buried in native ATIII and then becomes exposed when pentasaccharide binds to the inhibitor and activates it. This change suggested that Tyr(131) might serve as a switch for ATIII conformational activation. The hypothesis is supported by results from this study, which progressively removed atoms from the Tyr(131) side chain. Rates of heparin-independent Y131L and Y131A factor Xa inhibition were 25 and 29 times faster than for the control and Y131F, suggesting that Tyr(131) ring interactions with neighboring helix D and strand 2A residues shift the uncatalyzed native-to-activated conformational equilibrium toward the RCL-inserted state. Thermal denaturation experiments showed Y131A and Y131L were less stable than the control and Y131F, implying an increased tendency toward A-sheet mobility in these genetically activated molecules. Thus, the tight Tyr(131)-Asn(127)-Leu(130)-Leu(140)-Ser(142) cluster at the helix D-strand 2A interface of native antithrombin contributes significantly to the stability of the ground state conformation, and tyrosine 131 serves as a heparin-responsive molecular switch during the allosteric activation of ATIII anticoagulant activity.
Collapse
|
41
|
Jairajpuri MA, Lu A, Desai U, Olson ST, Bjork I, Bock SC. Antithrombin III phenylalanines 122 and 121 contribute to its high affinity for heparin and its conformational activation. J Biol Chem 2003; 278:15941-50. [PMID: 12556442 DOI: 10.1074/jbc.m212319200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [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: 12/23/2022] Open
Abstract
The dissociation equilibrium constant for heparin binding to antithrombin III (ATIII) is a measure of the cofactor's binding to and activation of the proteinase inhibitor, and its salt dependence indicates that ionic and non-ionic interactions contribute approximately 40 and approximately 60% of the binding free energy, respectively. We now report that phenylalanines 121 and 122 (Phe-121 and Phe-122) together contribute 43% of the total binding free energy and 77% of the energy of non-ionic binding interactions. The large contribution of these hydrophobic residues to the binding energy is mediated not by direct interactions with heparin, but indirectly, through contacts between their phenyl rings and the non-polar stems of positively charged heparin binding residues, whose terminal amino and guanidinium groups are thereby organized to form extensive and specific ionic and non-ionic contacts with the pentasaccharide. Investigation of the kinetics of heparin binding demonstrated that Phe-122 is critical for promoting a normal rate of conformational change and stabilizing AT*H, the high affinity-activated binary complex. Kinetic and structural considerations suggest that Phe-122 and Lys-114 act cooperatively through non-ionic interactions to promote P-helix formation and ATIII binding to the pentasaccharide. In summary, although hydrophobic residues Phe-122 and Phe-121 make minimal contact with the pentasaccharide, they play a critical role in heparin binding and activation of antithrombin by coordinating the P-helix-mediated conformational change and organizing an extensive network of ionic and non-ionic interactions between positively charged heparin binding site residues and the cofactor.
Collapse
Affiliation(s)
- Mohamad Aman Jairajpuri
- Departments of Medicine and Bioengineering, Health Science Center, University of Utah, 50 N. Medical Drive, Salt Lake City, UT 84132, USA
| | | | | | | | | | | |
Collapse
|
42
|
Jairajpuri MA, Lu A, Bock SC. Elimination of P1 arginine 393 interaction with underlying glutamic acid 255 partially activates antithrombin III for thrombin inhibition but not factor Xa inhibition. J Biol Chem 2002; 277:24460-5. [PMID: 11971909 DOI: 10.1074/jbc.m203127200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [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: 11/06/2022] Open
Abstract
The mechanism for heparin activation of antithrombin III has been postulated to involve disruption of interactions between its reactive loop P1 residue and Glu(255) on the underlying protein surface. To test this hypothesis, the potential P1-constraining Arg(393)-Glu(255) hydrogen bond and ionic interactions were eliminated by converting Glu(255) to alanine. E255A and wild-type ATIIIs have identical reactive loop sequences (including the P1 and P14 residues), but differ in that Glu(255)-mediated, P1-constraining interactions with the underlying surface cannot form in the mutant. Relative to its wild-type parent, E255A had a 5-fold higher affinity for heparin and pentasaccharide. In the absence of cofactor, E255A exhibited a 5-fold activation of thrombin inhibition but no activation of factor Xa inhibition. Pentasaccharide addition elicited no further activation of thrombin inhibition but increased the factor Xa inhibition rate 100-fold. E255A heparin-dependent thrombin and factor Xa inhibition rates were 1000- and 2-fold faster, respectively, than pentasaccharide-catalyzed rates. Although "approximation" is the predominant factor in heparin activation of ATIII thrombin inhibition, and removal of the P1 constraint plays a distinct but minor role, the primary determinant for activation of factor Xa inhibition is the pentasaccharide-induced conformational change, with approximation making a further minor contribution, and removal of the P1 constraint playing no role at all.
Collapse
|
43
|
Jairajpuri MA, Azam N, Baburaj K, Bulliraju E, Durani S. Charge and solvation effects in anion recognition centers: an inquiry exploiting reactive arginines. Biochemistry 1998; 37:10780-91. [PMID: 9692968 DOI: 10.1021/bi980058e] [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: 02/08/2023]
Abstract
Following a long-standing suggestion of Riordan et al. [Riordan, J. F., McElvany, K. D., and Borders, C. L., Jr. (1977) Science 195, 884-885], we sought to exploit chemically activated arginines as probes to characterize the microenvironmental effects in enzymes that mediate the recognition of anionic substrates. A micellar simulation study establishes that octylguanidine (OGn) becomes chemically activated upon incorporation into both cetyltrimethylammonium bromide (CTAB) and Triton X-100 micelles and that the activations correlate with the pKa diminutions induced in its guanidinium group by the effects of electrostatic or nonelectrostatic nature as reflected in the results of pH and salt titration experiments. Next, a protein modification study establishes that the modifiable arginines in a number of enzymes also have diminished pKa's, again due to effects of electrostatic or nonelectrostatic nature as reflected in the results of pH and salt titration experiments. Warwicker's finite difference Poisson--Boltzmann algorithm [Warwicker, J. (1992) J. Mol. Biol. 223, 247-257] is applied to several of the enzymes with available crystal structure coordinates, and indeed, their chemically activated arginines are found to be in an electrostatic microenvironment that can diminish their pKa's, with the magnitudes of these diminutions matching closely the diminutions measured experimentally. Finally, the chemically activated arginines are examined with respect to their atomic atmosphere and are thus found to occur in a local microenvironment that would facilitate their roles as anion anchors. Thus, electrostatic and solvation effects are found to be critical determinants of the arginine role as an anion anchor.
Collapse
Affiliation(s)
- M A Jairajpuri
- Biotechnology Center, Indian Institute of Technology Bombay, Mumbai, India
| | | | | | | | | |
Collapse
|