1
|
Serrano C, Teixeira CSS, Cooper DN, Carneiro J, Lopes-Marques M, Stenson PD, Amorim A, Prata MJ, Sousa SF, Azevedo L. Compensatory epistasis explored by molecular dynamics simulations. Hum Genet 2021; 140:1329-1342. [PMID: 34173867 DOI: 10.1007/s00439-021-02307-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/20/2021] [Indexed: 11/24/2022]
Abstract
A non-negligible proportion of human pathogenic variants are known to be present as wild type in at least some non-human mammalian species. The standard explanation for this finding is that molecular mechanisms of compensatory epistasis can alleviate the mutations' otherwise pathogenic effects. Examples of compensated variants have been described in the literature but the interacting residue(s) postulated to play a compensatory role have rarely been ascertained. In this study, the examination of five human X-chromosomally encoded proteins (FIX, GLA, HPRT1, NDP and OTC) allowed us to identify several candidate compensated variants. Strong evidence for a compensated/compensatory pair of amino acids in the coagulation FIXa protein (involving residues 270 and 271) was found in a variety of mammalian species. Both amino acid residues are located within the 60-loop, spatially close to the 39-loop that performs a key role in coagulation serine proteases. To understand the nature of the underlying interactions, molecular dynamics simulations were performed. The predicted conformational change in the 39-loop consequent to the Glu270Lys substitution (associated with hemophilia B) appears to impair the protein's interaction with its substrate but, importantly, such steric hindrance is largely mitigated in those proteins that carry the compensatory residue (Pro271) at the neighboring amino acid position.
Collapse
Affiliation(s)
- Catarina Serrano
- i3S, Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution Group, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Carla S S Teixeira
- UCIBIO/REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - João Carneiro
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
| | - Mónica Lopes-Marques
- i3S, Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution Group, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - António Amorim
- i3S, Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution Group, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Maria J Prata
- i3S, Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution Group, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Sérgio F Sousa
- UCIBIO/REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.
| | - Luísa Azevedo
- i3S, Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution Group, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre, s/n, 4169-007, Porto, Portugal.
| |
Collapse
|
2
|
Goettig P, Brandstetter H, Magdolen V. Surface loops of trypsin-like serine proteases as determinants of function. Biochimie 2019; 166:52-76. [PMID: 31505212 PMCID: PMC7615277 DOI: 10.1016/j.biochi.2019.09.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/06/2019] [Indexed: 02/07/2023]
Abstract
Trypsin and chymotrypsin-like serine proteases from family S1 (clan PA) constitute the largest protease group in humans and more generally in vertebrates. The prototypes chymotrypsin, trypsin and elastase represent simple digestive proteases in the gut, where they cleave nearly any protein. Multidomain trypsin-like proteases are key players in the tightly controlled blood coagulation and complement systems, as well as related proteases that are secreted from diverse immune cells. Some serine proteases are expressed in nearly all tissues and fluids of the human body, such as the human kallikreins and kallikrein-related peptidases with specialization for often unique substrates and accurate timing of activity. HtrA and membrane-anchored serine proteases fulfill important physiological tasks with emerging roles in cancer. The high diversity of all family members, which share the tandem β-barrel architecture of the chymotrypsin-fold in the catalytic domain, is conferred by the large differences of eight surface loops, surrounding the active site. The length of these loops alters with insertions and deletions, resulting in remarkably different three-dimensional arrangements. In addition, metal binding sites for Na+, Ca2+ and Zn2+ serve as regulatory elements, as do N-glycosylation sites. Depending on the individual tasks of the protease, the surface loops determine substrate specificity, control the turnover and allow regulation of activation, activity and degradation by other proteins, which are often serine proteases themselves. Most intriguingly, in some serine proteases, the surface loops interact as allosteric network, partially tuned by protein co-factors. Knowledge of these subtle and complicated molecular motions may allow nowadays for new and specific pharmaceutical or medical approaches.
Collapse
Affiliation(s)
- Peter Goettig
- Division of Structural Biology, Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria.
| | - Hans Brandstetter
- Division of Structural Biology, Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria
| | - Viktor Magdolen
- Clinical Research Unit, Department of Obstetrics and Gynecology, School of Medicine, Technical University of Munich, Ismaninger Strasse 22, 81675, München, Germany
| |
Collapse
|
3
|
Yang L, Rezaie AR. Characterization of Protein Z-Dependent Protease Inhibitor/Antithrombin Chimeras Provides Insight into the Serpin Specificity of Coagulation Proteases. ACS OMEGA 2017; 2:3276-3283. [PMID: 28782047 PMCID: PMC5537704 DOI: 10.1021/acsomega.7b00606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 06/28/2017] [Indexed: 06/07/2023]
Abstract
Protein Z (PZ)-dependent protease inhibitor (ZPI) and antithrombin (AT) are two physiological serpin inhibitors involved in the regulation of proteolytic activities of the blood coagulation cascade. ZPI has restricted protease specificity capable of inhibiting factors Xa (FXa) and XIa (FXIa) but exhibiting no reactivity with other coagulation proteases. Unlike ZPI, AT is a general inhibitor of all coagulation proteases and the only physiological inhibitor of factor IXa (FIXa). To understand the molecular determinants of protease specificity of the two serpins, we engineered two ZPI mutants in which the P12-P3' residues of the reactive center loop of ZPI were replaced with either P12-P3' or P12-P7' residues of AT (ZPI-ATP12-P3' and ZPI-ATP12-P7'). The reactivity of chimeras with FXa was improved ∼4-25-fold in the absence of PZ. Both chimeras inhibited FIXa with rate constants that were ∼2 orders of magnitude higher than the rate of the AT inhibition of the protease. PZ improved the reactivity of chimeras with FIXa by another 2 orders of magnitude, rendering the chimeras potent inhibitors of FIXa so that the PZ-mediated inhibitory activity of the ZPI-AT chimeras toward FIXa was ∼20-fold higher than that of the fondaparinux-catalyzed inhibition of FIXa by AT. Further studies revealed that the substitution of P1-Tyr of ZPI with an Arg is sufficient to convert the serpin to an effective inhibitor of FIXa. The potential therapeutic utility of the serpin chimeras as specific inhibitors of FIXa was diminished by findings that the chimeras function as effective substrates for other coagulation proteases.
Collapse
Affiliation(s)
- Likui Yang
- Cardiovascular
Biology Research Program, Oklahoma Medical
Research Foundation, Oklahoma
City, Oklahoma 73104, United States
| | - Alireza R. Rezaie
- Cardiovascular
Biology Research Program, Oklahoma Medical
Research Foundation, Oklahoma
City, Oklahoma 73104, United States
- Department
of Biochemistry and Molecular Biology, University
of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States
| |
Collapse
|
4
|
Qureshi SH, Lu Q, Manithody C, Yang L, Rezaie AR. Characterization of the protein Z-dependent protease inhibitor interactive-sites of protein Z. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1631-7. [PMID: 24960590 DOI: 10.1016/j.bbapap.2014.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 05/29/2014] [Accepted: 06/16/2014] [Indexed: 11/30/2022]
Abstract
BACKGROUND Protein Z (PZ) has been reported to promote the inactivation of factor Xa (FXa) by PZ-dependent protease inhibitor (ZPI) by about three orders of magnitude. Previously, we prepared a chimeric PZ in which its C-terminal pseudo-catalytic domain was grafted on FX light-chain (Gla and EGF-like domains) (PZ/FX-LC). Characterization of PZ/FX-LC revealed that the ZPI interactive-site is primarily located within PZ pseudo-catalytic domain. Nevertheless, the cofactor function and apparent Kd of PZ/FX-LC for interaction with ZPI remained impaired ~6-7-fold, suggesting that PZ contains a ZPI interactive-site outside pseudo-catalytic domain. X-ray structural data indicates that Tyr-240 of ZPI interacts with EGF2-domain of PZ. Structural data further suggests that 3 other ZPI surface loops make salt-bridge interactions with PZ pseudo-catalytic domain. To identify ZPI interactive-sites on PZ, we grafted the N-terminal EGF2 subdomain of PZ onto PZ/FX-LC chimera (PZ-EGF2/FX-LC) and also generated two compensatory charge reversal mutants of PZ pseudo-catalytic domain (Glu-244 and Arg-212) and ZPI surface loops (Lys-239 and Asp-293). METHODS PZ chimeras were expressed in mammalian cells and ZPI derivatives were expressed in Escherichia coli. RESULTS The PZ EGF2 subdomain fusion restored the defective cofactor function of PZ/FX-LC. The activities of PZ and ZPI mutants were all impaired if assayed individually, but partially restored if the compensatory charge reversal mutants were used in the assay. CONCLUSIONS PZ EGF2 subdomain constitutes an interactive-site for ZPI. Data with compensatory charge reversal mutants validates structural data that the identified residues are part of interactive-sites. GENERAL SIGNIFICANCE Insight is provided into mechanisms through which specificity of ZPI-PZ-FXa complex formation is determined.
Collapse
Affiliation(s)
- Shabir H Qureshi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA
| | - Qiuya Lu
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA
| | - Chandrashekhara Manithody
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA
| | - Likui Yang
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA
| | - Alireza R Rezaie
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA.
| |
Collapse
|