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Giulini M, Honorato RV, Rivera JL, Bonvin AMJJ. ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information. Commun Biol 2024; 7:49. [PMID: 38184711 PMCID: PMC10771469 DOI: 10.1038/s42003-023-05718-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/18/2023] [Indexed: 01/08/2024] Open
Abstract
The formation of a stable complex between proteins lies at the core of a wide variety of biological processes and has been the focus of countless experiments. The huge amount of information contained in the protein structural interactome in the Protein Data Bank can now be used to characterise and classify the existing biological interfaces. We here introduce ARCTIC-3D, a fast and user-friendly data mining and clustering software to retrieve data and rationalise the interface information associated with the protein input data. We demonstrate its use by various examples ranging from showing the increased interaction complexity of eukaryotic proteins, 20% of which on average have more than 3 different interfaces compared to only 10% for prokaryotes, to associating different functions to different interfaces. In the context of modelling biomolecular assemblies, we introduce the concept of "recognition entropy", related to the number of possible interfaces of the components of a protein-protein complex, which we demonstrate to correlate with the modelling difficulty in classical docking approaches. The identified interface clusters can also be used to generate various combinations of interface-specific restraints for integrative modelling. The ARCTIC-3D software is freely available at github.com/haddocking/arctic3d and can be accessed as a web-service at wenmr.science.uu.nl/arctic3d.
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Affiliation(s)
- Marco Giulini
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584, Utrecht, CH, The Netherlands
| | - Rodrigo V Honorato
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584, Utrecht, CH, The Netherlands
| | - Jesús L Rivera
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584, Utrecht, CH, The Netherlands
| | - Alexandre M J J Bonvin
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584, Utrecht, CH, The Netherlands.
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2
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Vulpetti A, Randl S, Rüdisser S, Ostermann N, Erbel P, Mac Sweeney A, Zoller T, Salem B, Gerhartz B, Cumin F, Hommel U, Dalvit C, Lorthiois E, Maibaum J. Structure-Based Library Design and Fragment Screening for the Identification of Reversible Complement Factor D Protease Inhibitors. J Med Chem 2017; 60:1946-1958. [PMID: 28157311 DOI: 10.1021/acs.jmedchem.6b01684] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Chronic dysregulation of alternative complement pathway activation has been associated with diverse clinical disorders including age-related macular degeneration and paroxysmal nocturnal hemoglobinurea. Factor D is a trypsin-like serine protease with a narrow specificity for arginine in the P1 position, which catalyzes the first enzymatic reaction of the amplification loop of the alternative pathway. In this article, we describe two hit finding approaches leading to the discovery of new chemical matter for this pivotal protease of the complement system: in silico active site mapping for hot spot identification to guide rational structure-based design and NMR screening of focused and diverse fragment libraries. The wealth of information gathered by these complementary approaches enabled the identification of ligands binding to different subpockets of the latent Factor D conformation and was instrumental for understanding the binding requirements for the generation of the first known potent noncovalent reversible Factor D inhibitors.
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Affiliation(s)
- Anna Vulpetti
- Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, CH-4056 Basel, Switzerland
| | - Stefan Randl
- Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, CH-4056 Basel, Switzerland
| | - Simon Rüdisser
- Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, CH-4056 Basel, Switzerland
| | - Nils Ostermann
- Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, CH-4056 Basel, Switzerland
| | - Paul Erbel
- Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, CH-4056 Basel, Switzerland
| | - Aengus Mac Sweeney
- Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, CH-4056 Basel, Switzerland
| | - Thomas Zoller
- Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, CH-4056 Basel, Switzerland
| | - Bahaa Salem
- Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, CH-4056 Basel, Switzerland
| | - Bernd Gerhartz
- Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, CH-4056 Basel, Switzerland
| | - Frederic Cumin
- Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, CH-4056 Basel, Switzerland
| | - Ulrich Hommel
- Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, CH-4056 Basel, Switzerland
| | - Claudio Dalvit
- Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, CH-4056 Basel, Switzerland
| | - Edwige Lorthiois
- Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, CH-4056 Basel, Switzerland
| | - Jürgen Maibaum
- Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, CH-4056 Basel, Switzerland
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3
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Chen YL, Li W, Liu Y, Guan Z, He YH. Trypsin-catalyzed direct asymmetric aldol reaction. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2012.10.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Shamaladevi N, Pattabhi V. Secondary Binding Site of Trypsin: Revealed by Crystal Structure of Trypsin-Peptide Complex. J Biomol Struct Dyn 2012; 22:635-42. [PMID: 15842169 DOI: 10.1080/07391102.2005.10507031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Designed synthetic heterochiral peptides, when added to porcine trypsin, resulted in reduction of enzyme activity. The crystal structure of a complex formed between porcine trypsin and a heterochiral hepta peptide Boc-Pro-DAsp-Aib-Leu-Aib-Leu-Ala-NHMe has been determined at 1.9 A resolution. The hepta peptide does not bind at the active site, but is located in the interstitial region, and interacts with the calcium-binding loop (residues 60-80). The bound peptide interacts with the active site residue Ser195 through an acetate ion, and with Lys 60 mediated by water molecules. The structure, when compared with the other trypsin-peptide complexes, suggests that the flexibility of surface loops, concerted movement of the loops towards the active site, and the interaction of the bound peptide with Lys 60, may be responsible for the reduction in enzyme activity. This study provides a structural evidence for the earlier biochemical observation regarding the role of surface loops in the catalysis of the enzyme.
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Affiliation(s)
- N Shamaladevi
- Dept. of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai-600025, India
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5
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Ben-Shem A, Fass D, Bibi E. Structural basis for intramembrane proteolysis by rhomboid serine proteases. Proc Natl Acad Sci U S A 2006; 104:462-6. [PMID: 17190827 PMCID: PMC1766407 DOI: 10.1073/pnas.0609773104] [Citation(s) in RCA: 151] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intramembrane proteases catalyze peptide bond cleavage of integral membrane protein substrates. This activity is crucial for many biological and pathological processes. Rhomboids are evolutionarily widespread intramembrane serine proteases. Here, we present the 2.3-A-resolution crystal structure of a rhomboid from Escherichia coli. The enzyme has six transmembrane helices, five of which surround a short TM4, which starts deep within the membrane at the catalytic serine residue. Thus, the catalytic serine is in an externally exposed cavity, which provides a hydrophilic environment for proteolysis. Our results reveal a mechanism to enable water-dependent catalysis at the depth of the hydrophobic milieu of the membrane and suggest how substrates gain access to the sequestered rhomboid active site.
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Affiliation(s)
- Adam Ben-Shem
- Departments of *Biological Chemistry and
- To whom correspondence may be addressed. E-mail:
or
| | - Deborah Fass
- Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eitan Bibi
- Departments of *Biological Chemistry and
- To whom correspondence may be addressed. E-mail:
or
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6
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Syed Ibrahim B, Pattabhi V. Trypsin inhibition by a peptide hormone: crystal structure of trypsin-vasopressin complex. J Mol Biol 2005; 348:1191-8. [PMID: 15854654 DOI: 10.1016/j.jmb.2005.03.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2005] [Revised: 03/07/2005] [Accepted: 03/15/2005] [Indexed: 10/25/2022]
Abstract
The large variety of serine protease inhibitors, available from various sources such as tissues, microorganisms, plants, etc., play an important role in regulating the proteolytic enzymes. The analysis of protease-inhibitor complexes helps in understanding the mechanism of action, as well as in designing inhibitors. Vasopressin, an anti-diuretic nonapeptide hormone, is found to be an effective inhibitor of trypsin, with a K(i) value of 5 nM. The crystal structure of the trypsin-vasopressin complex revealed that vasopressin fulfils all the important interactions for an inhibitor, without any break in the scissile peptide bond. The cyclic nature due to a disulfide bridge between Cys1 and Cys6 of vasopressin provides structural rigidity to the peptide hormone. The trypsin-binding site is located at the C terminus, while the neurophysin-binding site is at the N terminus of vasopressin. This study will assist in designing new peptide inhibitors. This study suggests that vasopressin inhibition of trypsin may have unexplored biological implications.
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Affiliation(s)
- B Syed Ibrahim
- Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
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Ibrahim BS, Shamaladevi N, Pattabhi V. Trypsin activity reduced by an autocatalytically produced nonapeptide. J Biomol Struct Dyn 2005; 21:737-44. [PMID: 15106996 DOI: 10.1080/07391102.2004.10506964] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Trypsin, a serine protease enzyme plays a pivotal role in digestion and is autocatalytic. The crystal structure of a complex formed between porcine trypsin and an auto catalytically produced peptide is reported here. This complex shows a reduction in enzyme activity as compared to native beta-trypsin. The nonapeptide has a lysine, which is recognized by Asp 189 at the specificity pocket. The auto catalytically produced native nonapeptide is bound at the active site cleft like other trypsin inhibitors but the important interactions with the oxyanion hole are absent. The peptide covers only a part of the active site cleft and hence the enzyme activity is reduced rather than being inhibited.
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Affiliation(s)
- B S Ibrahim
- Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Guindy, Chennai-600025, India
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Meijers R, Blagova EV, Levdikov VM, Rudenskaya GN, Chestukhina GG, Akimkina TV, Kostrov SV, Lamzin VS, Kuranova IP. The Crystal Structure of Glutamyl Endopeptidase from Bacillus intermedius Reveals a Structural Link between Zymogen Activation and Charge Compensation. Biochemistry 2004; 43:2784-91. [PMID: 15005613 DOI: 10.1021/bi035354s] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Extracellular glutamyl endopeptidase from Bacillus intermedius (BIEP) is a chymotrypsin-like serine protease which cleaves the peptide bond on the carboxyl side of glutamic acid. Its three-dimensional structure was determined for C222(1) and C2 crystal forms of BIEP to 1.5 and 1.75 A resolution, respectively. The topology of BIEP diverges from the most common chymotrypsin architecture, because one of the domains consists of a beta-sandwich consisting of two antiparallel beta-sheets and two helices. In the C2 crystals, a 2-methyl-2,4-pentanediol (MPD) molecule was found in the substrate binding site, mimicking a glutamic acid. This enabled the identification of the residues involved in the substrate recognition. The presence of the MPD molecule causes a change in the active site; the interaction between two catalytic residues (His47 and Ser171) is disrupted. The N-terminal end of the enzyme is involved in the formation of the substrate binding pocket. This indicates a direct relation between zymogen activation and substrate charge compensation.
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Affiliation(s)
- Rob Meijers
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
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Ibrahim BS, Pattabhi V. Crystal structure of trypsin–turkey egg white inhibitor complex. Biochem Biophys Res Commun 2004; 313:8-16. [PMID: 14672690 DOI: 10.1016/j.bbrc.2003.11.082] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Crystal structure of the complex between porcine beta-trypsin and the second domain of the Kazal-type ovomucoid turkey egg white trypsin inhibitor (OMTKY2) has been determined at 1.9A resolution. A peptide fragment from the first domain has been crystallized with the complex. Restrained-refinement of the structure led to an R-factor of 0.19 for the 32206 reflections. OMTKY2 exhibits the canonical Kazal-type fold with a central alpha-helix and a short two-stranded anti-parallel beta-sheet. The carbonyl carbon of the reactive site prefers trigonal geometry. The reactive site loop geometry of the inhibitor is complementary to the surface and charge of the binding site in beta-trypsin.
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Affiliation(s)
- B Syed Ibrahim
- Department of crystallography and Biophysics, University of Madras, Chennai 600 025, India
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Singh RK, Gourinath S, Sharma S, Roy I, Gupta MN, Betzel C, Srinivasan A, Singh TP. Enhancement of enzyme activity through three-phase partitioning: crystal structure of a modified serine proteinase at 1.5 A resolution. PROTEIN ENGINEERING 2001; 14:307-13. [PMID: 11438752 DOI: 10.1093/protein/14.5.307] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Three-phase partitioning is fast developing as a novel bioseparation strategy with a wide range of applications including enzyme stability and enhancement of its catalytic activity. Despite all this, the enzyme behaviour in this process still remains unknown. A serine proteinase, proteinase K, was subjected to three-phase partitioning (TPP). A 3 ml volume of proteinase K solution (3 mg/ml in 0.05 M acetate buffer, pH 6.0) was brought to 30% (w/v) ammonium sulphate saturation by addition of saturated ammonium sulphate. tert-Butanol (6 ml) was added to this solution and the mixture was incubated at 25 degrees C for 1 h. The precipitated protein in the mid-layer was dissolved in 3 ml of 0.05 M acetate buffer, pH 6.0. The specific activity of the processed enzyme was estimated and was found to be 210% of the original enzyme activity. In order to understand the basis of this remarkable enhancement of the enzyme activity, the structure of the TPP-treated enzyme was determined by X-ray diffraction at 1.5 A resolution. The overall structure of the TPP-treated enzyme is similar to the original structure in an aqueous environment. The hydrogen bonding system of the catalytic triad is intact. However, the water structure in the substrate binding site has undergone a rearrangement as some of the water molecules are either displaced or completely absent. Two acetate ions were identified in the structure. One is located in the active site and seems to mimic the role of water in the enzyme activity and stability. The other is located at the surface of the molecule and is involved in stabilizing the local structure of the enzyme. The most striking observation in respect of the present structure pertains to a relatively higher overall temperature factor (B = 19.7 A(2)) than the value of 9.3 A(2) in the original enzyme. As a result of a higher B-factor, a number of residues, particularly their side chains, were found to adopt more than one conformation. It appears that the protein exists in an excited state which might be helping the enzyme to function more rapidly than the original enzyme in aqueous media. Summarily, the basis of increased enzymatic activity could be attributed to (i) the presence of an acetate ion at the active site and (ii) its excited state as reflected by an overall higher B-factor.
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Affiliation(s)
- R K Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029
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