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De Filippis V, Acquasaliente L, Pierangelini A, Marin O. Chemical Synthesis and Structure-Activity Relationship Studies of the Coagulation Factor Xa Inhibitor Tick Anticoagulant Peptide from the Hematophagous Parasite Ornithodoros moubata. Biomimetics (Basel) 2024; 9:485. [PMID: 39194464 DOI: 10.3390/biomimetics9080485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 07/29/2024] [Accepted: 08/05/2024] [Indexed: 08/29/2024] Open
Abstract
Tick Anticoagulant Peptide (TAP), a 60-amino acid protein from the soft tick Ornithodoros moubata, inhibits activated coagulation factor X (fXa) with almost absolute specificity. Despite TAP and Bovine Pancreatic Trypsin Inhibitor (BPTI) (i.e., the prototype of the Kunitz-type protease inhibitors) sharing a similar 3D fold and disulphide bond topology, they have remarkably different amino acid sequence (only ~24% sequence identity), thermal stability, folding pathways, protease specificity, and even mechanism of protease inhibition. Here, fully active and correctly folded TAP was produced in reasonably high yields (~20%) by solid-phase peptide chemical synthesis and thoroughly characterised with respect to its chemical identity, disulphide pairing, folding kinetics, conformational dynamics, and fXa inhibition. The versatility of the chemical synthesis was exploited to perform structure-activity relationship studies on TAP by incorporating non-coded amino acids at positions 1 and 3 of the inhibitor. Using Hydrogen-Deuterium Exchange Mass Spectrometry, we found that TAP has a remarkably higher conformational flexibility compared to BPTI, and propose that these different dynamics could impact the different folding pathway and inhibition mechanisms of TAP and BPTI. Hence, the TAP/BPTI pair represents a nice example of divergent evolution, while the relative facility of TAP synthesis could represent a good starting point to design novel synthetic analogues with improved pharmacological profiles.
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Affiliation(s)
- Vincenzo De Filippis
- Laboratory of Protein Chemistry & Molecular Haematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, Via F. Marzolo 5, 35131 Padua, Italy
| | - Laura Acquasaliente
- Laboratory of Protein Chemistry & Molecular Haematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, Via F. Marzolo 5, 35131 Padua, Italy
| | - Andrea Pierangelini
- Laboratory of Protein Chemistry & Molecular Haematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, Via F. Marzolo 5, 35131 Padua, Italy
| | - Oriano Marin
- Department of Biomedical Sciences, School of Medicine, University of Padova, Via Trieste 75, 35121 Padua, Italy
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MacKenzie DWS, Schaefer A, Steckner J, Leo CA, Naser D, Artikis E, Broom A, Ko T, Shah P, Ney MQ, Tran E, Smith MTJ, Fuglestad B, Wand AJ, Brooks CL, Meiering EM. A fine balance of hydrophobic-electrostatic communication pathways in a pH-switching protein. Proc Natl Acad Sci U S A 2022; 119:e2119686119. [PMID: 35737838 PMCID: PMC9245636 DOI: 10.1073/pnas.2119686119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/29/2022] [Indexed: 12/24/2022] Open
Abstract
Allostery is the phenomenon of coupling between distal binding sites in a protein. Such coupling is at the crux of protein function and regulation in a myriad of scenarios, yet determining the molecular mechanisms of coupling networks in proteins remains a major challenge. Here, we report mechanisms governing pH-dependent myristoyl switching in monomeric hisactophilin, whereby the myristoyl moves between a sequestered state, i.e., buried within the core of the protein, to an accessible state, in which the myristoyl has increased accessibility for membrane binding. Measurements of the pH and temperature dependence of amide chemical shifts reveal protein local structural stability and conformational heterogeneity that accompany switching. An analysis of these measurements using a thermodynamic cycle framework shows that myristoyl-proton coupling at the single-residue level exists in a fine balance and extends throughout the protein. Strikingly, small changes in the stereochemistry or size of core and surface hydrophobic residues by point mutations readily break, restore, or tune myristoyl switch energetics. Synthesizing the experimental results with those of molecular dynamics simulations illuminates atomistic details of coupling throughout the protein, featuring a large network of hydrophobic interactions that work in concert with key electrostatic interactions. The simulations were critical for discerning which of the many ionizable residues in hisactophilin are important for switching and identifying the contributions of nonnative interactions in switching. The strategy of using temperature-dependent NMR presented here offers a powerful, widely applicable way to elucidate the molecular mechanisms of allostery in proteins at high resolution.
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Affiliation(s)
| | - Anna Schaefer
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Julia Steckner
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Christopher A. Leo
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Dalia Naser
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Efrosini Artikis
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109
| | - Aron Broom
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Travis Ko
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Purnank Shah
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Mikaela Q. Ney
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Elisa Tran
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Martin T. J. Smith
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Brian Fuglestad
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - A. Joshua Wand
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Charles L. Brooks
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109
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Best practices for resilient automation of biomolecular simulations. Methods Cell Biol 2022; 169:199-219. [DOI: 10.1016/bs.mcb.2021.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Abstract
Biomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their own structures and dynamics using as input seemingly random character strings of their sequence, following which they coalesce and perform integrated cellular functions. In large computational systems with finite interaction-codes, the appearance of conflicting goals is inevitable. Simple conflicting forces can lead to quite complex structures and behaviors, leading to the concept of frustration in condensed matter. We present here some basic ideas about frustration in biomolecules and how the frustration concept leads to a better appreciation of many aspects of the architecture of biomolecules, and especially how biomolecular structure connects to function by means of localized frustration. These ideas are simultaneously both seductively simple and perilously subtle to grasp completely. The energy landscape theory of protein folding provides a framework for quantifying frustration in large systems and has been implemented at many levels of description. We first review the notion of frustration from the areas of abstract logic and its uses in simple condensed matter systems. We discuss then how the frustration concept applies specifically to heteropolymers, testing folding landscape theory in computer simulations of protein models and in experimentally accessible systems. Studying the aspects of frustration averaged over many proteins provides ways to infer energy functions useful for reliable structure prediction. We discuss how frustration affects folding mechanisms. We review here how the biological functions of proteins are related to subtle local physical frustration effects and how frustration influences the appearance of metastable states, the nature of binding processes, catalysis and allosteric transitions. In this review, we also emphasize that frustration, far from being always a bad thing, is an essential feature of biomolecules that allows dynamics to be harnessed for function. In this way, we hope to illustrate how Frustration is a fundamental concept in molecular biology.
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Millers EKI, Trabi M, Masci PP, Lavin MF, de Jersey J, Guddat LW. Crystal structure of textilinin-1, a Kunitz-type serine protease inhibitor from the venom of the Australian common brown snake (Pseudonaja textilis). FEBS J 2009; 276:3163-75. [PMID: 19490116 DOI: 10.1111/j.1742-4658.2009.07034.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Textilinin-1 is a Kunitz-type serine protease inhibitor isolated from the venom of the Australian common brown snake, Pseudonaja textilis. This molecule binds to and blocks the activity of a range of serine proteases, including plasmin and trypsin. Textilinin-1's ability to inhibit plasmin, a protease involved in fibrinolysis, has raised the possibility that it could be used as an alternative to aprotinin (Trasylol) as a systemic antibleeding agent in surgery. Here, the crystal structure of free recombinant textilinin-1 has been determined to 1.63 A, with three molecules observed in the asymmetric unit. All of these have a similar overall fold to aprotinin, except that the canonical loop for one of the molecules is inverted such that the side chain of the P1' residue, Val18, is partially buried by intramolecular contacts to Pro15, Thr13, and Ile36. In aprotinin, the P1' residue is Ala16, whose side chain is too small to form similar contacts. The loop inversion in textilinin-1 is facilitated by changes in backbone dihedral angles for the P1 and P2' residues, such that they alternate between values in the beta-sheet and alpha-helical regions of the Ramachandran plot. In a comparison with the structures of all other known Kunitz-type serine protease inhibitors, no such conformational variability has been observed. The presence of the bulkier valine as the P1' residue in textilinin-1 appears to be a major contributor to reducing the binding affinity for plasmin as compared to aprotinin (3.5 nm versus 0.053 nm) and could also account for an observed narrower binding specificity.
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Affiliation(s)
- Emma-Karin I Millers
- School of Molecular and Microbial Sciences, The University of Queensland, Brisbane, Australia
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Flight S, Johnson L, Trabi M, Gaffney P, Lavin M, de Jersey J, Masci P. Comparison of Textilinin-1 with Aprotinin as Serine Protease Inhibitors and as Antifibrinolytic Agents. PATHOPHYSIOLOGY OF HAEMOSTASIS AND THROMBOSIS 2006; 34:188-93. [PMID: 16707925 DOI: 10.1159/000092421] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Textilinin-1 (Q8008) was isolated from the venom of the Pseudonaja textilis and has a 47% sequence identity to the antihaemorrhagic therapeutic agent aprotinin. When equimolar concentrations of enzyme and aprotinin were pre-incubated, plasmin was inhibited 100%, plasma kallikrein 58%, and tissue kallikrein 99%. Under the same conditions, textilinin-1 inhibited plasmin 98%, plasma kallikrein 16% and tissue kallikrein 17%. Whole blood clot lysis was inhibited strongly by both aprotinin and textilinin-1, as shown by thrombelastography. At 2 microM inhibitor lysis initiated by t-PA was greater than 99% inhibited by aprotinin (LY60 = 0.4 +/- 0.1) whereas textilinin-1, inhibited lysis by 91% (LY60 = 8.9 +/- 0.7). The same trend was found with the lysis of euglobulin fractions. From these data textilinin-1 appears to be a more specific plasmin inhibitor than aprotinin but aprotinin inhibits clot lysis to a greater extent.
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Affiliation(s)
- Simone Flight
- School of Medicine, University of Queensland, Princess Alexandra Hospital, Brisbane, Australia
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Hanson WM, Beeser SA, Oas TG, Goldenberg DP. Identification of a Residue Critical for Maintaining the Functional Conformation of BPTI. J Mol Biol 2003; 333:425-41. [PMID: 14529627 DOI: 10.1016/j.jmb.2003.08.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The effects of amino acid replacements on the backbone dynamics of bovine pancreatic trypsin inhibitor (BPTI) were examined using 15N NMR relaxation experiments. Previous studies have shown that backbone amide groups within the trypsin-binding region of the wild-type protein undergo conformational exchange processes on the micros time scale, and that replacement of Tyr35 with Gly greatly increases the number of backbone atoms involved in such motions. In order to determine whether these mutational effects are specific to the replacement of this residue with Gly, six additional replacements were examined in the present study. In two of these, Tyr35 was replaced with either Ala or Leu, and the other four were single replacements of Tyr23, Phe33, Asn43 or Asn44, all of which are highly buried in the native structure and conserved in homologous proteins. The Y35A and Y35L mutants displayed dynamic properties very similar to those of the Y35G mutant, with the backbone segments including residues 10-19 and 32-44 undergoing motions revealed by enhanced 15N transverse relaxation rates. On the other hand, the Y23L, N43G and N44A substitutions caused almost no detectable changes in backbone dynamics, on either the ns-ps or ms-micros time scales, even though each of these replacements significantly destabilizes the native conformation. Replacement of Phe33 with Leu caused intermediate effects, with several residues that have previously been implicated in motions in the wild-type protein displaying enhanced transverse relaxation rates. These results demonstrate that destabilizing amino acid replacements can be accommodated in a native protein with dramatically different effects on conformational dynamics and that Tyr35 plays a particularly important role in defining the conformation of the trypsin-binding site of BPTI.
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Affiliation(s)
- W Miachel Hanson
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112-0840, USA
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