Small Angle X-ray Scattering, Molecular Modeling, and Chemometric Studies from a Thrombin-Like (Lmr-47) Enzyme of Lachesis m. rhombeata Venom
INTRODUCTION: Snakebite envenomation is considered a neglected tropical disease, and SVTLEs critical elements are involved in serious coagulopathies that occur on envenoming. Although some enzymes of this group have been structurally investigated, it is essential to characterize other proteins to better understand their unique properties such as the Lachesis muta rhombeata 47 kDa (Lmr-47) venom serine protease.
METHODS: The structure of Lmr-47 was studied in solution, using SAXS, DLS, CD, and in silico by homology modeling. Molecular docking experiments simulated 21 competitive inhibitors.
RESULTS: At pH 8.0, Lmr-47 has an Rg of 34.5 ± 0.6 Å, Dmax of 130 Å, and SR of 50 Å, according to DLS data. Kratky plot analysis indicates a rigid shape at pH 8.0. Conversely, the pH variation does not change the center of mass's intrinsic fluorescence, possibly indicating the absence of fluorescent amino acids in the regions affected by pH variation. CD experiments show a substantially random coiled secondary structure not affected by pH. The low-resolution model of Lmr-47 presented a prolate elongated shape at pH 8.0. Using the 3D structure obtained by molecular modeling, docking experiments identified five good and three suitable competitive inhibitors.
CONCLUSION: Together, our work provided insights into the structure of the Lmr-47 and identified inhibitors that may enhance our understanding of thrombin-like family proteins.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2021 |
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| Erschienen: |
2021 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:26 |
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| Enthalten in: |
Molecules (Basel, Switzerland) - 26(2021), 13 vom: 28. Juni |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
De-Simone, Salvatore Giovanni [VerfasserIn] |
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| Links: |
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| Themen: |
Amidine inhibitors |
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| Anmerkungen: |
Date Completed 14.07.2021 Date Revised 02.04.2024 published: Electronic Citation Status MEDLINE |
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| doi: |
10.3390/molecules26133930 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM327498579 |
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| 100 | 1 | |a De-Simone, Salvatore Giovanni |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Small Angle X-ray Scattering, Molecular Modeling, and Chemometric Studies from a Thrombin-Like (Lmr-47) Enzyme of Lachesis m. rhombeata Venom |
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| 500 | |a Date Completed 14.07.2021 | ||
| 500 | |a Date Revised 02.04.2024 | ||
| 500 | |a published: Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a INTRODUCTION: Snakebite envenomation is considered a neglected tropical disease, and SVTLEs critical elements are involved in serious coagulopathies that occur on envenoming. Although some enzymes of this group have been structurally investigated, it is essential to characterize other proteins to better understand their unique properties such as the Lachesis muta rhombeata 47 kDa (Lmr-47) venom serine protease | ||
| 520 | |a METHODS: The structure of Lmr-47 was studied in solution, using SAXS, DLS, CD, and in silico by homology modeling. Molecular docking experiments simulated 21 competitive inhibitors | ||
| 520 | |a RESULTS: At pH 8.0, Lmr-47 has an Rg of 34.5 ± 0.6 Å, Dmax of 130 Å, and SR of 50 Å, according to DLS data. Kratky plot analysis indicates a rigid shape at pH 8.0. Conversely, the pH variation does not change the center of mass's intrinsic fluorescence, possibly indicating the absence of fluorescent amino acids in the regions affected by pH variation. CD experiments show a substantially random coiled secondary structure not affected by pH. The low-resolution model of Lmr-47 presented a prolate elongated shape at pH 8.0. Using the 3D structure obtained by molecular modeling, docking experiments identified five good and three suitable competitive inhibitors | ||
| 520 | |a CONCLUSION: Together, our work provided insights into the structure of the Lmr-47 and identified inhibitors that may enhance our understanding of thrombin-like family proteins | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Lachelis m. rhombeata | |
| 650 | 4 | |a SVTLE | |
| 650 | 4 | |a amidine inhibitors | |
| 650 | 4 | |a guanidine inhibitors | |
| 650 | 4 | |a protein shape | |
| 650 | 4 | |a serine protease | |
| 650 | 4 | |a solution structure | |
| 650 | 7 | |a Crotalid Venoms |2 NLM | |
| 650 | 7 | |a Lachesis venom |2 NLM | |
| 650 | 7 | |a Reptilian Proteins |2 NLM | |
| 650 | 7 | |a Thrombin |2 NLM | |
| 650 | 7 | |a EC 3.4.21.5 |2 NLM | |
| 700 | 1 | |a Lechuga, Guilherme Curty |e verfasserin |4 aut | |
| 700 | 1 | |a Napoleão-Pêgo, Paloma |e verfasserin |4 aut | |
| 700 | 1 | |a Gomes, Larissa Rodrigues |e verfasserin |4 aut | |
| 700 | 1 | |a Provance, David William |c Jr |e verfasserin |4 aut | |
| 700 | 1 | |a Nirello, Vinícius Dias |e verfasserin |4 aut | |
| 700 | 1 | |a Sodero, Ana Carolina Rennó |e verfasserin |4 aut | |
| 700 | 1 | |a Guedes, Herbert Leonel de Mattos |e verfasserin |4 aut | |
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