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Caballero I, Castellví A, Triviño J, Jiménez E, Soler N, Borges R, Usón I. ARCIMBOLDO at low resolution: Verification for coiled coils and globular proteins. Protein Sci 2024; 33:e5136. [PMID: 39150227 PMCID: PMC11328115 DOI: 10.1002/pro.5136] [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: 03/30/2024] [Revised: 07/07/2024] [Accepted: 07/22/2024] [Indexed: 08/17/2024]
Abstract
Crystallography at low resolution must determine the atomic model from less experimental observations, which is challenging in the absence of a model. In addition, model bias is more severe when independent experimental data are scarce. Our methods solve the phase problem by combining the location of accurate model fragments using Phaser with density modification and interpretation of the resulting maps using SHELXE. From a partial, correct structure, the density modification process and the stereochemical constraints draw the rest of the structure, validating the result. This same principle is now exploited at low resolution. Coiled coils are important, ubiquitous structures but notoriously difficult to phase and to predict. Both correct solutions and incorrect ones are poorly discriminated by the crystallographic figures of merit as long as helices are correctly oriented. We incorporate coiled-coil verification, designed to set up competing, incompatible structural hypotheses to probe both the results and establish the power of the data to discriminate them. Efficiency of coiled-coil phasing and validation in test cases from 3 to 4 Å is demonstrated in ARCIMBOLDO_LITE, placing single helices, and in ARCIMBOLDO_SHREDDER, with fragments derived from AlphaFold models. SHELXE tracing at low resolution has been enhanced, maintaining its local character but extending the environment assessment. For non-helical structures, verification is demonstrated in the fragment location process. Its use is exemplified with the solution of the VSR1 structure at 3.5 Å, depending on LLG optimization and the emergence of new features in the electron density. Relying on verification, we have extended the use of the ARCIMBOLDO software to low resolution.
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Affiliation(s)
- Iracema Caballero
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
| | - Albert Castellví
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
| | - Josep Triviño
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
| | - Elisabet Jiménez
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
| | - Nicolas Soler
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
| | - Rafael Borges
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
| | - Isabel Usón
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
- ICREA: Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
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Salvador GHM, Fernandes CAH, Borges RJ, Soares AM, Fontes MRM. Structural studies with crotoxin B from Crotalus durissus collilineatus venom suggest a heterodimeric assembly formed by two new isoforms. Biochimie 2024; 218:46-56. [PMID: 37659716 DOI: 10.1016/j.biochi.2023.08.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/07/2023] [Accepted: 08/31/2023] [Indexed: 09/04/2023]
Abstract
In accidents involving Crotalus snakes, the crotoxin complex (CTX) plays lethal action due to its neurotoxic activity. On the other hand, CTX have potential biotechnological application due to its anti-tumoral, anti-inflammatory, antimicrobial, analgesic and immunomodulatory properties. CTX is a heterodimer composed of Crotoxin A (CA or crotapotin), the acidic nontoxic and non-enzymatic component and; Crotoxin B (CB), a basic, toxic and catalytic PLA2. Currently, there are two classes of CTX isoforms, whose differences in their biological activities have been attributed to features presented in CB isoforms. Here, we present the crystal structure of CB isolated from the Crotalus durissus collilineatus venom. It amino acid sequence was assigned using the SEQUENCE SLIDER software, which revealed that the crystal structure is a heterodimer composed of two new CB isoforms (colCB-A and colCB-B). Bioinformatic and biophysical analyses showed that the toxin forms a tetrameric assembly in solution similar to CB from Crotalus durissus terrificus venom, despite some differences observed at the dimeric interface. By the previously proposed classification, the colCB-B presents features of the class I isoforms while colCB-A cannot be classified into classes I and II based on its amino acid sequence. Due to similar features observed for other CB isoforms found in the NCBI database and the results obtained for colCB-A, we suggest that there are more than two classes of CTX and CB isoforms in crotalic venoms.
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Affiliation(s)
- Guilherme H M Salvador
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - Carlos A H Fernandes
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil; UMR 7590, CNRS, Muséum National d'Histoire Naturelle, IRD, Institut de Minéralogie, Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Université, Paris, France
| | - Rafael J Borges
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil; Centro de Química Medicina (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade de Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Andreimar M Soares
- Laboratório de Biotecnologia de Proteínas e Compostos Bioativos Aplicados, Fundação Oswaldo Cruz (FIOCRUZ), Unidade Rondônia, Porto Velho, RO, Brazil; Inst Nac. de Epidemiologia da Amazônia Ocidental (INCT-EPIAMO), Rede de Pesquisa e Conhecimento de Excelência na Amazônia Ocidental (RED-CONEXAO), Brazil
| | - Marcos R M Fontes
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil; Instituto de Estudos Avançados do Mar (IEAMar), Universidade Estadual Paulista (UNESP), São Vicente, SP, Brazil.
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Solving the microheterogeneity of Bothrops asper myotoxin-II by high-resolution mass spectrometry: Insights into C-terminal region variability in Lys49-phospholipase A2 homologs. Toxicon 2022; 210:123-131. [DOI: 10.1016/j.toxicon.2022.02.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 11/21/2022]
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