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Natural Inhibitors of Snake Venom Metalloendopeptidases: History and Current Challenges

View Article: PubMed Central - PubMed

ABSTRACT

The research on natural snake venom metalloendopeptidase inhibitors (SVMPIs) began in the 18th century with the pioneering work of Fontana on the resistance that vipers exhibited to their own venom. During the past 40 years, SVMPIs have been isolated mainly from the sera of resistant animals, and characterized to different extents. They are acidic oligomeric glycoproteins that remain biologically active over a wide range of pH and temperature values. Based on primary structure determination, mammalian plasmatic SVMPIs are classified as members of the immunoglobulin (Ig) supergene protein family, while the one isolated from muscle belongs to the ficolin/opsonin P35 family. On the other hand, SVMPIs from snake plasma have been placed in the cystatin superfamily. These natural antitoxins constitute the first line of defense against snake venoms, inhibiting the catalytic activities of snake venom metalloendopeptidases through the establishment of high-affinity, non-covalent interactions. This review presents a historical account of the field of natural resistance, summarizing its main discoveries and current challenges, which are mostly related to the limitations that preclude three-dimensional structural determinations of these inhibitors using “gold-standard” methods; perspectives on how to circumvent such limitations are presented. Potential applications of these SVMPIs in medicine are also highlighted.

No MeSH data available.


Related in: MedlinePlus

Strategies for a structural view of SVMPIs. (Left) The experimental methods for structure determination, NMR spectroscopy and XRD crystallography, are the “gold-standard” techniques in protein structure elucidation, providing atomic resolution of individual proteins and their complexes. The SVMPIs DM43 and BJ46a represent a challenge for these techniques. For NMR spectroscopy, due to the molecular size of both molecules, costly and time-consuming methods for sample labeling and analysis are required. For XRD crystallography, crystals of DM43 produced low-resolution diffraction pattern while BJ46a could not be crystallized, highlighting the limiting character of the crystallization step. Hence, modeling becomes an important tool for the structural studies of these molecules. (Right) In molecular modeling, the main step is the identification of a homologous protein, whose experimental structure has already been determined, to be used as a template structure. The identification in structure databases of sequences evolutionarily correlated with sequential identity greater than 40% is done by standard pairwise sequence search methods, allowing the generation of high accuracy models. However, below this sequence identity threshold the correlation between two structures is difficult to address. In this range, sequences are correlated directly with proteins of known structure (fold recognition). A drawback is that, due to the low evolutionary correlation and the low sensitivity in the sequence alignment building, the accuracy of the produced models is lower. On the other hand, the ensemble of models produced can be filtered according to their agreement with experimental data. In our proposed strategy, these data would come from XL-MS, HDX-MS and SAXS assays, leading to the selection of accurate models, and shedding some light on the three-dimensional structural characteristics of these SVMPIs. Consequently, the molecular basis of the interaction between the inhibitors and their target toxins could be established.
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toxins-08-00250-f002: Strategies for a structural view of SVMPIs. (Left) The experimental methods for structure determination, NMR spectroscopy and XRD crystallography, are the “gold-standard” techniques in protein structure elucidation, providing atomic resolution of individual proteins and their complexes. The SVMPIs DM43 and BJ46a represent a challenge for these techniques. For NMR spectroscopy, due to the molecular size of both molecules, costly and time-consuming methods for sample labeling and analysis are required. For XRD crystallography, crystals of DM43 produced low-resolution diffraction pattern while BJ46a could not be crystallized, highlighting the limiting character of the crystallization step. Hence, modeling becomes an important tool for the structural studies of these molecules. (Right) In molecular modeling, the main step is the identification of a homologous protein, whose experimental structure has already been determined, to be used as a template structure. The identification in structure databases of sequences evolutionarily correlated with sequential identity greater than 40% is done by standard pairwise sequence search methods, allowing the generation of high accuracy models. However, below this sequence identity threshold the correlation between two structures is difficult to address. In this range, sequences are correlated directly with proteins of known structure (fold recognition). A drawback is that, due to the low evolutionary correlation and the low sensitivity in the sequence alignment building, the accuracy of the produced models is lower. On the other hand, the ensemble of models produced can be filtered according to their agreement with experimental data. In our proposed strategy, these data would come from XL-MS, HDX-MS and SAXS assays, leading to the selection of accurate models, and shedding some light on the three-dimensional structural characteristics of these SVMPIs. Consequently, the molecular basis of the interaction between the inhibitors and their target toxins could be established.

Mentions: During the second half of the 20th century, a large portion of the research in this field has been devoted to the isolation of SVMPIs for further physicochemical and chemical characterizations, including primary structure determination. However, over the last 15 years, the main goal of natural resistance research shifted from protein purification to mechanistic studies in an attempt to understand the interaction between inhibitors and target toxins at the molecular level. This review does not intend to present all known SVMPIs and their determined characteristics; this information can be found by the reader in a historical series of reviews [20,21,24,26,27,28,29]. In fact, with this contribution, we aimed to summarize the available knowledge in the field of SVMPIs (Figure 1) and to discuss novel perspectives in this research area, especially on how to address the actual bottleneck due to the lack of information on the three-dimensional structures of SVMPIs (Figure 2).


Natural Inhibitors of Snake Venom Metalloendopeptidases: History and Current Challenges
Strategies for a structural view of SVMPIs. (Left) The experimental methods for structure determination, NMR spectroscopy and XRD crystallography, are the “gold-standard” techniques in protein structure elucidation, providing atomic resolution of individual proteins and their complexes. The SVMPIs DM43 and BJ46a represent a challenge for these techniques. For NMR spectroscopy, due to the molecular size of both molecules, costly and time-consuming methods for sample labeling and analysis are required. For XRD crystallography, crystals of DM43 produced low-resolution diffraction pattern while BJ46a could not be crystallized, highlighting the limiting character of the crystallization step. Hence, modeling becomes an important tool for the structural studies of these molecules. (Right) In molecular modeling, the main step is the identification of a homologous protein, whose experimental structure has already been determined, to be used as a template structure. The identification in structure databases of sequences evolutionarily correlated with sequential identity greater than 40% is done by standard pairwise sequence search methods, allowing the generation of high accuracy models. However, below this sequence identity threshold the correlation between two structures is difficult to address. In this range, sequences are correlated directly with proteins of known structure (fold recognition). A drawback is that, due to the low evolutionary correlation and the low sensitivity in the sequence alignment building, the accuracy of the produced models is lower. On the other hand, the ensemble of models produced can be filtered according to their agreement with experimental data. In our proposed strategy, these data would come from XL-MS, HDX-MS and SAXS assays, leading to the selection of accurate models, and shedding some light on the three-dimensional structural characteristics of these SVMPIs. Consequently, the molecular basis of the interaction between the inhibitors and their target toxins could be established.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5037476&req=5

toxins-08-00250-f002: Strategies for a structural view of SVMPIs. (Left) The experimental methods for structure determination, NMR spectroscopy and XRD crystallography, are the “gold-standard” techniques in protein structure elucidation, providing atomic resolution of individual proteins and their complexes. The SVMPIs DM43 and BJ46a represent a challenge for these techniques. For NMR spectroscopy, due to the molecular size of both molecules, costly and time-consuming methods for sample labeling and analysis are required. For XRD crystallography, crystals of DM43 produced low-resolution diffraction pattern while BJ46a could not be crystallized, highlighting the limiting character of the crystallization step. Hence, modeling becomes an important tool for the structural studies of these molecules. (Right) In molecular modeling, the main step is the identification of a homologous protein, whose experimental structure has already been determined, to be used as a template structure. The identification in structure databases of sequences evolutionarily correlated with sequential identity greater than 40% is done by standard pairwise sequence search methods, allowing the generation of high accuracy models. However, below this sequence identity threshold the correlation between two structures is difficult to address. In this range, sequences are correlated directly with proteins of known structure (fold recognition). A drawback is that, due to the low evolutionary correlation and the low sensitivity in the sequence alignment building, the accuracy of the produced models is lower. On the other hand, the ensemble of models produced can be filtered according to their agreement with experimental data. In our proposed strategy, these data would come from XL-MS, HDX-MS and SAXS assays, leading to the selection of accurate models, and shedding some light on the three-dimensional structural characteristics of these SVMPIs. Consequently, the molecular basis of the interaction between the inhibitors and their target toxins could be established.
Mentions: During the second half of the 20th century, a large portion of the research in this field has been devoted to the isolation of SVMPIs for further physicochemical and chemical characterizations, including primary structure determination. However, over the last 15 years, the main goal of natural resistance research shifted from protein purification to mechanistic studies in an attempt to understand the interaction between inhibitors and target toxins at the molecular level. This review does not intend to present all known SVMPIs and their determined characteristics; this information can be found by the reader in a historical series of reviews [20,21,24,26,27,28,29]. In fact, with this contribution, we aimed to summarize the available knowledge in the field of SVMPIs (Figure 1) and to discuss novel perspectives in this research area, especially on how to address the actual bottleneck due to the lack of information on the three-dimensional structures of SVMPIs (Figure 2).

View Article: PubMed Central - PubMed

ABSTRACT

The research on natural snake venom metalloendopeptidase inhibitors (SVMPIs) began in the 18th century with the pioneering work of Fontana on the resistance that vipers exhibited to their own venom. During the past 40 years, SVMPIs have been isolated mainly from the sera of resistant animals, and characterized to different extents. They are acidic oligomeric glycoproteins that remain biologically active over a wide range of pH and temperature values. Based on primary structure determination, mammalian plasmatic SVMPIs are classified as members of the immunoglobulin (Ig) supergene protein family, while the one isolated from muscle belongs to the ficolin/opsonin P35 family. On the other hand, SVMPIs from snake plasma have been placed in the cystatin superfamily. These natural antitoxins constitute the first line of defense against snake venoms, inhibiting the catalytic activities of snake venom metalloendopeptidases through the establishment of high-affinity, non-covalent interactions. This review presents a historical account of the field of natural resistance, summarizing its main discoveries and current challenges, which are mostly related to the limitations that preclude three-dimensional structural determinations of these inhibitors using “gold-standard” methods; perspectives on how to circumvent such limitations are presented. Potential applications of these SVMPIs in medicine are also highlighted.

No MeSH data available.


Related in: MedlinePlus