The Experts below are selected from a list of 591 Experts worldwide ranked by ideXlab platform
Minna M. Poranen - One of the best experts on this subject based on the ideXlab platform.
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Structural comPArison strengthens the higher-order classification of proteases related to chymotrypsin.
PloS one, 2019Co-Authors: Heli A. M. Mönttinen, Janne J. Ravantti, Minna M. PoranenAbstract:Specific cleavage of proteins by proteases is essential for several cellular, physiological, and viral processes. Chymotrypsin-related proteases that form the PA Clan in the MEROPS classification of proteases is one of the largest and most diverse group of proteases. The PA Clan comprises serine proteases from bacteria, eukaryotes, archaea, and viruses and chymotrypsin-related cysteine proteases from positive-strand RNA viruses. Despite low amino acid sequence identity, all PA Clan proteases share a conserved double β-barrel structure. Using an automated structure-based hierarchical clustering method, we identified a common structural core of 72 amino acid residues for 143 PA Clan proteases that represent 12 protein families and 11 subfamilies. The identified core is located around the catalytic site between the two β-barrels and resembles the structures of the smallest PA Clan proteases. We constructed a structure-based distance tree derived from the properties of the identified common core. Our structure-based analyses support the current classification of these proteases at the subfamily level and largely at the family level. Structural alignment and structure-based distance trees could thus be used for directing objective classification of PA Clan proteases and to strengthen their higher order classification. Our results also indicate that the PA Clan proteases of positive-strand RNA viruses are related to cellular heat-shock proteases, which suggests that the exchange of protease genes between viruses and cells might have occurred more than once.
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Common structural fold for PA Clan proteases.
2019Co-Authors: Heli A. M. Mönttinen, Janne J. Ravantti, Minna M. PoranenAbstract:The common structural core for the PA Clan proteases was identified using the HSF program. The 72 equivalent residues deduced from the structural clustering are mapped in green on the structures of the 3C protease of the hePAtitis A virus (left; family C3, subfamily C3E, PDBid: 1HAV), MamO protease of Magnetospirillum magneticum (middle; family S1, subfamily S1C, PDBid: 5HMA), and trypsin of Fusarium oxysporum (right; family S1A, PDBid: 1GDQ). The other PArts of the protein structures are shown in grey.
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A structure-based distance tree for members of PA Clan proteases.
2019Co-Authors: Heli A. M. Mönttinen, Janne J. Ravantti, Minna M. PoranenAbstract:The structure-based distance tree was deduced based on the 72 equivalent amino acid residues located close to the catalytic site. The colors indicate the different families of the PA Clan according to the MEROPS database. The five clusters (I−V) are indicated. The split subfamily S1D groups are labeled with “S1Dtype” and “S1Dnew”. The branches corresponding to the protease PAralogs SMIPP-S-D1 and SMIPP-S-I1 (PDBids: 3H7T and 3H7O, respectively) are marked with asterisks. The names of the families/subfamilies that comprise viral proteases are in bold.
Chhabinath Mandal - One of the best experts on this subject based on the ideXlab platform.
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Modeling and structural analysis of PA Clan serine proteases.
BMC research notes, 2012Co-Authors: Aparna Laskar, Euan J. Rodger, Aniruddha Chatterjee, Chhabinath MandalAbstract:Background Serine proteases account for over a third of all known proteolytic enzymes; they are involved in a variety of physiological processes and are classified into Clans sharing structural homology. The PA Clan of endopeptidases is the most abundant and over two thirds of this Clan is comprised of the S1 family of serine proteases, which bear the archetyPAl trypsin fold and have a catalytic triad in the order Histidine, AsPArtate, Serine. These proteases have been studied in depth and many three dimensional structures have been experimentally determined. However, these structures mostly consist of bacterial and animal proteases, with a small number of plant and fungal proteases and as yet no structures have been determined for protozoa or archaea. The core structure and active site geometry of these proteases is of interest for many applications. This study investigated the structural properties of different S1 family serine proteases from a diverse range of taxa using molecular modeling techniques.
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Modeling and structural analysis of PA Clan serine proteases
BMC Research Notes, 2012Co-Authors: Aparna Laskar, Euan J. Rodger, Aniruddha Chatterjee, Chhabinath MandalAbstract:Background Serine proteases account for over a third of all known proteolytic enzymes; they are involved in a variety of physiological processes and are classified into Clans sharing structural homology. The PA Clan of endopeptidases is the most abundant and over two thirds of this Clan is comprised of the S1 family of serine proteases, which bear the archetyPAl trypsin fold and have a catalytic triad in the order Histidine, AsPArtate, Serine. These proteases have been studied in depth and many three dimensional structures have been experimentally determined. However, these structures mostly consist of bacterial and animal proteases, with a small number of plant and fungal proteases and as yet no structures have been determined for protozoa or archaea. The core structure and active site geometry of these proteases is of interest for many applications. This study investigated the structural properties of different S1 family serine proteases from a diverse range of taxa using molecular modeling techniques. Results Our predicted models from protozoa, archaea, fungi and plants were combined with the experimentally determined structures of 16 S1 family members and used for analysis of the catalytic core. Amino acid sequences were submitted to SWISS-MODEL for homology-based structure prediction or the LOOPP server for threading-based structure prediction. Predicted models were refined using INSIGHT II and SCRWL and validated against experimental structures. Investigation of secondary structures and electrostatic surface potential was performed using MOLMOL. The structural geometry of the catalytic core shows clear deviations between taxa, but the relative positions of the catalytic triad residues were conserved. Some highly conserved residues potentially contributing to the stability of the structural core were identified. Evolutionary divergence was also exhibited by large variation in secondary structure features outside the core, differences in overall amino acid distribution, and unique surface electrostatic potential PAtterns between species. Conclusions EncomPAssing a wide range of taxa, our structural analysis provides an evolutionary perspective on S1 family serine proteases. Focusing on the common core containing the catalytic site of the enzyme, this analysis is beneficial for future molecular modeling strategies and structural analysis of serine protease models.
Heli A. M. Mönttinen - One of the best experts on this subject based on the ideXlab platform.
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Structural comPArison strengthens the higher-order classification of proteases related to chymotrypsin.
PloS one, 2019Co-Authors: Heli A. M. Mönttinen, Janne J. Ravantti, Minna M. PoranenAbstract:Specific cleavage of proteins by proteases is essential for several cellular, physiological, and viral processes. Chymotrypsin-related proteases that form the PA Clan in the MEROPS classification of proteases is one of the largest and most diverse group of proteases. The PA Clan comprises serine proteases from bacteria, eukaryotes, archaea, and viruses and chymotrypsin-related cysteine proteases from positive-strand RNA viruses. Despite low amino acid sequence identity, all PA Clan proteases share a conserved double β-barrel structure. Using an automated structure-based hierarchical clustering method, we identified a common structural core of 72 amino acid residues for 143 PA Clan proteases that represent 12 protein families and 11 subfamilies. The identified core is located around the catalytic site between the two β-barrels and resembles the structures of the smallest PA Clan proteases. We constructed a structure-based distance tree derived from the properties of the identified common core. Our structure-based analyses support the current classification of these proteases at the subfamily level and largely at the family level. Structural alignment and structure-based distance trees could thus be used for directing objective classification of PA Clan proteases and to strengthen their higher order classification. Our results also indicate that the PA Clan proteases of positive-strand RNA viruses are related to cellular heat-shock proteases, which suggests that the exchange of protease genes between viruses and cells might have occurred more than once.
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Common structural fold for PA Clan proteases.
2019Co-Authors: Heli A. M. Mönttinen, Janne J. Ravantti, Minna M. PoranenAbstract:The common structural core for the PA Clan proteases was identified using the HSF program. The 72 equivalent residues deduced from the structural clustering are mapped in green on the structures of the 3C protease of the hePAtitis A virus (left; family C3, subfamily C3E, PDBid: 1HAV), MamO protease of Magnetospirillum magneticum (middle; family S1, subfamily S1C, PDBid: 5HMA), and trypsin of Fusarium oxysporum (right; family S1A, PDBid: 1GDQ). The other PArts of the protein structures are shown in grey.
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A structure-based distance tree for members of PA Clan proteases.
2019Co-Authors: Heli A. M. Mönttinen, Janne J. Ravantti, Minna M. PoranenAbstract:The structure-based distance tree was deduced based on the 72 equivalent amino acid residues located close to the catalytic site. The colors indicate the different families of the PA Clan according to the MEROPS database. The five clusters (I−V) are indicated. The split subfamily S1D groups are labeled with “S1Dtype” and “S1Dnew”. The branches corresponding to the protease PAralogs SMIPP-S-D1 and SMIPP-S-I1 (PDBids: 3H7T and 3H7O, respectively) are marked with asterisks. The names of the families/subfamilies that comprise viral proteases are in bold.
Aparna Laskar - One of the best experts on this subject based on the ideXlab platform.
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Modeling and structural analysis of PA Clan serine proteases.
BMC research notes, 2012Co-Authors: Aparna Laskar, Euan J. Rodger, Aniruddha Chatterjee, Chhabinath MandalAbstract:Background Serine proteases account for over a third of all known proteolytic enzymes; they are involved in a variety of physiological processes and are classified into Clans sharing structural homology. The PA Clan of endopeptidases is the most abundant and over two thirds of this Clan is comprised of the S1 family of serine proteases, which bear the archetyPAl trypsin fold and have a catalytic triad in the order Histidine, AsPArtate, Serine. These proteases have been studied in depth and many three dimensional structures have been experimentally determined. However, these structures mostly consist of bacterial and animal proteases, with a small number of plant and fungal proteases and as yet no structures have been determined for protozoa or archaea. The core structure and active site geometry of these proteases is of interest for many applications. This study investigated the structural properties of different S1 family serine proteases from a diverse range of taxa using molecular modeling techniques.
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Modeling and structural analysis of PA Clan serine proteases
BMC Research Notes, 2012Co-Authors: Aparna Laskar, Euan J. Rodger, Aniruddha Chatterjee, Chhabinath MandalAbstract:Background Serine proteases account for over a third of all known proteolytic enzymes; they are involved in a variety of physiological processes and are classified into Clans sharing structural homology. The PA Clan of endopeptidases is the most abundant and over two thirds of this Clan is comprised of the S1 family of serine proteases, which bear the archetyPAl trypsin fold and have a catalytic triad in the order Histidine, AsPArtate, Serine. These proteases have been studied in depth and many three dimensional structures have been experimentally determined. However, these structures mostly consist of bacterial and animal proteases, with a small number of plant and fungal proteases and as yet no structures have been determined for protozoa or archaea. The core structure and active site geometry of these proteases is of interest for many applications. This study investigated the structural properties of different S1 family serine proteases from a diverse range of taxa using molecular modeling techniques. Results Our predicted models from protozoa, archaea, fungi and plants were combined with the experimentally determined structures of 16 S1 family members and used for analysis of the catalytic core. Amino acid sequences were submitted to SWISS-MODEL for homology-based structure prediction or the LOOPP server for threading-based structure prediction. Predicted models were refined using INSIGHT II and SCRWL and validated against experimental structures. Investigation of secondary structures and electrostatic surface potential was performed using MOLMOL. The structural geometry of the catalytic core shows clear deviations between taxa, but the relative positions of the catalytic triad residues were conserved. Some highly conserved residues potentially contributing to the stability of the structural core were identified. Evolutionary divergence was also exhibited by large variation in secondary structure features outside the core, differences in overall amino acid distribution, and unique surface electrostatic potential PAtterns between species. Conclusions EncomPAssing a wide range of taxa, our structural analysis provides an evolutionary perspective on S1 family serine proteases. Focusing on the common core containing the catalytic site of the enzyme, this analysis is beneficial for future molecular modeling strategies and structural analysis of serine protease models.
Janne J. Ravantti - One of the best experts on this subject based on the ideXlab platform.
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Structural comPArison strengthens the higher-order classification of proteases related to chymotrypsin.
PloS one, 2019Co-Authors: Heli A. M. Mönttinen, Janne J. Ravantti, Minna M. PoranenAbstract:Specific cleavage of proteins by proteases is essential for several cellular, physiological, and viral processes. Chymotrypsin-related proteases that form the PA Clan in the MEROPS classification of proteases is one of the largest and most diverse group of proteases. The PA Clan comprises serine proteases from bacteria, eukaryotes, archaea, and viruses and chymotrypsin-related cysteine proteases from positive-strand RNA viruses. Despite low amino acid sequence identity, all PA Clan proteases share a conserved double β-barrel structure. Using an automated structure-based hierarchical clustering method, we identified a common structural core of 72 amino acid residues for 143 PA Clan proteases that represent 12 protein families and 11 subfamilies. The identified core is located around the catalytic site between the two β-barrels and resembles the structures of the smallest PA Clan proteases. We constructed a structure-based distance tree derived from the properties of the identified common core. Our structure-based analyses support the current classification of these proteases at the subfamily level and largely at the family level. Structural alignment and structure-based distance trees could thus be used for directing objective classification of PA Clan proteases and to strengthen their higher order classification. Our results also indicate that the PA Clan proteases of positive-strand RNA viruses are related to cellular heat-shock proteases, which suggests that the exchange of protease genes between viruses and cells might have occurred more than once.
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Common structural fold for PA Clan proteases.
2019Co-Authors: Heli A. M. Mönttinen, Janne J. Ravantti, Minna M. PoranenAbstract:The common structural core for the PA Clan proteases was identified using the HSF program. The 72 equivalent residues deduced from the structural clustering are mapped in green on the structures of the 3C protease of the hePAtitis A virus (left; family C3, subfamily C3E, PDBid: 1HAV), MamO protease of Magnetospirillum magneticum (middle; family S1, subfamily S1C, PDBid: 5HMA), and trypsin of Fusarium oxysporum (right; family S1A, PDBid: 1GDQ). The other PArts of the protein structures are shown in grey.
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A structure-based distance tree for members of PA Clan proteases.
2019Co-Authors: Heli A. M. Mönttinen, Janne J. Ravantti, Minna M. PoranenAbstract:The structure-based distance tree was deduced based on the 72 equivalent amino acid residues located close to the catalytic site. The colors indicate the different families of the PA Clan according to the MEROPS database. The five clusters (I−V) are indicated. The split subfamily S1D groups are labeled with “S1Dtype” and “S1Dnew”. The branches corresponding to the protease PAralogs SMIPP-S-D1 and SMIPP-S-I1 (PDBids: 3H7T and 3H7O, respectively) are marked with asterisks. The names of the families/subfamilies that comprise viral proteases are in bold.
