The Experts below are selected from a list of 47742 Experts worldwide ranked by ideXlab platform
Jens Wöhnert - One of the best experts on this subject based on the ideXlab platform.
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Structure-based redesign of docking domain interactions modulates the Product Spectrum of a rhabdopeptide-synthesizing NRPS
Nature Communications, 2018Co-Authors: Carolin Hacker, Xiaofeng Cai, Carsten Kegler, Lei Zhao, A. Katharina Weickhmann, Jan Philip Wurm, Helge B. Bode, Jens WöhnertAbstract:Rhabdopeptides are synthesized by non-ribosomal peptide synthetases (NRPSs) and the multiple NRPS subunits interact through docking domains (DD). Here the authors provide insights into DD interaction patterns and present the structures of three N-terminal docking domains (^NDD) and a ^NDD-^CDD complex and derive a set of recognition rules for DD interactions. Several peptides in clinical use are derived from non-ribosomal peptide synthetases (NRPS). In these systems multiple NRPS subunits interact with each other in a specific linear order mediated by specific docking domains (DDs), whose structures are not known yet, to synthesize well-defined peptide Products. In contrast to classical NRPSs, single-module NRPS subunits responsible for the generation of rhabdopeptide/xenortide-like peptides (RXPs) can act in different order depending on subunit stoichiometry thereby producing peptide libraries. To define the basis for their unusual interaction patterns, we determine the structures of all N-terminal DDs (^NDDs) as well as of an ^NDD-^CDD complex and characterize all putative DD interactions thermodynamically for such a system. Key amino acid residues for DD interactions are identified that upon their exchange change the DD affinity and result in predictable changes in peptide Production. Recognition rules for DD interactions are identified that also operate in other megasynthase complexes.
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Structure-based redesign of docking domain interactions modulates the Product Spectrum of a rhabdopeptide-synthesizing NRPS.
Nature communications, 2018Co-Authors: Carolin Hacker, Xiaofeng Cai, Carsten Kegler, Lei Zhao, A. Katharina Weickhmann, Jan Philip Wurm, Helge B. Bode, Jens WöhnertAbstract:Several peptides in clinical use are derived from non-ribosomal peptide synthetases (NRPS). In these systems multiple NRPS subunits interact with each other in a specific linear order mediated by specific docking domains (DDs), whose structures are not known yet, to synthesize well-defined peptide Products. In contrast to classical NRPSs, single-module NRPS subunits responsible for the generation of rhabdopeptide/xenortide-like peptides (RXPs) can act in different order depending on subunit stoichiometry thereby producing peptide libraries. To define the basis for their unusual interaction patterns, we determine the structures of all N-terminal DDs (NDDs) as well as of an NDD-CDD complex and characterize all putative DD interactions thermodynamically for such a system. Key amino acid residues for DD interactions are identified that upon their exchange change the DD affinity and result in predictable changes in peptide Production. Recognition rules for DD interactions are identified that also operate in other megasynthase complexes.
Carolin Hacker - One of the best experts on this subject based on the ideXlab platform.
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Structure-based redesign of docking domain interactions modulates the Product Spectrum of a rhabdopeptide-synthesizing NRPS
Nature Communications, 2018Co-Authors: Carolin Hacker, Xiaofeng Cai, Carsten Kegler, Lei Zhao, A. Katharina Weickhmann, Jan Philip Wurm, Helge B. Bode, Jens WöhnertAbstract:Rhabdopeptides are synthesized by non-ribosomal peptide synthetases (NRPSs) and the multiple NRPS subunits interact through docking domains (DD). Here the authors provide insights into DD interaction patterns and present the structures of three N-terminal docking domains (^NDD) and a ^NDD-^CDD complex and derive a set of recognition rules for DD interactions. Several peptides in clinical use are derived from non-ribosomal peptide synthetases (NRPS). In these systems multiple NRPS subunits interact with each other in a specific linear order mediated by specific docking domains (DDs), whose structures are not known yet, to synthesize well-defined peptide Products. In contrast to classical NRPSs, single-module NRPS subunits responsible for the generation of rhabdopeptide/xenortide-like peptides (RXPs) can act in different order depending on subunit stoichiometry thereby producing peptide libraries. To define the basis for their unusual interaction patterns, we determine the structures of all N-terminal DDs (^NDDs) as well as of an ^NDD-^CDD complex and characterize all putative DD interactions thermodynamically for such a system. Key amino acid residues for DD interactions are identified that upon their exchange change the DD affinity and result in predictable changes in peptide Production. Recognition rules for DD interactions are identified that also operate in other megasynthase complexes.
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Structure-based redesign of docking domain interactions modulates the Product Spectrum of a rhabdopeptide-synthesizing NRPS.
Nature communications, 2018Co-Authors: Carolin Hacker, Xiaofeng Cai, Carsten Kegler, Lei Zhao, A. Katharina Weickhmann, Jan Philip Wurm, Helge B. Bode, Jens WöhnertAbstract:Several peptides in clinical use are derived from non-ribosomal peptide synthetases (NRPS). In these systems multiple NRPS subunits interact with each other in a specific linear order mediated by specific docking domains (DDs), whose structures are not known yet, to synthesize well-defined peptide Products. In contrast to classical NRPSs, single-module NRPS subunits responsible for the generation of rhabdopeptide/xenortide-like peptides (RXPs) can act in different order depending on subunit stoichiometry thereby producing peptide libraries. To define the basis for their unusual interaction patterns, we determine the structures of all N-terminal DDs (NDDs) as well as of an NDD-CDD complex and characterize all putative DD interactions thermodynamically for such a system. Key amino acid residues for DD interactions are identified that upon their exchange change the DD affinity and result in predictable changes in peptide Production. Recognition rules for DD interactions are identified that also operate in other megasynthase complexes.
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Structure-based redesign of docking domain interactions modulates the Product Spectrum of a rhabdopeptide-synthesizing NRPS
2018Co-Authors: Carolin Hacker, Xiaofeng Cai, Carsten Kegler, Lei Zhao, Helge B. Bode, Katharina Weickhmann, Jens WoehnertAbstract:Abstract Several peptides in clinical use are derived from non-ribosomal peptide synthetases (NRPS). In these systems multiple NRPS subunits interact with each other in a specific linear order mediated by docking domains (DDs) to synthesize well-defined peptide Products. In contrast to these classical NRPSs, the subunits of rhabdopeptide/xenortide producing NRPSs can act iteratively and in different order resulting in libraries of peptide Products. In order to define the structural and thermodynamic basis for their unusual interaction patterns, we determined the structures of all N-terminal DDs (NDDs) as well as of an NDD-CDD complex and characterized all putative DD interactions thermodynamically for one such system. Key amino acid residues for DD interactions were identified that upon their exchange not only changed the DD affinity but also resulted in rationally predictable changes in peptide Production. A simple set of ‘recognition rules’ for DD interactions was identified that also operates in other megasynthase complexes.
Miguel Mauricio-iglesias - One of the best experts on this subject based on the ideXlab platform.
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A metabolic model for targeted volatile fatty acids Production by cofermentation of carbohydrates and proteins.
Bioresource technology, 2019Co-Authors: Alberte Regueira, R. Bevilacqua, Juan M. Lema, Marta Carballa, Miguel Mauricio-iglesiasAbstract:Anaerobic mixed-culture fermentations are interesting processes to valorise organic wastes by converting them to volatile fatty acids. One of the main issues is that certain operational conditions (e.g. pH or different substrate concentrations) can vary significantly the Product Spectrum. So far, there are no tools that take into the account the characteristic features of cofermentation processes, which hinders the possibility of designing processes that use real wastes as substrates. In this work a mathematical model was developed for the Production of volatile fatty acids from organic wastes with a high concentration of carbohydrates and proteins. The model reproduces satisfactorily experimental results and is also able of giving mechanistic insight into the interactions between carbohydrates and proteins that explain the observed changes in the Product Spectrum. We envision this model as the core of an early-stage design tool for anaerobic cofermentation processes, as shown in this work with different examples.
Kuldip K Paliwal - One of the best experts on this subject based on the ideXlab platform.
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Product of power Spectrum and group delay function for speech recognition
International Conference on Acoustics Speech and Signal Processing, 2004Co-Authors: Donglai Zhu, Kuldip K PaliwalAbstract:Mel-frequency cepstral coefficients (MFCCs) are the most widely used features for speech recognition. These are derived from the power Spectrum of the speech signal. Recently, the cepstral features derived from the modified group delay function (MGDF) have been studied by Murthy and Gadde (Proc. ICASSP, vol.1, p.68-71, 2003) for speech recognition. In this paper, we propose to use the Product of the power Spectrum and the group delay function (GDF), and derive the MFCCs from the Product Spectrum. This Spectrum combines the information from the magnitude Spectrum as well as the phase Spectrum. The MFCCs of the MGDF are also investigated in this paper. Results show that the cepstral features derived from the power Spectrum perform better than that from the MGDF, and the Product Spectrum based features provide the best performance.
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ICASSP (1) - Product of power Spectrum and group delay function for speech recognition
2004 IEEE International Conference on Acoustics Speech and Signal Processing, 1Co-Authors: Donglai Zhu, Kuldip K PaliwalAbstract:Mel-frequency cepstral coefficients (MFCCs) are the most widely used features for speech recognition. These are derived from the power Spectrum of the speech signal. Recently, the cepstral features derived from the modified group delay function (MGDF) have been studied by Murthy and Gadde (Proc. ICASSP, vol.1, p.68-71, 2003) for speech recognition. In this paper, we propose to use the Product of the power Spectrum and the group delay function (GDF), and derive the MFCCs from the Product Spectrum. This Spectrum combines the information from the magnitude Spectrum as well as the phase Spectrum. The MFCCs of the MGDF are also investigated in this paper. Results show that the cepstral features derived from the power Spectrum perform better than that from the MGDF, and the Product Spectrum based features provide the best performance.
Helge B. Bode - One of the best experts on this subject based on the ideXlab platform.
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Structure-based redesign of docking domain interactions modulates the Product Spectrum of a rhabdopeptide-synthesizing NRPS
Nature Communications, 2018Co-Authors: Carolin Hacker, Xiaofeng Cai, Carsten Kegler, Lei Zhao, A. Katharina Weickhmann, Jan Philip Wurm, Helge B. Bode, Jens WöhnertAbstract:Rhabdopeptides are synthesized by non-ribosomal peptide synthetases (NRPSs) and the multiple NRPS subunits interact through docking domains (DD). Here the authors provide insights into DD interaction patterns and present the structures of three N-terminal docking domains (^NDD) and a ^NDD-^CDD complex and derive a set of recognition rules for DD interactions. Several peptides in clinical use are derived from non-ribosomal peptide synthetases (NRPS). In these systems multiple NRPS subunits interact with each other in a specific linear order mediated by specific docking domains (DDs), whose structures are not known yet, to synthesize well-defined peptide Products. In contrast to classical NRPSs, single-module NRPS subunits responsible for the generation of rhabdopeptide/xenortide-like peptides (RXPs) can act in different order depending on subunit stoichiometry thereby producing peptide libraries. To define the basis for their unusual interaction patterns, we determine the structures of all N-terminal DDs (^NDDs) as well as of an ^NDD-^CDD complex and characterize all putative DD interactions thermodynamically for such a system. Key amino acid residues for DD interactions are identified that upon their exchange change the DD affinity and result in predictable changes in peptide Production. Recognition rules for DD interactions are identified that also operate in other megasynthase complexes.
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Structure-based redesign of docking domain interactions modulates the Product Spectrum of a rhabdopeptide-synthesizing NRPS.
Nature communications, 2018Co-Authors: Carolin Hacker, Xiaofeng Cai, Carsten Kegler, Lei Zhao, A. Katharina Weickhmann, Jan Philip Wurm, Helge B. Bode, Jens WöhnertAbstract:Several peptides in clinical use are derived from non-ribosomal peptide synthetases (NRPS). In these systems multiple NRPS subunits interact with each other in a specific linear order mediated by specific docking domains (DDs), whose structures are not known yet, to synthesize well-defined peptide Products. In contrast to classical NRPSs, single-module NRPS subunits responsible for the generation of rhabdopeptide/xenortide-like peptides (RXPs) can act in different order depending on subunit stoichiometry thereby producing peptide libraries. To define the basis for their unusual interaction patterns, we determine the structures of all N-terminal DDs (NDDs) as well as of an NDD-CDD complex and characterize all putative DD interactions thermodynamically for such a system. Key amino acid residues for DD interactions are identified that upon their exchange change the DD affinity and result in predictable changes in peptide Production. Recognition rules for DD interactions are identified that also operate in other megasynthase complexes.
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Structure-based redesign of docking domain interactions modulates the Product Spectrum of a rhabdopeptide-synthesizing NRPS
2018Co-Authors: Carolin Hacker, Xiaofeng Cai, Carsten Kegler, Lei Zhao, Helge B. Bode, Katharina Weickhmann, Jens WoehnertAbstract:Abstract Several peptides in clinical use are derived from non-ribosomal peptide synthetases (NRPS). In these systems multiple NRPS subunits interact with each other in a specific linear order mediated by docking domains (DDs) to synthesize well-defined peptide Products. In contrast to these classical NRPSs, the subunits of rhabdopeptide/xenortide producing NRPSs can act iteratively and in different order resulting in libraries of peptide Products. In order to define the structural and thermodynamic basis for their unusual interaction patterns, we determined the structures of all N-terminal DDs (NDDs) as well as of an NDD-CDD complex and characterized all putative DD interactions thermodynamically for one such system. Key amino acid residues for DD interactions were identified that upon their exchange not only changed the DD affinity but also resulted in rationally predictable changes in peptide Production. A simple set of ‘recognition rules’ for DD interactions was identified that also operates in other megasynthase complexes.