The Experts below are selected from a list of 19305 Experts worldwide ranked by ideXlab platform
G Timp - One of the best experts on this subject based on the ideXlab platform.
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reading the primary structure of a Protein with 0 07 nm3 resolution using a subnanometre diameter pore
2016Co-Authors: Eamonn Kennedy, Zhuxin Dong, Clare Tennant, G TimpAbstract:The primary structure of a Protein consists of a sequence of amino acids and is a key factor in determining how a Protein folds and functions. However, conventional methods for sequencing Proteins, such as mass spectrometry and Edman degradation, suffer from short reads and lack sensitivity, so alternative approaches are sought. Here, we show that a subnanometre-diameter pore, sputtered through a thin silicon nitride membrane, can be used to detect the primary structure of a Denatured Protein molecule. When a Denatured Protein immersed in electrolyte is driven through the pore by an electric field, measurements of a blockade in the current reveal nearly regular fluctuations, the number of which coincides with the number of residues in the Protein. Furthermore, the amplitudes of the fluctuations are highly correlated with the volumes that are occluded by quadromers (four residues) in the primary structure. Each fluctuation, therefore, represents a read of a quadromer. Scrutiny of the fluctuations reveals that the subnanometre pore is sensitive enough to read the occluded volume that is related to post-translational modifications of a single residue, measuring volume differences of ∼0.07 nm3, but it is not sensitive enough to discriminate between the volumes of all twenty amino acids. A pore with a subnanometre diameter, created in a thin silicon nitride membrane, can be used to detect the primary structure of a Denatured Protein molecule.
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reading the primary structure of a Protein with 0 07 nm3 resolution using a subnanometre diameter pore
2016Co-Authors: Eamonn Kennedy, Zhuxin Dong, Clare Tennant, G TimpAbstract:The primary structure of a Protein consists of a sequence of amino acids and is a key factor in determining how a Protein folds and functions. However, conventional methods for sequencing Proteins, such as mass spectrometry and Edman degradation, suffer from short reads and lack sensitivity, so alternative approaches are sought. Here, we show that a subnanometre-diameter pore, sputtered through a thin silicon nitride membrane, can be used to detect the primary structure of a Denatured Protein molecule. When a Denatured Protein immersed in electrolyte is driven through the pore by an electric field, measurements of a blockade in the current reveal nearly regular fluctuations, the number of which coincides with the number of residues in the Protein. Furthermore, the amplitudes of the fluctuations are highly correlated with the volumes that are occluded by quadromers (four residues) in the primary structure. Each fluctuation, therefore, represents a read of a quadromer. Scrutiny of the fluctuations reveals that the subnanometre pore is sensitive enough to read the occluded volume that is related to post-translational modifications of a single residue, measuring volume differences of ∼0.07 nm3, but it is not sensitive enough to discriminate between the volumes of all twenty amino acids.
Eamonn Kennedy - One of the best experts on this subject based on the ideXlab platform.
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reading the primary structure of a Protein with 0 07 nm3 resolution using a subnanometre diameter pore
2016Co-Authors: Eamonn Kennedy, Zhuxin Dong, Clare Tennant, G TimpAbstract:The primary structure of a Protein consists of a sequence of amino acids and is a key factor in determining how a Protein folds and functions. However, conventional methods for sequencing Proteins, such as mass spectrometry and Edman degradation, suffer from short reads and lack sensitivity, so alternative approaches are sought. Here, we show that a subnanometre-diameter pore, sputtered through a thin silicon nitride membrane, can be used to detect the primary structure of a Denatured Protein molecule. When a Denatured Protein immersed in electrolyte is driven through the pore by an electric field, measurements of a blockade in the current reveal nearly regular fluctuations, the number of which coincides with the number of residues in the Protein. Furthermore, the amplitudes of the fluctuations are highly correlated with the volumes that are occluded by quadromers (four residues) in the primary structure. Each fluctuation, therefore, represents a read of a quadromer. Scrutiny of the fluctuations reveals that the subnanometre pore is sensitive enough to read the occluded volume that is related to post-translational modifications of a single residue, measuring volume differences of ∼0.07 nm3, but it is not sensitive enough to discriminate between the volumes of all twenty amino acids. A pore with a subnanometre diameter, created in a thin silicon nitride membrane, can be used to detect the primary structure of a Denatured Protein molecule.
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reading the primary structure of a Protein with 0 07 nm3 resolution using a subnanometre diameter pore
2016Co-Authors: Eamonn Kennedy, Zhuxin Dong, Clare Tennant, G TimpAbstract:The primary structure of a Protein consists of a sequence of amino acids and is a key factor in determining how a Protein folds and functions. However, conventional methods for sequencing Proteins, such as mass spectrometry and Edman degradation, suffer from short reads and lack sensitivity, so alternative approaches are sought. Here, we show that a subnanometre-diameter pore, sputtered through a thin silicon nitride membrane, can be used to detect the primary structure of a Denatured Protein molecule. When a Denatured Protein immersed in electrolyte is driven through the pore by an electric field, measurements of a blockade in the current reveal nearly regular fluctuations, the number of which coincides with the number of residues in the Protein. Furthermore, the amplitudes of the fluctuations are highly correlated with the volumes that are occluded by quadromers (four residues) in the primary structure. Each fluctuation, therefore, represents a read of a quadromer. Scrutiny of the fluctuations reveals that the subnanometre pore is sensitive enough to read the occluded volume that is related to post-translational modifications of a single residue, measuring volume differences of ∼0.07 nm3, but it is not sensitive enough to discriminate between the volumes of all twenty amino acids.
Clare Tennant - One of the best experts on this subject based on the ideXlab platform.
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reading the primary structure of a Protein with 0 07 nm3 resolution using a subnanometre diameter pore
2016Co-Authors: Eamonn Kennedy, Zhuxin Dong, Clare Tennant, G TimpAbstract:The primary structure of a Protein consists of a sequence of amino acids and is a key factor in determining how a Protein folds and functions. However, conventional methods for sequencing Proteins, such as mass spectrometry and Edman degradation, suffer from short reads and lack sensitivity, so alternative approaches are sought. Here, we show that a subnanometre-diameter pore, sputtered through a thin silicon nitride membrane, can be used to detect the primary structure of a Denatured Protein molecule. When a Denatured Protein immersed in electrolyte is driven through the pore by an electric field, measurements of a blockade in the current reveal nearly regular fluctuations, the number of which coincides with the number of residues in the Protein. Furthermore, the amplitudes of the fluctuations are highly correlated with the volumes that are occluded by quadromers (four residues) in the primary structure. Each fluctuation, therefore, represents a read of a quadromer. Scrutiny of the fluctuations reveals that the subnanometre pore is sensitive enough to read the occluded volume that is related to post-translational modifications of a single residue, measuring volume differences of ∼0.07 nm3, but it is not sensitive enough to discriminate between the volumes of all twenty amino acids. A pore with a subnanometre diameter, created in a thin silicon nitride membrane, can be used to detect the primary structure of a Denatured Protein molecule.
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reading the primary structure of a Protein with 0 07 nm3 resolution using a subnanometre diameter pore
2016Co-Authors: Eamonn Kennedy, Zhuxin Dong, Clare Tennant, G TimpAbstract:The primary structure of a Protein consists of a sequence of amino acids and is a key factor in determining how a Protein folds and functions. However, conventional methods for sequencing Proteins, such as mass spectrometry and Edman degradation, suffer from short reads and lack sensitivity, so alternative approaches are sought. Here, we show that a subnanometre-diameter pore, sputtered through a thin silicon nitride membrane, can be used to detect the primary structure of a Denatured Protein molecule. When a Denatured Protein immersed in electrolyte is driven through the pore by an electric field, measurements of a blockade in the current reveal nearly regular fluctuations, the number of which coincides with the number of residues in the Protein. Furthermore, the amplitudes of the fluctuations are highly correlated with the volumes that are occluded by quadromers (four residues) in the primary structure. Each fluctuation, therefore, represents a read of a quadromer. Scrutiny of the fluctuations reveals that the subnanometre pore is sensitive enough to read the occluded volume that is related to post-translational modifications of a single residue, measuring volume differences of ∼0.07 nm3, but it is not sensitive enough to discriminate between the volumes of all twenty amino acids.
Zhuxin Dong - One of the best experts on this subject based on the ideXlab platform.
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reading the primary structure of a Protein with 0 07 nm3 resolution using a subnanometre diameter pore
2016Co-Authors: Eamonn Kennedy, Zhuxin Dong, Clare Tennant, G TimpAbstract:The primary structure of a Protein consists of a sequence of amino acids and is a key factor in determining how a Protein folds and functions. However, conventional methods for sequencing Proteins, such as mass spectrometry and Edman degradation, suffer from short reads and lack sensitivity, so alternative approaches are sought. Here, we show that a subnanometre-diameter pore, sputtered through a thin silicon nitride membrane, can be used to detect the primary structure of a Denatured Protein molecule. When a Denatured Protein immersed in electrolyte is driven through the pore by an electric field, measurements of a blockade in the current reveal nearly regular fluctuations, the number of which coincides with the number of residues in the Protein. Furthermore, the amplitudes of the fluctuations are highly correlated with the volumes that are occluded by quadromers (four residues) in the primary structure. Each fluctuation, therefore, represents a read of a quadromer. Scrutiny of the fluctuations reveals that the subnanometre pore is sensitive enough to read the occluded volume that is related to post-translational modifications of a single residue, measuring volume differences of ∼0.07 nm3, but it is not sensitive enough to discriminate between the volumes of all twenty amino acids. A pore with a subnanometre diameter, created in a thin silicon nitride membrane, can be used to detect the primary structure of a Denatured Protein molecule.
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reading the primary structure of a Protein with 0 07 nm3 resolution using a subnanometre diameter pore
2016Co-Authors: Eamonn Kennedy, Zhuxin Dong, Clare Tennant, G TimpAbstract:The primary structure of a Protein consists of a sequence of amino acids and is a key factor in determining how a Protein folds and functions. However, conventional methods for sequencing Proteins, such as mass spectrometry and Edman degradation, suffer from short reads and lack sensitivity, so alternative approaches are sought. Here, we show that a subnanometre-diameter pore, sputtered through a thin silicon nitride membrane, can be used to detect the primary structure of a Denatured Protein molecule. When a Denatured Protein immersed in electrolyte is driven through the pore by an electric field, measurements of a blockade in the current reveal nearly regular fluctuations, the number of which coincides with the number of residues in the Protein. Furthermore, the amplitudes of the fluctuations are highly correlated with the volumes that are occluded by quadromers (four residues) in the primary structure. Each fluctuation, therefore, represents a read of a quadromer. Scrutiny of the fluctuations reveals that the subnanometre pore is sensitive enough to read the occluded volume that is related to post-translational modifications of a single residue, measuring volume differences of ∼0.07 nm3, but it is not sensitive enough to discriminate between the volumes of all twenty amino acids.
Vijay S Pande - One of the best experts on this subject based on the ideXlab platform.
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modeling the mechanism of cln025 beta hairpin formation
2017Co-Authors: Keri A. Mckiernan, Brooke E. Husic, Vijay S PandeAbstract:Beta-hairpins are substructures found in Proteins that can lend insight into more complex systems. Furthermore, the folding of beta-hairpins is a valuable test case for benchmarking experimental and theoretical methods. Here, we simulate the folding of CLN025, a miniProtein with a beta-hairpin structure, at its experimental melting temperature using a range of state-of-the-art Protein force fields. We construct Markov state models in order to examine the thermodynamics, kinetics, mechanism, and rate-determining step of folding. Mechanistically, we find the folding process is rate-limited by the formation of the turn region hydrogen bonds, which occurs following the downhill hydrophobic collapse of the extended Denatured Protein. These results are presented in the context of established and contradictory theories of the beta-hairpin folding process. Furthermore, our analysis suggests that the AMBER-FB15 force field, at this temperature, best describes the characteristics of the full experimental CLN025 con...
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modeling the mechanism of cln025 beta hairpin formation
2017Co-Authors: Keri A. Mckiernan, Brooke E. Husic, Vijay S PandeAbstract:Beta-hairpins are a substructure found in Proteins that can lend insight into more complex systems. Furthermore, the folding of betahairpins is a valuable test case for benchmarking experimental and theoretical methods. Here, we simulate the folding of CLN025, a miniProtein with a beta-hairpin structure, at its experimental melting temperature using a range of state-of-the-art Protein force fields. We construct Markov state models in order to examine the thermodynamics, kinetics, mechanism, and rate-determining step of folding. Mechanistically, we find the folding process is rate-limited by the formation of the turn region hydrogen bonds, which occurs following the downhill hydrophobic collapse of the extended Denatured Protein. These results are presented in the context of established and contradictory theories of the beta-hairpin folding process. Furthermore, our analysis suggests that the AMBER-FB15 force field, at this temperature, best describes the characteristics of the full experimental CLN025 conformational ensemble, while the AMBER ff99SB-ILDN and CHARMM22* force fields display a tendency to overstabilize the native state.