The Experts below are selected from a list of 37029 Experts worldwide ranked by ideXlab platform
K Binder - One of the best experts on this subject based on the ideXlab platform.
-
computer simulation of bottle brush polymers with flexible Backbone good solvent versus theta solvent conditions
arXiv: Soft Condensed Matter, 2011Co-Authors: Panagiotis E. Theodorakis, Hsiaoping Hsu, Wolfgang Paul, K BinderAbstract:By Molecular Dynamics simulation of a coarse-grained bead-spring type model for a cylindrical molecular brush with a Backbone Chain of $N_b$ effective monomers to which with grafting density $\sigma$ side Chains with $N$ effective monomers are tethered, several characteristic length scales are studied for variable solvent quality. Side Chain lengths are in the range $5 \le N \le 40$, Backbone Chain lengths are in the range $50 \le N_b \le 200$, and we perform a comparison to results for the bond fluctuation model on the simple cubic lattice (for which much longer Chains are accessible, $N_b \le 1027$, and which corresponds to an athermal, very good, solvent). We obtain linear dimensions of side Chains and the Backbone Chain and discuss their $N$-dependence in terms of power laws and the associated effective exponents. We show that even at the Theta point the side Chains are considerably stretched, their linear dimension depending on the solvent quality only weakly. Effective persistence lengths are extracted both from the orientational correlations and from the Backbone end-to-end distance; it is shown that different measures of the persistence length (which would all agree for Gaussian Chains) are not mutually consistent with each other, and depend distinctly both on $N_b$ and the solvent quality. A brief discussion of pertinent experiments is given.
-
computer simulation of bottle brush polymers with flexible Backbone good solvent versus theta solvent conditions
Journal of Chemical Physics, 2011Co-Authors: Panagiotis E. Theodorakis, Hsiaoping Hsu, Wolfgang Paul, K BinderAbstract:By molecular dynamics simulation of a coarse-grained bead-spring-type model for a cylindrical molecular brush with a Backbone Chain of Nb effective monomers to which with grafting density σ side Chains with N effective monomers are tethered, several characteristic length scales are studied for variable solvent quality. Side Chain lengths are in the range 5 ⩽ N ⩽ 40, Backbone Chain lengths are in the range 50 ⩽ Nb ⩽ 200, and we perform a comparison to results for the bond fluctuation model on the simple cubic lattice (for which much longer Chains are accessible, Nb ⩽ 1027, and which corresponds to an athermal, very good, solvent). We obtain linear dimensions of the side Chains and the Backbone Chain and discuss their N-dependence in terms of power laws and the associated effective exponents. We show that even at the theta point the side Chains are considerably stretched, their linear dimension depending on the solvent quality only weakly. Effective persistence lengths are extracted both from the orientatio...
Douglas W Lowman - One of the best experts on this subject based on the ideXlab platform.
-
differential high affinity interaction of dectin 1 with natural or synthetic glucans is dependent upon primary structure and is influenced by polymer Chain length and side Chain branching
Journal of Pharmacology and Experimental Therapeutics, 2008Co-Authors: Elizabeth L Adams, Peter J Rice, Harry E Ensley, Bridget M Graves, Siamon Gordon, Mario A Monteiro, Erzsebet Pappszabo, Douglas W Lowman, Trevor D PowerAbstract:Glucans are structurally diverse fungal biopolymers that stimulate innate immunity and are fungal pathogen-associated molecular patterns. Dectin-1 is a C-type lectin-like pattern recognition receptor that binds glucans and induces innate immune responses to fungal pathogens. We examined the effect of glucan structure on recognition and binding by murine recombinant Dectin-1 with a library of natural product and synthetic (1-->3)-beta/(1-->6)-beta-glucans as well as nonglucan polymers. Dectin-1 is highly specific for glucans with a pure (1-->3)-beta-linked Backbone structure. Although Dectin-1 is highly specific for (1-->3)-beta-d-glucans, it does not recognize all glucans equally. Dectin-1 differentially interacted with (1-->3)-beta-d-glucans over a very wide range of binding affinities (2.6 mM-2.2 pM). One of the most striking observations that emerged from this study was the remarkable high-affinity interaction of Dectin-1 with certain glucans (2.2 pM). These data also demonstrated that synthetic glucan ligands interact with Dectin-1 and that binding affinity increased in synthetic glucans containing a single glucose side-Chain branch. We also observed differential recognition of glucans derived from saprophytes and pathogens. We found that glucan derived from a saprophytic yeast was recognized with higher affinity than glucan derived from the pathogen Candida albicans. Structural analysis demonstrated that glucan Backbone Chain length and (1-->6)-beta side-Chain branching strongly influenced Dectin-1 binding affinity. These data demonstrate: 1) the specificity of Dectin-1 for glucans; 2) that Dectin-1 differentiates between glucan ligands based on structural determinants; and 3) that Dectin-1 can recognize and interact with both natural product and synthetic glucan ligands.
-
differential high affinity interaction of dectin 1 with natural or synthetic glucans is dependent upon primary structure and is influenced by polymer Chain length and side Chain branching
Journal of Pharmacology and Experimental Therapeutics, 2008Co-Authors: Elizabeth L Adams, Peter J Rice, Harry E Ensley, Bridget M Graves, Siamon Gordon, Mario A Monteiro, Erzsebet Pappszabo, Hai Yu, Gordon D Brown, Douglas W LowmanAbstract:Glucans are structurally diverse fungal biopolymers that stimulate innate immunity and are fungal pathogen-associated molecular patterns. Dectin-1 is a C-type lectin-like pattern recognition receptor that binds glucans and induces innate immune responses to fungal pathogens. We examined the effect of glucan structure on recognition and binding by murine recombinant Dectin-1 with a library of natural product and synthetic (1→3)-β/(1→6)-β-glucans as well as nonglucan polymers. Dectin-1 is highly specific for glucans with a pure (1→3)-β-linked Backbone structure. Although Dectin-1 is highly specific for (1→3)-β-d-glucans, it does not recognize all glucans equally. Dectin-1 differentially interacted with (1→3)-β-d-glucans over a very wide range of binding affinities (2.6 mM–2.2 pM). One of the most striking observations that emerged from this study was the remarkable high-affinity interaction of Dectin-1 with certain glucans (2.2 pM). These data also demonstrated that synthetic glucan ligands interact with Dectin-1 and that binding affinity increased in synthetic glucans containing a single glucose side-Chain branch. We also observed differential recognition of glucans derived from saprophytes and pathogens. We found that glucan derived from a saprophytic yeast was recognized with higher affinity than glucan derived from the pathogen Candida albicans . Structural analysis demonstrated that glucan Backbone Chain length and (1→6)-β side-Chain branching strongly influenced Dectin-1 binding affinity. These data demonstrate: 1) the specificity of Dectin-1 for glucans; 2) that Dectin-1 differentiates between glucan ligands based on structural determinants; and 3) that Dectin-1 can recognize and interact with both natural product and synthetic glucan ligands.
Milagros Medina - One of the best experts on this subject based on the ideXlab platform.
-
involvement of the pyrophosphate and the 2 phosphate binding regions of ferredoxin nadp reductase in coenzyme specificity
Journal of Biological Chemistry, 2003Co-Authors: Jesus Tejero, Alejandra Luquita, Juan A Hermoso, Tomas Mayoral, J Sanzaparicio, Carlos Gomezmoreno, Marta Martinezjulvez, John K Hurley, Gordon Tollin, Milagros MedinaAbstract:Previous studies indicated that the determinants of coenzyme specificity in ferredoxin-NADP+ reductase (FNR) from Anabaena are situated in the 2′-phosphate (2′-P) NADP+ binding region, and also suggested that other regions must undergo structural rearrangements of the protein Backbone during coenzyme binding. Among the residues involved in such specificity could be those located in regions where interaction with the pyrophosphate group of the coenzyme takes place, namely loops 155–160 and 261–268 in Anabaena FNR. In order to learn more about the coenzyme specificity determinants, and to better define the structural basis of coenzyme binding, mutations in the pyrophosphate and 2′-P binding regions of FNR have been introduced. Modification of the pyrophosphate binding region, involving residues Thr-155, Ala-160, and Leu-263, indicates that this region is involved in determining coenzyme specificity and that selected alterations of these positions produce FNR enzymes that are able to bind NAD+. Thus, our results suggest that slightly different structural rearrangements of the Backbone Chain in the pyrophosphate binding region might determine FNR specificity for the coenzyme. Combined mutations at the 2′-P binding region, involving residues Ser-223, Arg-224, Arg-233, and Tyr-235, in combination with the residues mentioned above in the pyrophosphate binding region have also been carried out in an attempt to increase the FNR affinity for NAD+/H. However, in most cases the analyzed mutants lost the ability for NADP+/H binding and electron transfer, and no major improvements were observed with regard to the efficiency of the reactions with NAD+/H. Therefore, our results confirm that determinants for coenzyme specificity in FNR are also situated in the pyrophosphate binding region and not only in the 2′-P binding region. Such observations also suggest that other regions of the protein, yet to be identified, might also be involved in this process.
-
probing the determinants of coenzyme specificity in ferredoxin nadp reductase by site directed mutagenesis
Journal of Biological Chemistry, 2001Co-Authors: Milagros Medina, Alejandra Luquita, Jesus Tejero, Juan A Hermoso, Tomas Mayoral, J Sanzaparicio, Koert Grever, Carlos GomezmorenoAbstract:On the basis of sequence and three-dimensional structure comparison between Anabaena PCC7119 ferredoxin-NADP+ reductase (FNR) and other reductases from its structurally related family that bind either NADP+/H or NAD+/H, a set of amino acid residues that might determine the FNR coenzyme specificity can be assigned. These residues include Thr-155, Ser-223, Arg-224, Arg-233 and Tyr-235. Systematic replacement of these amino acids was done to identify which of them are the main determinants of coenzyme specificity. Our data indicate that all of the residues interacting with the 2′-phosphate of NADP+/H in Anabaena FNR are not involved to the same extent in determining coenzyme specificity and affinity. Thus, it is found that Ser-223 and Tyr-235 are important for determining NADP+/H specificity and orientation with respect to the protein, whereas Arg-224 and Arg-233 provide only secondary interactions in Anabaena FNR. The analysis of the T155G FNR form also indicates that the determinants of coenzyme specificity are not only situated in the 2′-phosphate NADP+/H interacting region but that other regions of the protein must be involved. These regions, although not interacting directly with the coenzyme, must produce specific structural arrangements of the Backbone Chain that determine coenzyme specificity. The loop formed by residues 261–268 inAnabaena FNR must be one of these regions.
Elizabeth L Adams - One of the best experts on this subject based on the ideXlab platform.
-
differential high affinity interaction of dectin 1 with natural or synthetic glucans is dependent upon primary structure and is influenced by polymer Chain length and side Chain branching
Journal of Pharmacology and Experimental Therapeutics, 2008Co-Authors: Elizabeth L Adams, Peter J Rice, Harry E Ensley, Bridget M Graves, Siamon Gordon, Mario A Monteiro, Erzsebet Pappszabo, Douglas W Lowman, Trevor D PowerAbstract:Glucans are structurally diverse fungal biopolymers that stimulate innate immunity and are fungal pathogen-associated molecular patterns. Dectin-1 is a C-type lectin-like pattern recognition receptor that binds glucans and induces innate immune responses to fungal pathogens. We examined the effect of glucan structure on recognition and binding by murine recombinant Dectin-1 with a library of natural product and synthetic (1-->3)-beta/(1-->6)-beta-glucans as well as nonglucan polymers. Dectin-1 is highly specific for glucans with a pure (1-->3)-beta-linked Backbone structure. Although Dectin-1 is highly specific for (1-->3)-beta-d-glucans, it does not recognize all glucans equally. Dectin-1 differentially interacted with (1-->3)-beta-d-glucans over a very wide range of binding affinities (2.6 mM-2.2 pM). One of the most striking observations that emerged from this study was the remarkable high-affinity interaction of Dectin-1 with certain glucans (2.2 pM). These data also demonstrated that synthetic glucan ligands interact with Dectin-1 and that binding affinity increased in synthetic glucans containing a single glucose side-Chain branch. We also observed differential recognition of glucans derived from saprophytes and pathogens. We found that glucan derived from a saprophytic yeast was recognized with higher affinity than glucan derived from the pathogen Candida albicans. Structural analysis demonstrated that glucan Backbone Chain length and (1-->6)-beta side-Chain branching strongly influenced Dectin-1 binding affinity. These data demonstrate: 1) the specificity of Dectin-1 for glucans; 2) that Dectin-1 differentiates between glucan ligands based on structural determinants; and 3) that Dectin-1 can recognize and interact with both natural product and synthetic glucan ligands.
-
differential high affinity interaction of dectin 1 with natural or synthetic glucans is dependent upon primary structure and is influenced by polymer Chain length and side Chain branching
Journal of Pharmacology and Experimental Therapeutics, 2008Co-Authors: Elizabeth L Adams, Peter J Rice, Harry E Ensley, Bridget M Graves, Siamon Gordon, Mario A Monteiro, Erzsebet Pappszabo, Hai Yu, Gordon D Brown, Douglas W LowmanAbstract:Glucans are structurally diverse fungal biopolymers that stimulate innate immunity and are fungal pathogen-associated molecular patterns. Dectin-1 is a C-type lectin-like pattern recognition receptor that binds glucans and induces innate immune responses to fungal pathogens. We examined the effect of glucan structure on recognition and binding by murine recombinant Dectin-1 with a library of natural product and synthetic (1→3)-β/(1→6)-β-glucans as well as nonglucan polymers. Dectin-1 is highly specific for glucans with a pure (1→3)-β-linked Backbone structure. Although Dectin-1 is highly specific for (1→3)-β-d-glucans, it does not recognize all glucans equally. Dectin-1 differentially interacted with (1→3)-β-d-glucans over a very wide range of binding affinities (2.6 mM–2.2 pM). One of the most striking observations that emerged from this study was the remarkable high-affinity interaction of Dectin-1 with certain glucans (2.2 pM). These data also demonstrated that synthetic glucan ligands interact with Dectin-1 and that binding affinity increased in synthetic glucans containing a single glucose side-Chain branch. We also observed differential recognition of glucans derived from saprophytes and pathogens. We found that glucan derived from a saprophytic yeast was recognized with higher affinity than glucan derived from the pathogen Candida albicans . Structural analysis demonstrated that glucan Backbone Chain length and (1→6)-β side-Chain branching strongly influenced Dectin-1 binding affinity. These data demonstrate: 1) the specificity of Dectin-1 for glucans; 2) that Dectin-1 differentiates between glucan ligands based on structural determinants; and 3) that Dectin-1 can recognize and interact with both natural product and synthetic glucan ligands.
Carlos Gomezmoreno - One of the best experts on this subject based on the ideXlab platform.
-
involvement of the pyrophosphate and the 2 phosphate binding regions of ferredoxin nadp reductase in coenzyme specificity
Journal of Biological Chemistry, 2003Co-Authors: Jesus Tejero, Alejandra Luquita, Juan A Hermoso, Tomas Mayoral, J Sanzaparicio, Carlos Gomezmoreno, Marta Martinezjulvez, John K Hurley, Gordon Tollin, Milagros MedinaAbstract:Previous studies indicated that the determinants of coenzyme specificity in ferredoxin-NADP+ reductase (FNR) from Anabaena are situated in the 2′-phosphate (2′-P) NADP+ binding region, and also suggested that other regions must undergo structural rearrangements of the protein Backbone during coenzyme binding. Among the residues involved in such specificity could be those located in regions where interaction with the pyrophosphate group of the coenzyme takes place, namely loops 155–160 and 261–268 in Anabaena FNR. In order to learn more about the coenzyme specificity determinants, and to better define the structural basis of coenzyme binding, mutations in the pyrophosphate and 2′-P binding regions of FNR have been introduced. Modification of the pyrophosphate binding region, involving residues Thr-155, Ala-160, and Leu-263, indicates that this region is involved in determining coenzyme specificity and that selected alterations of these positions produce FNR enzymes that are able to bind NAD+. Thus, our results suggest that slightly different structural rearrangements of the Backbone Chain in the pyrophosphate binding region might determine FNR specificity for the coenzyme. Combined mutations at the 2′-P binding region, involving residues Ser-223, Arg-224, Arg-233, and Tyr-235, in combination with the residues mentioned above in the pyrophosphate binding region have also been carried out in an attempt to increase the FNR affinity for NAD+/H. However, in most cases the analyzed mutants lost the ability for NADP+/H binding and electron transfer, and no major improvements were observed with regard to the efficiency of the reactions with NAD+/H. Therefore, our results confirm that determinants for coenzyme specificity in FNR are also situated in the pyrophosphate binding region and not only in the 2′-P binding region. Such observations also suggest that other regions of the protein, yet to be identified, might also be involved in this process.
-
probing the determinants of coenzyme specificity in ferredoxin nadp reductase by site directed mutagenesis
Journal of Biological Chemistry, 2001Co-Authors: Milagros Medina, Alejandra Luquita, Jesus Tejero, Juan A Hermoso, Tomas Mayoral, J Sanzaparicio, Koert Grever, Carlos GomezmorenoAbstract:On the basis of sequence and three-dimensional structure comparison between Anabaena PCC7119 ferredoxin-NADP+ reductase (FNR) and other reductases from its structurally related family that bind either NADP+/H or NAD+/H, a set of amino acid residues that might determine the FNR coenzyme specificity can be assigned. These residues include Thr-155, Ser-223, Arg-224, Arg-233 and Tyr-235. Systematic replacement of these amino acids was done to identify which of them are the main determinants of coenzyme specificity. Our data indicate that all of the residues interacting with the 2′-phosphate of NADP+/H in Anabaena FNR are not involved to the same extent in determining coenzyme specificity and affinity. Thus, it is found that Ser-223 and Tyr-235 are important for determining NADP+/H specificity and orientation with respect to the protein, whereas Arg-224 and Arg-233 provide only secondary interactions in Anabaena FNR. The analysis of the T155G FNR form also indicates that the determinants of coenzyme specificity are not only situated in the 2′-phosphate NADP+/H interacting region but that other regions of the protein must be involved. These regions, although not interacting directly with the coenzyme, must produce specific structural arrangements of the Backbone Chain that determine coenzyme specificity. The loop formed by residues 261–268 inAnabaena FNR must be one of these regions.
