23397-23-1Relevant articles and documents
Chemical Mapping Exposes the Importance of Active Site Interactions in Governing the Temperature Dependence of Enzyme Turnover
Winter, Samuel D.,Jones, Hannah B. L.,R?s?dean, Dora M.,Crean, Rory M.,Danson, Michael J.,Panto?, G. Dan,Katona, Gergely,Prentice, Erica,Arcus, Vickery L.,van der Kamp, Marc W.,Pudney, Christopher R.
, p. 14854 - 14863 (2021/12/09)
Uncovering the role of global protein dynamics in enzyme turnover is needed to fully understand enzyme catalysis. Recently, we have demonstrated that the heat capacity of catalysis, ΔCP?, can reveal links between the protein free energy landscape, global protein dynamics, and enzyme turnover, suggesting that subtle changes in molecular interactions at the active site can affect long-range protein dynamics and link to enzyme temperature activity. Here, we use a model promiscuous enzyme (glucose dehydrogenase from Sulfolobus solfataricus) to chemically map how individual substrate interactions affect the temperature dependence of enzyme activity and the network of motions throughout the protein. Utilizing a combination of kinetics, red edge excitation shift (REES) spectroscopy, and computational simulation, we explore the complex relationship between enzyme–substrate interactions and the global dynamics of the protein. We find that changes in ΔCP? and protein dynamics can be mapped to specific substrate–enzyme interactions. Our study reveals how subtle changes in substrate binding affect global changes in motion and flexibility extending throughout the protein.
Chemoenzymatic synthesis of sialosides containing C7-modified sialic acids and their application in sialidase substrate specificity studies
Khedri, Zahra,Li, Yanhong,Muthana, Saddam,Muthana, Musleh M.,Hsiao, Ching-Wen,Yu, Hai,Chen, Xi
, p. 100 - 111 (2014/05/20)
Modifications at the glycerol side chain of sialic acid in sialosides modulate their recognition by sialic acid-binding proteins and sialidases. However, limited work has been focused on the synthesis and functional studies of sialosides with C7-modified
Substrate specificity of galactokinase from Streptococcus pneumoniae TIGR4 towards galactose, glucose, and their derivatives
Zou, Yang,Wang, Wenjun,Cai, Li,Chen, Leilei,Xue, Mengyang,Zhang, Xiaomei,Shen, Jie,Chen, Min
scheme or table, p. 3540 - 3543 (2012/07/03)
Galactokinases (GalKs) have attracted significant research attention for their potential applications in the enzymatic synthesis of unique sugar phosphates. The galactokinase (GalKSpe4) cloned from Streptococcus pneumoniae TIGR4 presents a remarkably broad substrate range including 14 diverse natural and unnatural sugars. TLC and MS studies revealed that GalKSpe4 had relaxed activity towards galactose derivatives with modifications on the C-6, 4- or 2-positions. Additionally, GalKSpe4 can also tolerate glucose while glucose derivatives with modifications on the C-6, 4- or 2-positions were unacceptable. More interestingly, GalKSpe4 can phosphorylate l-mannose in moderate yield (43%), while other l-sugars such as l-Gal cannot be recognized by this enzyme. These results are very significant because there is rarely enzyme reported that can phosphorylate such uncommon substrates as l-mannose.
Structure of the major O-specific polysaccharide from the lipopolysaccharide of Pseudomonas fluorescens BIM B-582: Identification of 4-deoxy-d-xylo-hexose as a component of bacterial polysaccharides
Valueva, Olga A.,Rakhuba, Dzianis,Shashkov, Alexander S.,Zdorovenko, Evelina L.,Kiseleva, Elena,Novik, Galina,Knirel, Yuriy A.
experimental part, p. 2161 - 2167 (2011/12/14)
A novel constituent of bacterial polysaccharides, 4-deoxy-d-xylo-hexose (d-4dxylHex), was found in the major O-specific polysaccharide from the lipopolysaccharide of Pseudomonas fluorescens BIM B-582. d-4dxylHex was isolated in the free state by paper chromatography after full acid hydrolysis of the polysaccharide and identified by GLC-mass spectrometry, 1H and 13C NMR spectroscopy, and specific rotation. It occurs as a lateral substituent in ～40% of the oligosaccharide repeating units, making the polysaccharide devoid of strict regularity. The structure of the polysaccharide was established by sugar analysis, Smith degradation, and two-dimensional 1H and 13C NMR spectroscopy. In addition, a minor polysaccharide was isolated from the same lipopolysaccharide and found to contain 4-O-methylrhamnose.
Thermodynamics of binding of D-galactose and deoxy derivatives thereof to the L-arabinose-binding protein
Hernandez Daranas, Antonio,Shimizu, Hiroki,Homans, Steve W.
, p. 11870 - 11876 (2007/10/03)
We report the thermodynamics of binding of D-galactose and deoxy derivatives thereof to the arabinose binding protein (ABP). The "intrinsic" (solute-solute) free energy of binding ΔG°int at 308 K for the 1-, 2-, 3-, and 6-hydroxyl groups of gal
The preparation of deoxy derivatives of mannose-1-phosphate and their substrate specificity towards recombinant GDP-mannose pyrophosphorylase from Salmonella enterica, group B
Watt, Gregory M.,Flitsch, Sabine L.,Fey, Sven,Elling, Lothar,Kragl, Udo
, p. 621 - 628 (2007/10/03)
2-Deoxy-α-D-glucose-1-phosphate, 3-deoxy-α-D-arabino-hexose-1-phosphate, 4-deoxy-α-D-lyxo-hexose-1-phosphate, and α-D-lyxose-1-phosphate were synthesised chemically, and evaluated as substrates for a recombinant GDP-mannose pyrophosphorylase (Salmonella enterica, group B, cloned in Escherichia coli). The deoxy derivatives were all substrates for the enzyme, with slightly reduced V(max) values but significantly higher K(m) values than those recorded for the native substrate, mannose-1-phosphate. The pyrophosphorylase was used for the synthesis of GDP-mannose analogues GDP-2-deoxy-glucose and GDP-lyxose on a milligram scale. Copyright (C) 2000 Elsevier Science Ltd.
Chemical mapping of the active site of the glucoamylase of Aspergillus niger
Lemieux, Raymond U.,Spohr, Ulrike,Bach, Mimi,Cameron, Dale R.,Frandsen, Torben P.,Stoffer, Bjarne B.,Svensson, Birte,Palcic, Monica M.
, p. 319 - 335 (2007/10/03)
A recently developed technique for the probing of the combining sites of lectins and antibodies, to establish the structure of the epitope that is involved in the binding of an oligosaccharide, is used to study the binding of methyl α-isomaltoside by the enzyme glucoamylase. The procedure involved the determination of the effects on the kinetics of hydrolysis of both monodeoxygenation and mono-O-methylation at each of the seven hydroxyl groups in order to gain an estimate of the differential changes in the free energies of activation, ΔΔG(paragraph). As expected, from previous publications, both deoxygenation and O-methylation of OH-4 (reducing unit), OH-4', or OH-6' strongly hindered hydrolysis, whereas the kinetics were virtually unaffected by either the substitutions at OH-2 or structural changes at C-1. The substitutions at OH-3 caused increases of 2.1 and 1.9 kcal/mol in the ΔΔG(paragraph). In contrast, whereas deoxygenation of either OH-2' or OH-3' caused much smaller (0.96 and 0.52 kcal/mol) increases in ΔΔG(paragraph), the mono-O-methylations resulted in severe steric hindrance to the formation of the activated complex. The relatively weak effects of deoxygenation suggest that the hydroxyl groups are replaced by water molecules and thereby participate in the binding by contributing effective complementarity. Methyl α-isomaltoside was docked into the combining site of the X-ray crystal structure at 2.4 A resolution of the complex with the inhibitor acarbose. A fit free of steric interactions with the protein was found that has the methyl α-glucopyranoside unit in the normal 4C1 conformation and the other glucose unit approaching a half-chair conformation with the interunit fragment defined by the torsion angles Φ/ψ/ω = 74°/134°/166° (O-5'-C-1'(φ)-O-6(ψ)-C-6(ω)-C-5-O-5). The model provides a network of hydrogen bonds that appears to well represent the activated complex formed by the glucoamylase with both maltose and isomaltose since the structures appear to provide a sound rationale for both the specificity and catalysis provided by the enzyme. A recently developed technique for the probing of the combining sites of lectins and antibodies, to establish the structure of the epitope that is involved in the binding of an oligosaccharide, is used to study the binding of methyl α-isomaltoside by the enzyme glucoamylase. The procedure involved the determination of the effects on the kinetics of hydrolysis of both monodeoxygenation and mono-O-methylation at each of the seven hydroxyl groups in order to gain an estimate of the differential changes in the free energies of activation. A model has been developed which provides a network of hydrogen bonds that appears to well represent the activated complex formed by the glucoamylase with both maltose and isomaltose because the structures appear to provide a sound rationale for both the specificity and catalysis provided by the enzyme.
Synthesis of modified aldonic acids and studies of their substrate efficiency for dihydroxy acid dehydratase (DHAD)
Limberg, Gerrit,Thiem, Joachim
, p. 349 - 356 (2007/10/03)
Modified aldopentonic and aldohexonic acids were synthesized in order to study the electronic requirements for a successful enzymatic conversion into their corresponding 2-keto 3-deoxy analogues by dihydroxy acid dehydratase (DHAD), an enzyme from the biosynthetic pathway of branched chain amino acids. Analytical tests with the novel artificial substrates (18)-(21) and (27) provided evidence that the amount of conversion could be enhanced by replacement of the hydroxy group at C 4 of L-arabinonic acid (21) with less electron-withdrawing, ambivalent or electron-donating substituents. Modified aldohexonic acids were no substrates for DHAD, perhaps due to less perfect binding to the active site presumably for steric reasons. For 4-deoxy-L-threo-pentonic acid (18) the enzymatic conversion into 3,4-dideoxy-2-ketopentonic acid (29) by DHAD could be achieved on a preparative scale.
