Carbohydrate and Protein-based Inhibitors of Porcine Pancreatic α-Amylase: Structure Analysis and Comparison of Their Binding Characteristics

Machius, Mischa; Vertesy, L.; Huber, Robert; Wiegand, Georg

doi:10.1006/jmbi.1996.0410

Cited by 117 publications

(131 citation statements)

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“…As was pointed out in section I.6 we study the loop of N ) 7 residues, 304-310 (Gly-His-Gly-Ala-Gly-Gly-Ser), of PPA in two microstates related to the free and bound loop structures. The starting point is the available crystal structures of PPA II, 1pif and 1pig, 59 respectively. Because the structures of these proteins are almost identical, we have chosen to carry out the calculations with the 1pif structure, where the loop structure of 1pig is attached to the 1pif structure by superimposing the structure of 1pig on that of 1pif (the ligand was discarded); this would enable one to study the stability of the bound microstate of the loop in the structure of the free protein, as discussed in the previous section I.…”

Section: Theory and Methodologymentioning

confidence: 99%

“…PPA is a single polypeptide chain of 496 amino acid residues [56][57][58][59] consisting of three structural domains, domain A (residues 1-99, 170-404), domain B (residues 100-169), and domain C (residues 405-496). Domain A adopts a ( / R) 8 barrel structure and contains the three catalytic residues Asp197, Glu233, and Asp300.…”

Section: I1 the Role Of Free Energy In Structural Biologymentioning

confidence: 99%

“…A deep cleft in domain A is accepted to be the substratebinding site. [56][57][58][59][60][61][62] An essential chloride ion and a calcium ion are located closer to this V-shaped depression and have been suggested to enhance the catalytic activity. [62][63][64][65] While substantial evidence is available for the role of catalytic residues in amylases, very few studies have been carried out on the role of loops surrounding the active site that interact with the substrate.…”

Section: I1 the Role Of Free Energy In Structural Biologymentioning

confidence: 99%

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Stability of the Free and Bound Microstates of a Mobile Loop of α-Amylase Obtained from the Absolute Entropy and Free Energy

Cheluvaraja

Meirovitch

2007

J. Chem. Theory Comput.

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Abstract:The hypothetical scanning molecular dynamics (HSMD) method is a relatively new technique for calculating the absolute entropy, S, and free energy, F, from a given sample generated by any simulation procedure. Thus, each sample conformation, i, is reconstructed by calculating transition probabilities that their product leads to the probability of i, hence to the entropy. HSMD is an exact method where all interactions are considered, and the only approximation is due to insufficient sampling. In previous studies HSMD (and HS Monte Carlo -HSMC) has been applied very successfully to liquid argon, TIP3P water, self-avoiding walks, and peptides in a R-helix, extended, and hairpin microstates. In this paper HSMD is developed further as applied to the flexible 7-residue surface loop, 304-310 (Gly-His-Gly-Ala-Gly-GlySer) of the enzyme porcine pancreatic R-amylase. We are mainly interested in entropy and free energy differences ∆S ) S free -S bound (and ∆F)F free -F bound ) between the free and bound microstates of the loop, which are obtained from two separate MD samples of these microstates without the need to carry out thermodynamic integration. As for peptides, we find that relatively large systematic errors in S free and S bound (and F free and F bound ) are cancelled in ∆S (∆F) which is thus obtained efficiently with high accuracy, i.e., with a statistical error of 0.1-0.2 kcal/mol (T)300 K) using the AMBER force field and AMBER with the implicit solvation GB/SA. We provide theoretical arguments in support of this cancellation, discuss in detail the problems involved in the computational definition of a microstate in conformational space, suggest potential ways for enhancing efficiency further, and describe the next development where explicit water will replace implicit solvation.

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Section: Theory and Methodologymentioning

confidence: 99%

Section: I1 the Role Of Free Energy In Structural Biologymentioning

confidence: 99%

Section: I1 the Role Of Free Energy In Structural Biologymentioning

confidence: 99%

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Stability of the Free and Bound Microstates of a Mobile Loop of α-Amylase Obtained from the Absolute Entropy and Free Energy

Cheluvaraja

Meirovitch

2007

J. Chem. Theory Comput.

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“…ATase has the highest sequence identity (42%) with CGTases (14), and the protein is most likely organized in five domains (A-E), similar to CGTases. The substrate of ATase, acarbose, is a pseudotetrasaccharide, composed of the C7-cyclitol valienamine, 4-amino-4,6-dideoxyglucose, and maltose (Figure 3) (20)(21)(22)(23)(24)(25). In ATase, in contrast, acarbose must bind at the -2 to +2 subsites to allow catalysis of the acarviosyl transferase reaction (Figure 1).…”

mentioning

confidence: 99%

“…Protein crystallography studies have shown that acarbose inhibits R-amylase family enzymes by binding in the active site with the acarviosyl moiety at the -1 and +1 subsites (20)(21)(22)(23)(24)(25). In ATase, in contrast, acarbose must bind at the -2 to +2 subsites to allow catalysis of the acarviosyl transferase reaction (Figure 1).…”

mentioning

confidence: 99%

Single Amino Acid Mutations Interchange the Reaction Specificities of Cyclodextrin Glycosyltransferase and the Acarbose-Modifying Enzyme Acarviosyl Transferase

2004

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Single amino acid mutations interchange the reaction specificities of cyclodextrin glycosyltransferase and the acarbose-modifying enzyme acarviosyl transferase Leemhuis, H.; Wehmeier, U.F.; Dijkhuizen, Lubbert Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. D-42079 Wuppertal, Germany ReceiVed May 15, 2004; ReVised Manuscript ReceiVed July 22, 2004 ABSTRACT: Acarviosyl transferase (ATase) from Actinoplanes sp. SE50/110 is a bacterial enzyme that transfers the acarviosyl moiety of the diabetic drug acarbose to sugar acceptors. The enzyme exhibits 42% sequence identity with cyclodextrin glycosyltransferases (CGTase), and both enzymes are members of the R-amylase family, a large clan of enzymes acting on starch and related compounds. ATase is virtually inactive on starch, however. In contrast, ATase is the only known enzyme to efficiently use acarbose as substrate (2 µmol min -1 mg -1 ); acarbose is a strong inhibitor of CGTase and of most other R-amylase family enzymes. This distinct reaction specificity makes ATase an interesting enzyme to investigate the variation in reaction specificity of R-amylase family enzymes. Here we show that a G140H mutation in ATase, introducing the typical His of the conserved sequence region I of the R-amylase family, changed ATase into an enzyme with 4-R-glucanotransferase activity (3.4 µmol min -1 mg -1 ). Moreover, this mutation introduced cyclodextrin-forming activity into ATase, converting 2% of starch into cyclodextrins. The opposite experiment, removing this typical His side chain in CGTase (H140A), introduced acarviosyl transferase activity in CGTase (0.25 µmol min -1 mg -1 ).The R-amylase family, or glycoside hydrolase family 13 (1), is a large family of enzymes acting on R-glycosidic bonds in starch and related compounds (2). About 20 different reaction specificities have been identified in this family, including hydrolysis of R-(1,4)-and R-(1,6)-glycosidic linkages (e.g., R-amylase and isoamylase, respectively), as well as the formation of R-(1,4)-and R-(1,6)-glycosidic bonds (e.g., amylosucrase, acarviosyl transferase, cyclodextrin glycosyltransferase, and branching enzyme, respectively; Figure 1) (2, 3). All members use an R-retaining double displacement mechanism (4) in which reactions proceed via a covalent glycosyl-enzyme intermediate (5). Glycosidic bond cleavage occurs between subsites -1 and +1 ( Figure 2A), and after cleavage the glycosyl reaction intermediate re...

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X‐Ray Crystallography in Drug Discovery

Livingston¹,

Buchanan²,

D’Amico³

et al. 2003

Burger's Medicinal Chemistry and Drug Discovery

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The focus of this chapter is the methods, recent advances, and the applications of X‐ray protein crystallography in the discovery of new drug targets and candidate drugs. It begins with a basic description of the various steps involved in solving a structure, including recent advances in technique and technology, and the major challenges that are faced in executing the process. The underlying theory, various crystallization methods, data collection equipment and techniques, and computational reduction of the data to give the final structure are all covered in this section. The accessible databases that contain large collections of structures are also described. The application to drug discovery is then briefly addressed with a discussion of co‐crystallization methods and issues, which is followed by a comprehensive table enumerating the published structures of the known drug targets and close homologs. Applications to discovering and validating protein targets of therapeutic relevance are then covered in a section on the very new field of structural genomics. Genome annotation by structural homology, elucidating pathways and the potential for the rational design of multitarget drugs, and advances in the field of protein structure modeling that are enabled by crystallographic databases are described and exemplified with very recent results from the field.

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Carbohydrate and Protein-based Inhibitors of Porcine Pancreatic α-Amylase: Structure Analysis and Comparison of Their Binding Characteristics

Cited by 117 publications

References 37 publications

Stability of the Free and Bound Microstates of a Mobile Loop of α-Amylase Obtained from the Absolute Entropy and Free Energy

Stability of the Free and Bound Microstates of a Mobile Loop of α-Amylase Obtained from the Absolute Entropy and Free Energy

Single Amino Acid Mutations Interchange the Reaction Specificities of Cyclodextrin Glycosyltransferase and the Acarbose-Modifying Enzyme Acarviosyl Transferase

X‐Ray Crystallography in Drug Discovery

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