Alpha-amylase tertiary structures and their interactions with polysaccharides

The gut microbiome of nonhuman primates: Lessons in ecology and evolution

The mammalian gastrointestinal (GI) tract is home to trillions of bacteria that play a substantial role in host metabolism and immunity. While progress has been made in understanding the role that microbial communities play in human health and disease, much less attention has been given to host-associated microbiomes in nonhuman primates (NHPs). Here we review past and current research exploring the gut microbiome of NHPs. First, we summarize methods for characterization of the NHP gut microbiome. Then we discuss variation in gut microbiome composition and function across different NHP taxa. Finally, we highlight how studying the gut microbiome offers new insights into primate nutrition, physiology, and immune system function, as well as enhances our understanding of primate ecology and evolution. Microbiome approaches are useful tools for studying relevant issues in primate ecology. Further study of the gut microbiome of NHPs will offer new insight into primate ecology and evolution as well as human health.

Synthetic Assembly of Bifluorescence-Labeled Glycopolymers as Substrates for Assaying α-Amylase by Resonance Energy Transfer

To meet the need for a convenient substrate for sensitive and continuous assay for α-amylase, we developed a fluorescence resonance energy transfer (FRET)-based polymer substrate. Radical copolymerization of FRET-component monomers in different ratios of fluorogenic donor and acceptor was utilized to prepare such polymers. A glycomonomer as a fluorogenic donor was derived from naphthylmethylated maltotetraose, and a dansyl derivative monomer was used as an acceptor. Their mixture and acryl amide were copolymerized in a typical radical polymerization to yield a bifluorescence-labeled polymer in good yield. All of the polymers showed effective FRET and were used for the continuous assay of human salivary α-amylase. The time course of α-amylase reactions led to the apparent kinetic parameters of K_m = 4 μM and V_max = 0.29 nmol/min. The results strongly suggested that FRET-sensitive polymers are conveniently accessible and applicable for the sensitive determination of biochemical events.

Subsite mapping of porcine pancreatic alpha-amylase I and II using 4-nitrophenyl-alpha-maltooligosaccharides

The catalytic efficiency (kcat/Km) and the cleaved bond distribution for the nitrophenylated maltooligosaccharides, p-NPGlcn (2 < or = n < or = 7) hydrolysed by porcine pancreatic alpha-amylase isozymes I and II were determined. The subsite affinities (Ai) were calculated from the p-NPGlcn (4 < or = n < or = 7) hydrolysis data. Five subsites (-3 to 2) bind glucosidic residues with a positive affinity. No additional subsites could be detected both at the reducing end (3, 4, 5) and at the nonreducing end (-4, -5, -6). The energetic profiles of both isozymes are similar. The energetic profile of PPA differs from other alpha-amylases by having both a small number of subsites, and a catalytic subsite with a high positive affinity. Excellent agreement was found between observed catalytic efficiency values and those calculated from the subsite affinities.

Multi-functional roles of a histidine residue in human pancreatic alpha-amylase

Functional roles of histidine residues at the active site in human pancreatic alpha-amylase were examined by protein engineering. Three histidine residues at 101, 201, and 299 were converted to asparagine residues, respectively. It was found that His201 played multi-functional roles concerning so many functions; substrate binding, control of optimum pH, change in substrate specificity, activation by chloride ion, and inhibition by a proteinaceous inhibitor.

Effect of limited proteolysis in the 8th loop of the barrel and of antibodies on porcine pancreas amylase activity

The porcine pancreatic alpha-amylase is a (beta/alpha)8-barrel protein, containing domains A and B (peptide sequence 1-403) and a distinct C-domain (peptide sequence 404-496). Separation of the terminal C-domain from the A and B domains has been attempted by limited proteolysis in the hinge region. Subtilisin was found to hydrolyse amylase between residues 369 and 370 situated in the loop between the eighth beta-strand and alpha-helix. The cleaved amylase was isolated by chromatofocusing and found to retain about 60% of the activity of the native enzyme, while the isolated fragments were inactive. Antigen binding fragments prepared from polyclonal antibodies to native amylase and the CNBr-fragment P1 (peptide sequence 395-496) respectively, were tested for influence on the enzyme activity. Antibodies directed against P1 had no effect whereas antibodies against the peptide sequence 1-394 and amylase respectively inhibited hydrolysis of substrates having four or more glucose residues but not of shorter oligomaltosides. Crystallographic analysis revealed that changes in the region of residue 369 might affect the conformation of the active site as well as of a second binding site. This site, located on the enzyme surface, is proposed to be required for the hydrolysis of larger substrates.

Hydrophobic cluster analysis of the primary sequences of alpha-amylases

The amino acid sequences of 18 alpha-amylases have been compared by hydrophobic cluster analysis. The method was first calibrated with two alpha-amylases (Aspergillus oryzae and pig pancreas) whose three-dimensional structures are known. It was then applied to the other alpha-amylases resulting in straightforward sequence alignments which could be used for structure prediction. It was found that all alpha-amylases which were investigated display the same basic super-secondary structure with a (beta alpha)8 barrel. Most of the secondary structure elements of the protein cores could be assigned to segments of the amino acid sequences. In addition, six sub-families could be identified, based upon specific similarities occurring in the variable regions of alpha-amylases.