FOLD TYPE II PYRIDOXAL 5 `-PHOSPHATE DEPENDENT ENZYMES: STRUCTURE, SUBSTRATE RECOGNITION AND CATALYSIS

Enzymes utilizing pyridoxal 5'-phosphate dependent mechanism for catalysis are observed in all cellular forms of living organisms. PLP-dependent enzymes catalyze a wide variety of reactions involving amino acid substrates and their analogs. Structurally, these ubiquitous enzymes have been classified into four major fold types. We have carried out investigations on the structure and function of fold type I enzymes serine hydroxymethyl transferase and acetylornithine amino transferase, fold type n enzymes catabolic threonine deaminase, D-serine deaminase, D-cysteine desulfhydrase and diaminopropionate ammonia lyase. This review summarizes the major findings of investigations on fold type II enzymes in the context of similar studies on other PLP-dependent enzymes. Fold type II enzymes participate in pathways of both degradation and synthesis of amino acids. Polypeptide folds of these enzymes, features of their active sites, nature of interactions between the cofactor and the polypeptide, oligomeric structure, catalytic activities with various ligands, origin of specificity and plausible regulation of activity are briefly described. Analysis of the available crystal structures of fold type II enzymes revealed five different classes. The dimeric interfaces found in these enzymes vary across the classes and probably have functional significance.

Exploring the Consequences of a Representative ``Disallowed'' Conformation of Aib on a 3(10)-Helical Fold

The structural effects of a representative disallowed conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D (H-1, C-13) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)-helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib*-Oxa) of 2, in a conformation (phi, =180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)-helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations. (c) 2014 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 104: 21-36, 2015.

Exploring the Consequences of a Representative ``Disallowed'' Conformation of Aib on a 3(10)-Helical Fold

The structural effects of a representative ``disallowed'' conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D (H-1, C-13) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)- helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib(star)-Oxa) of 2, in a conformation (phi, psi = 180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)- helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations. (C) 2014 Wiley Periodicals, Inc. Biopolymers

Exploring the Consequences of a Representative ``Disallowed'' Conformation of Aib on a 3(10)-Helical Fold

The structural effects of a representative ``disallowed'' conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D (H-1, C-13) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)- helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib(star)-Oxa) of 2, in a conformation (phi, psi = 180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)- helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations. (C) 2014 Wiley Periodicals, Inc. Biopolymers

Evolutionary and structural analyses of heterodimeric proteins composed of subunits with same fold

Heterodimeric proteins with homologous subunits of same fold are involved in various biological processes. The objective of this study is to understand the evolution of structural and functional features of such heterodimers. Using a non-redundant dataset of 70 such heterodimers of known 3D structure and an independent dataset of 173 heterodimers from yeast, we note that the mean sequence identity between interacting homologous subunits is only 23-24% suggesting that, generally, highly diverged paralogues assemble to form such a heterodimer. We also note that the functional roles of interacting subunits/domains are generally quite different. This suggests that, though the interacting subunits/domains are homologous, the high evolutionary divergence characterize their high functional divergence which contributes to a gross function for the heterodimer considered as a whole. The inverse relationship between sequence identity and RMSD of interacting homologues in heterodimers is not followed. We also addressed the question of formation of homodimers of the subunits of heterodimers by generating models of fictitious homodimers on the basis of the 3D structures of the heterodimers. Interaction energies associated with these homodimers suggests that, in overwhelming majority of the cases, such homodimers are unlikely to be stable. Majority of the homologues of heterodimers of known structures form heterodimers (51.8%) and a small proportion (14.6%) form homodimers. Comparison of 3D structures of heterodimers with homologous homodimers suggests that interfacial nature of residues is not well conserved. In over 90% of the cases we note that the interacting subunits of heterodimers are co-localized in the cell. Proteins 2015; 83:1766-1786. (c) 2015 Wiley Periodicals, Inc.

Physiological role of FolD (methylenetetrahydrofolate dehydrogenase), FchA (methenyltetrahydrofolate cyclohydrolase) and Fhs (formyltetrahydrofolate synthetase) from Clostridium perfringens in a heterologous model of Escherichia coli

Most organisms possess bifunctional FolD 5,10-methylenetetrahydrofolate (5,10-CH2-THF) dehydrogenase-cyclohydrolase] to generate NADPH and 10-formyltetrandrofolate (10-CHO-THF) required in various metabolic steps. In addition, some organisms including Clostridium perfringens possess another protein, Fhs (formyltetrahydrofolate synthetase), to synthesize 10-CHO-THF. Here, we show that unlike the bifunctional FolD of Escherichia coli (Eco FolD), and contrary to its annotated bifunctional nature, C. perfringens FolD (Cpe FoID) is a monofunctional 5,10-CH2-THF dehydrogenase. The dehydrogenase activity of Cpe FoID is about five times more efficient than that of Eco FolD. The 5,10-methenyltetrahydrofolate (5,10-CH+-THF) cyclohydrolase activity in C. perfringens is provided by another protein, FchA (5,10-CH+-THF cyclohydrolase), whose cyclohydrolase activity is similar to 10 times more efficient than that of Eco FolD. Kinetic parameters for Cpe Fhs were also determined for utilization of all of its substrates. Both Cpe FoID and Cpe FchA are required to substitute for the single bifunctional FolD in E. coli. The simultaneous presence of Cpe FoID and Cpe FchA is also necessary to rescue an E coli folD deletion strain (harbouring Cpe Fhs support) for its formate and glycine auxotrophies, and to alleviate its susceptibility to trimethoprim (an antifolate drug) or UV light. The presence of the three clostridial proteins (FolD, FchA and Fhs) is required to maintain folate homeostasis in the cell.

Controllable group velocity of the probe light in a Lambda-type system with two fold levels

The group velocities of the probe laser field are studied in a A-type system where one lower state has two fold levels coupled by a control field. It is found that the interaction of double dark states leads to controllable group velocity of the probe field in this system. It can be easily realized, due to the interacting double dark resonances, that one of the group velocities at transparency positions is much slower than the other by tuning the control field to be off resonance. In particular, when the control field is on resonance. we can obtain two equal slow group velocities with a broader EIT width, which provides potential applications in quantum storage and retrieval of light. (c) 2005 Elsevier B.V. All rights reserved.

Enhancement of stimulated emission in 12-fold symmetric quasi-crystals

In this paper, we investigate the stimulated emission in a 12-fold symmetric quasiperiodic photonic crystal. The stimulated emission peaks in the quasiperiodic photonic crystal are more abundant and stronger than those in a periodic crystal. Also, more stimulated emission peaks appear as the crystal size and the gain increase, and some frequencies of the peaks are independent of the incident direction. These phenomena may be due to wave localization in the quasiperiodic photonic crystal.

Characteristics of a 4-fold segmented clover detectore

Four high-purity germanium 4-fold segmented Clover detectors have been applied in the experiment of neutron-rich nucleus N-21. The performance of those, four Clovers have been tested with radioactive sources and in-beam experiments and the main results including energy resolution, peak-to-total ratios, the variation of the hit pattern distribution in difficult crystals of one Clover detector with the energy of gamma ray, and absolute full energy peak detection efficiency curve, were presented.

2-D and 3-D processing and interpretation of multi-fold ground penetrating radar data:a case history from an archaeological site

A 2.5-D and 3-D multi-fold GPR survey was carried out in the Archaeological Park of Aquileia (northern Italy). The primary objective of the study was the identification of targets of potential archaeological interest in an area designated by local archaeological authorities. The second geophysical objective was to test 2-D and 3-D multi-fold methods and to study localised targets of unknown shape and dimensions in hostile soil conditions. Several portions of the acquisition grid were processed in common offset (CO), common shot (CSG) and common mid point (CMP) geometry. An 8×8 m area was studied with orthogonal CMPs thus achieving a 3-D subsurface coverage with azimuthal range limited to two normal components. Coherent noise components were identified in the pre-stack domain and removed by means of FK filtering of CMP records. Stack velocities were obtained from conventional velocity analysis and azimuthal velocity analysis of 3-D pre-stack gathers. Two major discontinuities were identified in the area of study. The deeper one most probably coincides with the paleosol at the base of the layer associated with activities of man in the area in the last 2500 years. This interpretation is in agreement with the results obtained from nearby cores and excavations. The shallow discontinuity is observed in a part of the investigated area and it shows local interruptions with a linear distribution on the grid. Such interruptions may correspond to buried targets of archaeological interest. The prominent enhancement of the subsurface images obtained by means of multi-fold techniques, compared with the relatively poor quality of the conventional single-fold georadar sections, indicates that multi-fold methods are well suited for the application to high resolution studies in archaeology.

Effect of the fold surface of the lamellae on the behavior of the trapped radicals in irradiated polyamide-1010

Two types of macromolecular free radicals -CH2CONHCHCH2- (a) and -CH2C=O (b) trapped in irradiated Polyamide-1010 (PA1010) and PA1010 filled with neodymium oxide (Nd2O3) were characterized by an ESR approach. It was found out that a was mainly trapped in the fold surface of the lamellae and b in the amorphous phase. This result suggested that trapped radicals mainly existed in the noncrystalline phases. The effect of the fold surface area of the lamellae on the behavior of the trapped radicals are discussed in this article. Whether for the specimens with similar crystallinities but different crystallite sizes or for those with the same concentration of neodymium oxide but different crystallinities, radical a exists dominantly in a specimen with a larger fold surface area of the lamellae. Under a certain circumstance, radical a can transform into radical b for a specimen with a larger fold surface area of the lamellae. It means that the fold surface area of the lamellae plays an important role in the transformation of radical a to b. (C) 1998 John Wiley & Sons, Inc.

Influence of the fold surface of the lamellae on radiation effects - Research on irradiated polyamide-1010 containing heterogeneous nuclei

Irradiated polyamide-1010 (PA1010) and PA1010 containing 0.5% (wt) heterogeneous nuclei were studied by ESR, WAXD, DSC and the determination of gel fractions. The fold surface of the lamellae plays an important role in the effects of radiation on crystalline PA1010. The results show that the direct radiation effects on both samples vary, while after being heated to 220 degrees C, the final radiation effects are identical, regardless of the difference in the amount of the fold surface of the lamellae. The post-radiation effects result predominantly from the fold surface.