Influence of phosphate ligands in abolishing the conformational difference between ribonuclease A and its acid-denatured derivative

The initial structural alteration of RNAase A due to acid denaturation (0.5 N HCl, 30 degrees C) that accompanies deamidation (without altering enzymic activity) has been dectected by spectrophotometric titration, fluorescence and ORD/CD measurements. It is shown that acid treated RNAase A has an altered conformation at neutral pH, 25 degrees C. This is characterized by the increased accessibility of buried tyrosine residue(s) towards the solvent. The most altered conformation of RNAase A is found in the 10 h acid-treated derivative. This has about 1.5 additional exposed tyrosine residues and a lesser amount of secondary structure than RNAase A. All three methods (titration, fluorescence and CD) established that the structural transition of RNAase A is biphasic. The first phase occurs within 1 h and the resulting subtle conformational change is constant up to 7 h. Following this, after the release of 0.55 mol of ammonia, the major conformational change begins. The altered conformation of the acid-denatured RNAase A could be reversed completely to the native state through a conformational change induced by substrate analogs like 2'- or 3'-CMP. Thus the monodeamidated derivative isolated from the acid-denatured RNAase A by phosphate is very similar to RNAase A in over-all conformation. The results suggest the possibility of flexibility in the RNAase A molecule that does not affect its catalytic activity, as probed through the tyrosine residues.

Beta-turns in nascent procollagen are sites of posttranslational enzymatic hydroxylation of proline

The selective hydroxylation of proline residues in nascent procollagen chains by prolyl hydroxylase (EC 1.14.11.2) can be understood in terms of the conformational feature of the -Pro-Gly-segments in linear peptides and globular proteins. The folded beta-turn conformation in such segments appears to be the conformational requirement for proline hydroxylation. The available data on the hydroxylation of native and synthetic substrates of prolyl hydroxylase are explained on the basis of the extent of beta-turn formation in them. Taken in conjunction with the conformational features of the hydroxyproline residue, our results bring out the conformational reason for the posttranslational proline hydroxylation which, it is proposed, leads to the "straightening" of the beta-turn segments into the linear triple-helical conformation.

Molecular conformation of alamethicin in dimethylsulfoxide solution A two-dimensional n.m.r. study

The solution conformation of alamethicin, a 20-residue antibiotic peptide, has been investigated using two-dimensional n.m.r. spectroscopy. Complete proton resonance assignments of this peptide have been carried out using COSY, SUPERCOSY, RELAY COSY and NOESY two-dimensional spectroscopies. Observation of a large number of nuclear Overhauser effects between sequential backbone amide protons, between backbone amide protons and CβH protons of preceding residues and extensive intramolecular hydrogen bonding patterns of NH protons has established that this polypeptide is in a largely helical conformation. This result is in conformity with earlier reported solid state X-ray results and a recent n.m.r. study in methanol solution (Esposito et al. (1987) Biochemistry26, 1043-1050) but is at variance with an earlier study which favored an extended conformation for the C-terminal half of alamethicin (Bannerjee et al.

Some implications of an alternative structure for DNA

We have constructed a space-filling (Corey-Pauling-Koltun) model of an alternative structure for DNA. This structure is not a double helix, but consists of a pair of polynucleotide strands lying side by side and held together by Watson-Crick base pairing. Each of the two strands has alternating right- and left-handed helical segments approximately five base pairs in length. Sugar residues in alternating segments along a strand point in opposite directions. A structure slightly different from the present one proposed earlier by ourselves and another group and in which sugars in a strand all point in the same direction is ruled out. The present structure yields natural solutions to the problems of supercoiling of DNA and of strand separation during DNA replication. This model is energetically more favorable than the double helix.

Discovery of oxidative enzymes for food engineering : Tyrosinase and sulfhydryl oxidase

Enzymes offer many advantages in industrial processes, such as high specificity, mild treatment conditions and low energy requirements. Therefore, the industry has exploited them in many sectors including food processing. Enzymes can modify food properties by acting on small molecules or on polymers such as carbohydrates or proteins. Crosslinking enzymes such as tyrosinases and sulfhydryl oxidases catalyse the formation of novel covalent bonds between specific residues in proteins and/or peptides, thus forming or modifying the protein network of food. In this study, novel secreted fungal proteins with sequence features typical of tyrosinases and sulfhydryl oxidases were iden-tified through a genome mining study. Representatives of both of these enzyme families were selected for heterologous produc-tion in the filamentous fungus Trichoderma reesei and biochemical characterisation. Firstly, a novel family of putative tyrosinases carrying a shorter sequence than the previously characterised tyrosinases was discovered. These proteins lacked the whole linker and C-terminal domain that possibly play a role in cofactor incorporation, folding or protein activity. One of these proteins, AoCO4 from Aspergillus oryzae, was produced in T. reesei with a production level of about 1.5 g/l. The enzyme AoCO4 was correctly folded and bound the copper cofactors with a type-3 copper centre. However, the enzyme had only a low level of activity with the phenolic substrates tested. Highest activity was obtained with 4-tert-butylcatechol. Since tyrosine was not a substrate for AoCO4, the enzyme was classified as catechol oxidase. Secondly, the genome analysis for secreted proteins with sequence features typical of flavin-dependent sulfhydryl oxidases pinpointed two previously uncharacterised proteins AoSOX1 and AoSOX2 from A. oryzae. These two novel sulfhydryl oxidases were produced in T. reesei with production levels of 70 and 180 mg/l, respectively, in shake flask cultivations. AoSOX1 and AoSOX2 were FAD-dependent enzymes with a dimeric tertiary structure and they both showed activity on small sulfhydryl compounds such as glutathione and dithiothreitol, and were drastically inhibited by zinc sulphate. AoSOX2 showed good stabil-ity to thermal and chemical denaturation, being superior to AoSOX1 in this respect. Thirdly, the suitability of AoSOX1 as a possible baking improver was elucidated. The effect of AoSOX1, alone and in combi-nation with the widely used improver ascorbic acid was tested on yeasted wheat dough, both fresh and frozen, and on fresh water-flour dough. In all cases, AoSOX1 had no effect on the fermentation properties of fresh yeasted dough. AoSOX1 nega-tively affected the fermentation properties of frozen doughs and accelerated the damaging effects of the frozen storage, i.e. giving a softer dough with poorer gas retention abilities than the control. In combination with ascorbic acid, AoSOX1 gave harder doughs. In accordance, rheological studies in yeast-free dough showed that the presence of only AoSOX1 resulted in weaker and more extensible dough whereas a dough with opposite properties was obtained if ascorbic acid was also used. Doughs containing ascorbic acid and increasing amounts of AoSOX1 were harder in a dose-dependent manner. Sulfhydryl oxidase AoSOX1 had an enhancing effect on the dough hardening mechanism of ascorbic acid. This was ascribed mainly to the produc-tion of hydrogen peroxide in the SOX reaction which is able to convert the ascorbic acid to the actual improver dehydroascorbic acid. In addition, AoSOX1 could possibly oxidise the free glutathione in the dough and thus prevent the loss of dough strength caused by the spontaneous reduction of the disulfide bonds constituting the dough protein network. Sulfhydryl oxidase AoSOX1 is therefore able to enhance the action of ascorbic acid in wheat dough and could potentially be applied in wheat dough baking.

Stereochemistry of collagen

This review article, based on a lecture delivered in Madras in 1985, is an account of the author's experience in the working out of the molecular structure and conformation of the collagen triple-helix over the years 1952–78. It starts with the first proposal of the correct triple-helix in 1954, but with three residues per turn, which was later refined in 1955 into a coiled-coil structure with approximately 3.3 residues per turn. The structure readily fitted proline and hydroxyproline residues and required glycine as every third residue in each of the three chains. The controversy regarding the number of hydrogen bonds per tripeptide could not be resolved by X-ray diffraction or energy minimization, but physicochemical data, obtained in other laboratories during 1961–65, strongly pointed to two hydrogen bonds, as suggested by the author. However, it was felt that the structure with one straight NH … O bond was better. A reconciliation of the two was obtained in Chicago in 1968, by showing that the second hydrogen bond is via a water molecule, which makes it weaker, as found in the physicochemical studies mentioned above. This water molecule was also shown, in 1973, to take part in further cross-linking hydrogen bonds with the OH group of hydroxyproline, which occurred always in the location previous to glycine, and is at the right distance from the water. Thus, almost all features of the primary structure, X-ray pattern, optical and hydrodynamic data, and the role of hydroxyproline in stabilising the triple helical structure, have been satisfactorily accounted for. These also lead to a confirmation of Pauling's theory that vitamin C improves immunity to diseases, as explained in the last section.

Interaction of water molecules in non-identical protein structures

The interaction of the protein atoms with the surrounding water oxygen atoms has been computed for 392 protein chains from 369 protein structures belonging to 90% non-homologous high resolution (<= 1.5 angstrom) protein Structures with a crystallographic R-factor <= 20%. The percentage composition of the polar atoms is found to be 36.3%. An average of 82.55% of water oxygen atoms are found to be in the primary hydration shell and 15.12% in the secondary hydration shell. The average Percentage of interactions of water oxygen atoms with the polar atoms of the main chain and side chain are 54% and 46%. respectively. The interaction of the acidic residues, aspartate and glutamate, with the water oxygen atoms is more when compared to that of the other residues.

Studies on active site mutants of P-falciparum adenylosuccinate synthetase: Insights into enzyme catalysis and activation

Adenylosuccinate synthetase catalyzes a reversible reaction utilizing IMP, GTP and aspartate in the presence of Mg2+ to form adenylosuccinate, GDP and inorganic phosphate. Comparison of similarly liganded complexes of Plasmodium falciparum, mouse and Escherichia coil AdSS reveals H-bonding interactions involving nonconserved catalytic loop residues (Asn429, Lys62 and Thr307) that are unique to the parasite enzyme. Site-directed mutagenesis has been used to examine the role of these interactions in catalysis and structural organization of P. falciparum adenylosuccinate synthetase (PfAdSS). Mutation of Asn429 to Val, Lys62 to Leu and Thr307 to Val resulted in an increase in K-m values for IMP, GTP and aspartate, respectively along with a 5 fold drop in the k(cat) value for N429V mutant suggesting the role of these residues in ligand binding and/or catalysis. We have earlier shown that the glycolytic intermediate, fructose 1,6 bisphosphate, which is an inhibitor of mammalian AdSS is an activator of the parasite enzyme. Enzyme kinetics along with molecular docking suggests a mechanism for activation wherein F16BP seems to be binding to the Asp loop and inducing a conformation that facilitates aspartate binding to the enzyme active site. Like in other AdSS, a conserved arginine residue (Arg155) is involved in dimer crosstalk and interacts with IMP in the active site of the symmetry related subunit of PfAdSS. We also report on the iochemical characterization of the arginine mutants (R155L, R155K and R155A) which suggests that unlike in E. coil AdSS, Arg155 in PfAdSS influences both ligand binding and catalysis. (C) 2010 Elsevier B.V. All rights reserved.

Synthetic peptide models for the redox-active disulfide loop of glutaredoxin. Conformational studies

Two cyclic peptide disulfides Boc-Cys-Pro-X-Cys-NHMe (X = L-Tyr or L-Phe) have been synthesized as models for the 14-membered redox-active disulfide loop of glutaredoxin. 'H NMR studies at 270 MHz in chloroform solutions establish a type I 0-turn conformation for the Pro-X segment in both peptides, stabilized by a 4-1 hydrogen bond between the Cys(1) CO and Cys(4) NH groups. Nuclear Overhauser effects establish that the aromatic ring in the X = Phe peptide is oriented over the central peptide unit. In dimethyl sulfoxide solutions two conformational species are observed in slow exchange on the NMR time scale, for both peptides. These are assigned to type I and type I1 p-turn structures with -Pro-Tyr(Phe)-as the corner residues. The structural assignments are based on correlation of NMR parameters with model 14-membered cyclic cystine peptides with Pro-X spacers. Circular dichroism studies based on the -S-Sn- u* transition suggest a structural change in the disulfide bridge with changing solvent polarity, establishing conformational coupling between the peptide backbone and the disulfide linkage in these systems.

Confirmation of pauling's theory that vitamin C improves immunity to infection

It is pointed out that the complement Clq, associated with the immune response system, has a part containing about 80 residues with a collagen-like sequence, with Gly at every third location and having also a number of Hyp and Hyl residues in locations before Gly, and that it takes the triple-helical conformation characteristic of collagen. As with collagen biosynthesis, ascorbic acid is therefore expected to be required for its production. Also, collagen itself, in the extracellular matrix, is connected with the fibroblast surface protein (FSP), whose absence leads to cell proliferation, and whose addition leads to suppression of malignancy in tissue culture. All these show the great importance of vitamin C for resistance to diseases, and even to cancer, as has been widely advocated by Pauling.

Crystal Structure of Staphylococcus aureus Metallopeptidase (Sapep) Reveals Large Domain Motions between the Manganese-bound and Apo-states

Proteases belonging to the M20 family are characterized by diverse substrate specificity and participate in several metabolic pathways. The Staphylococcus aureus metallopeptidase, Sapep, is a member of the aminoacylase-I/M20 protein family. This protein is a Mn2+-dependent dipeptidase. The crystal structure of this protein in the Mn2+-bound form and in the open, metal-free state suggests that large interdomain movements could potentially regulate the activity of this enzyme. We note that the extended inactive conformation is stabilized by a disulfide bond in the vicinity of the active site. Although these cysteines, Cys(155) and Cys(178), are not active site residues, the reduced form of this enzyme is substantially more active as a dipeptidase. These findings acquire further relevance given a recent observation that this enzyme is only active in methicillin-resistant S. aureus. The structural and biochemical features of this enzyme provide a template for the design of novel methicillin-resistant S. aureus-specific therapeutics.

Generation of a Manganese Specific Restriction Endonuclease with Nicking Activity

A typical feature of type II restriction endonucleases (REases) is their obligate sequence specificity and requirement for Mg2+ during catalysis. R.KpnI is an exception. Unlike most other type II REases, the active site of this enzyme can accommodate Mg2+, Mn2+, Ca2+, or Zn2+ and cleave DNA. The enzyme belongs to the HNH superfamily of nucleases and is characterized by the presence of a beta beta alpha-Me finger motif. Residues D148, H149, and Q175 together form the HNH active site and are essential for Mg2+ binding and catalysis. The unique ability of the enzyme to cleave DNA in the presence of different metal ions is exploited to generate mutants that are specific to one particular metal ion. We describe the generation of a Mn2+-dependent sequence specific endonuclease, defective in DNA cleavage with Mg2+ and other divalent metal ions. In the engineered mutant, only Mn2+ is selectively bound at the active site, imparting Mn2+-mediated cleavage. The mutant is impaired in concerted double-stranded DNA cleavage, leading to accumulation of nicked intermediates. The nicking activity of the mutant enzyme is further enhanced by altered reaction conditions. The active site fluidity of R Eases allowing flexible accommodation of catalytic cofactors thus forms a basis for engineering selective metal ion-dependent REase additionally possessing nicking activity.

Identifying N60D mutation in omega subunit of Escherichia coli RNA polymerase by bottom-up proteomic approach

Escherichia coli RNA polymerase is a multi-subunit enzyme containing alpha(2)beta beta'omega sigma, which transcribes DNA template to intermediate RNA product in a sequence specific manner. Although most of the subunits are essential for its function, the smallest subunit omega (average molecular mass similar to 10,105 Da) can be deleted without affecting bacterial growth. Creating a mutant of the omega subunit can aid in improving the understanding of its role. Sequencing of rpoZ gene that codes for omega subunit from a mutant variant suggested a substitution mutation at position 60 of the protein: asparagine (N) -> aspartic acid (D). This mutation was verified at the protein level by following a typical mass spectrometry (MS) based bottom-up proteomic approach. Characterization of in-gel trypsin digested samples by reverse phase liquid chromatography (LC) coupled to electrospray ionization (ESI)-tandem mass spectrometry (MS/MS) enabled in ascertaining this mutation. Electron transfer dissociation (ETD) of triply charged (M + 3H)(3+)] tryptic peptides (residues 53-67]), EIEEGLINNQILDVR from wild-type and EIEEGLIDNQILDVR from mutant, facilitated in unambiguously determining the site of mutation at residue 60.

Isolation and characterization of heat-stable allergens from shrimp (Penaeus indicus)

Shrimp are among the more common causes of immediate hypersensitivity reactions to food. To characterize better the allergenic substances within shrimp, extracts from heated shrimp were systematically examined with solid-phase radioimmunoassay and sera from patients clinically sensitive to shrimp. Two heat-stable protein allergens, designated as Sa-I and Sa-II, were identified from boiled shrimp (Penaeus indicus) extracts. Sa-I was isolated by ultrafiltration, Sephadex G-25, and diethylaminoethyl-Sephacel chromatography, whereas Sa-II, the major allergen, was purified by successive chromatography on diethylaminoethyl-Sephacel, Bio-Gel P-200, and Sepharose 4B columns. Sa-I, which was homogeneous by polyacrylamide gel electrophoresis (PAGE), elicited a single band on sodium dodecyl sulfate-PAGE corresponding to a molecular weight of 8.2 kd. Sa-II was also found to be homogeneous by PAGE, crossed immunoelectrophoresis, and immunoblotting. On sodium dodecyl sulfate-PAGE, it elicited a single band with a molecular weight of 34 kd. Sa-II was found to contain 301 amino acid residues and was particularly rich in glutamate/glutamine and aspartate/asparagine. Solid-phase radioimmunoassay-inhibition studies revealed that Sa-I and Sa-II share 54% of the allergenic epitopes, suggesting that Sa-I may be a fragment of Sa-II.SDS-PAGE, Sodium dodecyl sulfate-polyacrylamide gel electrophoresis; MW, Molecular weight; BSA, Bovine serum albumin; DEAE, Diethylaminoethyl; SPRIA, Solid-phase radioimmunoassay; CIE, Crossed immunoelectrophoresis .

Prediction of protein-protein interactions in dengue virus coat proteins guided by low resolution cryoEM structures

Background: Dengue virus along with the other members of the flaviviridae family has reemerged as deadly human pathogens. Understanding the mechanistic details of these infections can be highly rewarding in developing effective antivirals. During maturation of the virus inside the host cell, the coat proteins E and M undergo conformational changes, altering the morphology of the viral coat. However, due to low resolution nature of the available 3-D structures of viral assemblies, the atomic details of these changes are still elusive. Results: In the present analysis, starting from C alpha positions of low resolution cryo electron microscopic structures the residue level details of protein-protein interaction interfaces of dengue virus coat proteins have been predicted. By comparing the preexisting structures of virus in different phases of life cycle, the changes taking place in these predicted protein-protein interaction interfaces were followed as a function of maturation process of the virus. Besides changing the current notion about the presence of only homodimers in the mature viral coat, the present analysis indicated presence of a proline-rich motif at the protein-protein interaction interface of the coat protein. Investigating the conservation status of these seemingly functionally crucial residues across other members of flaviviridae family enabled dissecting common mechanisms used for infections by these viruses. Conclusions: Thus, using computational approach the present analysis has provided better insights into the preexisting low resolution structures of virus assemblies, the findings of which can be made use of in designing effective antivirals against these deadly human pathogens.