bluuebunny/crossref_metadata_2025 huggingface dataset:
A PHOTOLABILE PROTECTING GROUP FOR THE PHENOLIC HYDROXYL FUNCTION OF TYROSINE
Authors: Amit Boaz , Hazum Eli , Fridkin Mati , Patchornik Abraham
Published: August 2010

The ortho‐nitrobenzyl group (ONBzl) was utilized to protect the phenolic function of the side chain of tyrosine. Optimal conditions for its mild photolytic removal were established. This paper describes the preparation and properties of some (O‐ONBzl)‐tyrosine derivatives of potential value in the synthesis of tyrosine‐containing peptides. Their use in the synthesis of the dipeptide, N‐benzyloxycarbonyl‐L‐tyrosyl‐glycine ethyl ester is presented as an example.
PURIFICATION OF PROTECTED SYNTHETIC PEPTIDES BY PREPARATIVE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY ON SILICA GEL 60
Authors: Gabriel Thomas F. , Jimenez Manuel H. , Felix Arthur M. , Michalewsky Joseph , Meienhofer Johannes
Published: August 2010

A simple preparative system is described for rapid and efficient purification of protected synthetic peptides on a gram scale by high performance liquid chromatography on prepacked silica gel 60 columns. A variety of protected peptides up to tetradecapeptides have been chromatographed at pressures of 50 to 150 psi and obtained in analytically pure form within 2 to 4h. With such commonly used protecting groups as N‐benzyloxycarbonyl (Z), N‐2‐(p‐biphenylyl)‐2‐propyloxycarbonyl (Bpoc), N‐t‐butyloxycarbonyl (Boc), O‐ and S‐t‐butyl (But), and S‐acetamidomethyl (Acm), compounds were sufficiently soluble in chloroform, alcohols, acetic acid, or mixtures of these solvents for column loading. Dimethylformamide was also used as a solvent for loading. Solvent systems for column elution in isocratic, stepwise, or gradient modes were composed of chloroform, isopropanol, ethanol or methanol and acetic acid in ratios that differed for each protected peptide depending on Rf values on t.l.c. plates. A simple chromatograph is described which was self‐assembled using standard instruments commonly in use in most laboratories. A shut‐off valve was designed to prevent loss of material between fractions.
STEREOCHEMICAL RESTRICTIONS ON THE OCCURRENCE OF AMINO ACID RESIDUES IN THE COLLAGEN STRUCTURE
Authors: Bansal M.
Published: August 2010

The primary structure of collagen is characterized by the repeating tripeptide sequence (Gly‐R2‐R3)n. The results of theoretical studies, carried out using contact criteria to compute the stereochemically allowed orientations for various side chains at locations 2 and 3, are reported here. It is found that side chains with only γ‐atoms, as in valine, serine and threonine, or with only one δ‐methyl group, as in isoleucine, can occur equally well at locations 2 and 3, as is actually the case in collagen. Side chains with two Cδ‐atoms, as in leucine and phenyl‐alanine, can also be accommodated at both positions. However, if they occur as R3 their freedom of orientation is severely restricted in the presence of a proline residue as R2 in a neighbouring chain.

If water molecules bound to the chains of the triple helix are assumed to be present, then location 3 is virtually impossible for leucine and phenylalanine residues. Location 2 is, however, unaffected, and their presence as R2 can help to shield the water molecules from disturbance by the solvent medium. This may be the reason for the preferential occurrence of Leu and Phe residues in location 2 in the collagen triplets, although the polypeptides (Gly‐Pro‐Leu)n and (Gly‐Pro‐Phe)n form collagen‐like structures.
SOME OBSERVATIONS ON THE CARBOHYDRATE COMPOSITION OF PURIFIED TRANSFERRIN
Authors: Wong K.‐L. , Regoeczi E.
Published: August 2010

Five subfractions were isolated on DEAE‐cellulose from samples of a commercially available human transferrin preparation and their carbohydrate composition was analysed. Hexosamine, galactose and total hexose were determined in four subfractions and sialic acid in all five.

The data obtained indicate that the excess number of electrophoretic bands observed in transferrin from this source is due to the loss of carbohydrates which only affects sialic acid and none of the other sugar types. The availability of the penultimate galactose residues as the terminal residues in the subfractions deficient in sialic acid was also confirmed by a biological test utilizing the rat liver.

The reason for the gradual loss of sialic acid from transferrin is unknown. Freezing‐thawing and lyophilization did not detectably affect the sialic acid content of purified transferrin. However, free sialic acid did appear in some preparations on storage.

It is concluded that similar changes in the carbohydrate composition of other plasma glycoproteins before, during, or after purification can be expected to exert an adverse effect on their usefulness as metabolic tracers.
SYNTHESIS OF N‐ACETYL‐MURAMYL‐L‐ALANYL‐D‐ISOGLUTAMINE, AN ADJUVANT OF THE IMMUNE RESPONSE, AND OF SOME N‐ACETYL‐MURAMYL‐PEPTIDE ANALOGS
Authors: Lefrancier P. , Choay J. , Derrien M. , Lederman I.
Published: August 2010

A relatively easy synthetic method is reported for the production of the immunoadjuvant glycopeptide, N‐acetyl‐muramyl‐L‐alanyl‐D‐isoglutamine (MDP). Most of the details in this method were also applied to the preparation of some analogs, that were synthesized in order to study structure‐activity relationships.
THERMOPHILIC AMINOPEPTIDASE:
Authors: Deranleau David A. , Zuber Herbert
Published: August 2010

Aminopeptidase I is a membrane‐bound metalloenzyme isolated from B. stearothermophilus which is thermostable and requires Co2+ for activity. The Co, Zn, and metal‐free enzyme were titrated with ANS,* and cooperative binding was noted with the active Co enzyme but not with the Zn (5% active) or apo (inactive) enzymes. There are a number of sites for ANS on each of the three enzyme forms and the agreement between the association constants of the Zn enzyme (identical and independent sites) and the non‐cooperative sites of the Co enzyme suggest that these sites are intrinsically similar. However, binding to the first of these sites in the Co enzyme triggers a cooperative binding of a second molecule of ANS, and this cooperative binding is related to a concomitant decrease in enzymatic activity. The correspondence can be shown by comparison of the inhibition constant for the hydrolysis of Gly‐Leu‐Tyr (Ki‐1 = 13,300 cm3/mmol) and the association constant for the cooperating site (12, 500 cm3/mmol). The significance of these observations is discussed in terms of the nature of the binding sites and the possible consequences of the interactions on the regulation of aminopeptidase I activity.
CONFORMATIONAL STUDIES ON CYCLIC DIPEPTIDES*
Authors: Ramani R. , Sasisekharan V. , Venkatesan K.
Published: August 2010

An analysis of 11 crystal structures of cyclic dipeptides so far reported in the literature is made, with main reference to the internal parameters of these molecules. Preferred conformations of the side chains of cyclic dipeptides with different α‐amino acid residues have been studied by classical energy calculations. The possible conformations of the DKP ring are also studied. The significance of the non‐bonded interaction in deciding the pathway for conformational change has also been investigated. The agreement between theoretical results and experimental observations is quite good, both with respect to the conformation of these molecules as well as the enthalpy difference as estimated from n.m.r. studies between different conformers.
FLUORESCENT LABELLING OF 6–PHOSPHOGLUCONATE DEHYDROGENASE FROMBACILLUS STEAROTHERMOPHILUS:
Authors: Fontana Angelo , Mantovanelli Ludovico , Boccu Enrico , Veronese Francesco M.
Published: August 2010

The thermophilic 6–phosphogluconate dehydrogenase from Bacillus stearo‐thermophilus was inhibited upon specific modification of the ‐SH group of cysteine residues by 7–chloro‐4–nitrobenzo‐2–oxa‐1, 3–diazole (NBD‐Cl) at pH 7.0. By using 20–100–fold molar excess of NBD‐CL the reaction occurs slowly at pH 7.0 as a first order process. Partial protection from inactivation was observed when the substrate 6–phosphogluconate or the coenzyme NADP was added to the reaction mixture. Complete inactivation was achieved upon modification of 1.9 of the six cystine residues per mole of enzyme, which corresponds to nearly one residue per enzyme subunit.

Circular dichroism measurements suggest that the gross structure of the protein molecule is practically unchanged upon reaction of the enzyme with NBD‐Cl. Melting profile experiments revealed a single transition occurring at about 65d̀C. Analogously, the profile of intensity of the fluorescence emission at 520 nm of the enzyme‐bound S‐NBD groups versus temperature indicated a midpoint of transition near 65d̀C.

Since this melting temperature corresponds closely to that observed with the native enzyme, these results would indicate that the molecular organizations of the native and modified enzyme are similar and stabilized by similar interactions within the polypeptide chain.
SEQUENCE COMPARISON OF HUMAN PLASMA α1‐ACID GLYCOPROTEIN AND THE IMMUNOGLOBULINS
Authors: Schmid K. , Emura J. , Schmid M.F. , Stevens R.L. , Nimberg R.B.
Published: August 2010

The amino acid sequence of human plasma α1‐acid glycoprotein, upon comparison with the sequences of other blood proteins, was shown to possess significant similarity with the immunoglobulins. Employing direct and corrected sequence identity, the average mutation value and two different computer comparisons for the evaluation of sequence similarity, the following two regions of this α‐globulin, which account for approximately half of the total amino acid sequence of the protein, were found to possess sequence similarity with the immunoglobulins. a) The region from residues 77 through 125 proved to be related to the variable region of several human H and L chains, and b) the region from residues 136 through 166 was found to be related not only to the constant region of a human and a mouse L chain but also to the third and fourth constant region of a rabbit and a human H chain, respectively. These results suggest that α1‐acid glycoprotein is probably related to the immunoglobulins and further suggest that it possibly diverged from the immunoglobulin evolutionary tree prior to the formation of the primitive L chain.
SELECTIVE CLEAVAGE AT THE SINGLE TRYPTOPHAN RESIDUE IN BOVINE SOMATOTROPIN BY 2‐(2‐NITROPHENYLSULFENYL)‐3‐METHYL‐3‘‐BROMOINDOLEMINE
Authors: Houghten Richard A. , Li Choh Hao
Published: August 2010

SELECTIVE CLEAVAGE AT THE SINGLE TRYPTOPHAN RESIDUE IN BOVINE SOMATOTROPIN BY 2‐(2‐NITROPHENYLSULFENYL)‐3‐METHYL‐3′‐BROMOINDOLEMINE

The single tryptophan residue at position 86 in bovine somatotropin has been cleaved by the use of 2‐(2‐nitrophenylsulfenyl)‐3‐methyl‐3′‐bromoindolemine. This reaction was carried out with native bovine growth hormone as well as its reduced and alkylated derivative. When performed on the intact hormone, followed by the reduction and alkylation of the disulfides to liberate the two fragments, the cleavage reaction yielded the fragment containing residues 87–191 in a monomeric state. The other fragment, containing residues 1–86, could only be obtained in a highly aggregated form admixed with other material. When the cleavage reaction was carried out on the reduced and alkylated hormone, both the N‐terminal fragment of reduced‐carbamidomethylated bovine somatotropin as a monomer and the C‐terminal fragment as a dimer were obtained in 35–40% yield. Since the cleavage reaction also oxidized methionine to methionine sulfoxide, the sulfoxides were reduced back to the methionine with N‐methylmercapto acetamide. In this manner the following new derivatives and fragments of bovine somatotropin have been prepared: completely reduced and alkylated hormone, reduced and alkylated hormone with its methionines and tryptophan oxidized, reduced and alkylated hormone with its tryptophan oxidized, the N‐terminal fragment of the hormone containing residues 1–86 with its methionine and tryptophan oxidized, the C‐terminal fragment containing residues 87–191, both with its methionines oxidized and in their native state. The chemical and physical properties of these derivatives and fragments have been determined. Biological activity in the rat tibia was found to be negligible for all derivatives and fragments.
THE ACTIVE SITE OF AN INDUCIBLE ARYLACYLAMIDASE FROM PSEUDOMONAS ACIDOVORANS
Authors: Heymann Eberhard , Rix Hella
Published: August 2010

Though very effectively ibhibited by both SH‐group directed reagents and inhibitors typical for serine hydrolases, the inducible arylacylamidase from Pseudomonas acidovorans is a serine enzyme rather than a sulfhydryl enzyme. The amino acid sequence around the reactive serine residue is Gly‐Ser‐Ile. The sequence of a larger peptide from the active site is described.
A THEORETICAL STUDY OF THE STRUCTURES OF (GLY‐PRO‐LEU)n AND (GLY‐LEU‐PRO)n*
Authors: Bansal M. , Ramachandran G.N.
Published: August 2010

Theoretical conformation studies have been carried out for the polytripeptides (Gly‐Pro‐Leu)n and (Gly‐Leu‐Pro)n and the Fourier transforms of the structures have been calculated. X‐ray powder patterns of these polymers had indicated that both these polymers take up coiled‐coil triple‐helical structures, but in the case of (Gly‐Pro‐Leu)n it was not clear whether the triple helix is formed by three parallel polypeptide chains or by a single chain folding back on itself (Scatturin et al 1975). Our studies show that both the polytripeptides can take up stereochemically satisfactory triple‐helical structures with three parallel chains. There is also very good agreement between the calculated intensity distribution and that of the observed X‐ray pattern, in each case.
SYNTHESIS AND β‐CONFORMATION OF COPOLYPEPTIDES WITH ALTERNATING HYDROPHILIC AND HYDROPHOBIC RESIDUES
Authors: Brack Andrae , Caille Anita
Published: August 2010

Copolypeptides with alternating hydrophilic and hydrophobic residues were prepared, and their ability to form β‐structures in aqueous solutions was investigated by circular dichroism. Optically pure samples of poly (Lys‐Leu‐Lys‐Leu) and poly (Leu‐Glu‐Leu‐Glu), obtained via the 2‐hydroxyphenyl esters, undergo a coil‐to‐β transition in presence of salt. The β‐structures obtained under identical conditions with partially racemized samples of poly (Leu‐Lys)Np and poly (Leu‐Glu)Np, prepared by polycondensation of the corresponding dipeptide p‐nitrophenyl esters, appear to be less regular. Non‐alternating poly (Gly‐Lys‐Leu‐Lys‐Leu) does not form β‐structures in presence of NaCl as does alternating poly (Lys‐Leu‐Lys‐Leu) indicating that the amino acid sequence can dramatically change the tendency to form β‐structures.
β‐ENDORPHIN: SYNTHESIS AND BIOLOGICAL ACTIVITY OF SHORTENED PEPTIDE CHAINS
Authors: Li Choh Hao , Yamashiro Donald , Tseng Liang‐Fu , Loh Horace H.
Published: August 2010

Three analogs of β‐endorphin have been synthesized by the solid‐phase method: βc‐endorphin‐(1–5)‐(28–31), βc‐endorphin‐(6–31) and βh‐endorphin‐(1–5)‐(16–31). The analgesic activities of these synthetic peptides relative to that of the parent molecule are reported. All three peptides at high doses exhibit either no or much weaker analgesic activity than β‐endorphin. These data suggest that the entire β‐endorphin molecule is necessary for full in vivoanalgesicactivity.
SYNTHESIS OF SOME NEW ANALOGS OF THE IMMUNOADJUVANT GLYCOPEPTIDE MDP (N‐ACETYL‐MURAMYL‐L‐ALANYL‐D‐ISOGLUTAMINE)
Authors: Lefrancier P. , Derrien M. , Lederman I. , Nief F. , Choay J. , Lederer E.
Published: August 2010

In our continued efforts to elucidate the relationship between the structure and the immunoadjuvant, antiinfectious or mitogenic activity of N‐acetyl‐muramyl‐L‐alanyl‐D‐isoglutamine (MDP), we report the synthesis of 11 new analogs. Five of them present some modifications in the N‐acetyl‐muramyl moiety.
CYCLIC PEPTIDES
Authors: Shimohigashi Yasuyuki , Izumiya Nobuo
Published: August 2010

A cyclic tetradepsipeptide with a sequence corresponding to AM‐toxin II (a phytotoxic peptide) was synthesized in order to confirm the proposed structure by a conventional method. This was mediated through a dehydration reaction of cyclodepsipeptide containing a D‐Ser residue, by methanesulfonyl chloride containing sulfur dioxide. The synthetic peptide and natural AM‐toxin II were identical as regards t.l.c, crystal form, several kinds of spectra measurements and biological activity in causing necrosis on apple leaves. An analog, [L‐Phe1]‐AM‐toxin, containing the lower homolog (L‐phenylalanine) instead of L‐2‐amino‐5‐phenylpentanoic acid in position 1 of natural toxin II, was synthesized simultaneously. [L‐Phe1] ‐AM‐toxin showed extremely weak activity; the relationship between the bulkiness of an aromatic side chain and the biological activity of AM‐toxin II is discussed.
SIDE REACTIONS IN PEPTIDE SYNTHESIS. VI.
Authors: Bodanszky Miklos , Tolle John C. , Deshmane Sharad S. , Bodanszky Agnes
Published: August 2010

The acid catalyzed O → C migration of the benzyl group in the side chain of tyrosine could be reduced by applying HBr in a mixture of phenol and p‐cresol instead of HBr in trifluoroacetic acid for acidolytic deprotection. This side reaction occurs also during the removal of Boc groups. The loss of O‐benzyl protection and the formation of 3‐benzyltyrosine residues could be suppressed by the application of a 7:3 mixture of trifluoroacetic acid and acetic acid.

The acid‐ and base‐catalyzed ring closure of β‐benzylaspartyl residues to aminosuccinyl derivatives was also studied. In this case HBr in trifluoroacetic acid was found to be relatively harmless. Deprotection with HBr in a mixture of trifluoroacetic acid and p‐cresol can be applied for peptides that contain both β‐benzylaspartyl and O‐benzyltyrosyl residues. An attempt to reduce the rate of the base‐catalyzed side reaction by application of hindered tertiary amines was abandoned because the tertiary amines which were effective in this respect led to significant reduction of the rate of the desired reaction, the aminolysis of active esters, as well. A satisfactory solution for the problem was found in the selective catalysis of the active ester reaction with 1‐hydroxybenzotriazole o 4‐dimethylaminopyridine. These catalysts do not enhance the rate of ring closure and in their presence essentially pure β‐benzylaspartyl peptides can be produced in good yield.
PURIFICATION AND CHARACTERIZATION OF THE SURFACE ACTIVE PROTEINS OF BLACK GRAM (PHASEOLUS MUNGO)
Authors: Susheelamma N.S , Rao M.V.L.
Published: August 2010

The surface active globulin from black gram has been resolved into two components with high foam‐forming activity. They were found to be homogeneous by electrophoresis and ultracentrifugal examinations and had high molecular weights around 100,000 daltons.

They were rich in acidic as well as basic amino acids but low in sulphur amino acids. Heat treatment, proteolysis and treatment with certain inorganic salts such as copper, and mercurous mercury, group specific reagents P‐chloromercury benzoate and N‐ethylmalemide (PCMB, NEM) and protein denaturants were found to have an adverse effect, while oxidizing agents had no effect. The free sulphydryl content was low (3 and 4 μmol/mol), but essential for full manifestation of surface activity. Other purified proteins also needed free sulphydryl groups.
ALKALINE ISOMERIZATION OF HORSE AND YEAT CYTOCHROMES C
Authors: Looze Yvan , Polastro Enrico , Deconinck Marc , Leonis Jose
Published: August 2010

Spectrophotometric studies of the alkaline isomerization of horse heart and yeast cytochrome c show that the haemoproteins from Saccharomyces cerevisiae differ significantly from the mammalian cytochrome c.

Apparent pKa values of 8.41, 8.40 and 8.73 for iso‐l‐ (the methylated and unmethylated forms) and iso‐2‐cytochrome c respectively, from baker's yeast were determined and compared with the value of 9.40 found for horse heart cytochrome c.

The transitions, measured by observing the decrease of the absorbance at 695 nm as the pH increases, have been found to strictly parallel the decrease in amplitude of the negative circular dichroism band centered at 417 nm. This observation gives additional evidence that this negative band is closely related to the ligation of the heme iron by the sulfur atom of methionine 8u for each of the four haemoproteins examined.
SPECTRAL STUDIES ON TWO GENETIC FORMS OF THE HUMAN SERUM PROTEINASE INHIBITOR, ALPHA‐1‐ANTITRYPSIN*
Authors: Glaser Charles B. , Karic Lucija
Published: August 2010

Alpha‐1‐antitrypsin, the major inhibitor of proteolytic enzymes in human serum, was isolated from normal individuals (protease inhibitor type MM) and from those with an inherited deficiency (protease inhibitor type ZZ) of circulatory protein.

The two proteins were compared by circular dichroism spectroscopy, and by fluorescence quenching experiments using anionic (I‐), and neutral (acrylamide) probes.

Both proteins share a similar secondary structure, i.e. ˜45–50%α‐helix and 15–20%β‐structure. Evidence was accumulated to show that the micro‐environment in the vicinity of the three tryptophanyl residues is altered in Z form as compared to the M form as shown by (a) the absence of the positive dichroic band in the region 290–300nm of the circular dichroism spectra, (b) a > 50% increase in quantum yield in the tryptophanyl fluorescence emission spectra, (c) an increased accessibility of tryptophan to quenching by iodide, and (d) acrylamide quenching experiments which indicate that all tryptophanyl residues in the Z protein are quenched equally or that quenching is dominated by a single residue, while in the M protein, heterogeneous quenching occurs. The potential significance of these findings in terms of alpha‐1‐antitrypsin deficiency state are discussed.
THE SEPARATION OF PEPTIDE HORMONE DIASTEREOISOMERS BY REVERSE PHASE HIGH PRESSURE LIQUID CHROMATOGRAPHY
Authors: LARSEN BRENT , FOX B. LAWRENCE , BURKE MICHAEL F. , HRUBY VICTOR J.
Published: August 2010

Experimental conditions and parameters involved in high performance liquid chromatography (HPLC) separations of the peptide hormone oxytocin and seven of its diastereoisomers, namely [1‐hemi‐d‐cystine]‐, [2‐d‐tyrosine]‐, [4‐d‐glutamine]‐, [5‐d‐asparagine]‐, [6‐hemi‐d‐cystine‐], [7‐d‐proline]‐, and [8‐d‐leucine]‐oxytocin, on reverse phase columns were investigated. The effects of solvent, pH, and salt concentration were studied. Using the solvent systems 10% tetrahydrofuran‐ammonium acetate buffer or 18% acetonitrile‐ammonium acetate buffer and the üBondapak C18 support, oxytocin was separated from each of its diastereoisomers under all conditions studied, but the order of elution of diastereoisomers was highly dependent on solvent and to a lesser extent on pH. Separations of the hormone and its diastereoisomers on reverse phase HPLC and on classical partition chromatography on Sephadex G‐25 were compared. The results are discussed in terms of the interactions of the solute with the reverse phase column and the solvent system. Implications of these findings in terms of the different solution conformations of the peptides are discussed.
STUDIES ON POLYPEPTIDES
Authors: VOSKUYL‐HOLTKAMP INGRID , SCHATTENKERK CECILE
Published: August 2010

A description is given of the synthesis by fragment condensation of 12‐(3‐Pyd) Ala** S‐peptide (1–14), the 1–14 peptide sequence of ribonuclease A in which the histidine‐12 residue is replaced by β‐(3‐pyridyl)‐L‐alanine. The peptide binds strongly and stoichiometrically to S‐protein; the resulting complex is enzymatically inactive.
CYCLIC PEPTIDES
Authors: LEE SANNAMU , KANMERA TATSUHIKO , AOYAGI HARUHIKO , IZUMIYA NOBUO
Published: August 2010

Several cyclo (‐l‐aminoacyl‐ΔAla‐) (aminoacyl = Ala, Val, Leu, Phe, Pro and Lys (∍‐Ac)) were prepared by tosylation and successive detosylation of cyclo (‐l‐aminoacyl‐l‐Ser‐), which were synthesized via the Nitecki and Fischer methods. Hydrogenation of the double bond of dehydroalanine residues in cyclodipeptides was carried out using Pd black in methanol at 1‐atm pressure and room temperature. The degree of asymmetric hydrogenation was assessed by determining the amounts of l‐ and d‐alanine by a modified Manning and Moore procedure. When l‐valine was used as a chiral source, l‐alanine residue with chiral induction of 98.4% was derived from cyclo (‐l‐Val‐ΔAla‐). l‐Amino acids other than l‐proline also were effective in inducing remarkable asymmetric hydrogenation. Hydrogenation of α, β‐dehydro‐α‐aminobutanoic acid residues in cyclodipeptides produced l‐α‐aminobutanoic acid residues with effective chiral induction to the same extent as observed with dehydroalanine residues. Optically pure l‐alanine was prepared from cyclo (‐l‐Lys(∍‐Ac)‐ΔAla‐) via asymmetric hydrogenation. A mechanism of chiral induction is discussed.
PROTEIN DENSITIES
Authors: KUNTZ I.D. , CRIPPEN G.M.
Published: August 2010

The calculation of protein densities from atomic coordinates is not straightforward and requires very careful attention to the determination of the protein‐solvent boundary. Interior densities are more readily obtained and are in reasonable agreement with those estimated from solvent accessibility studies.

The interior of globular proteins has very significant density inhomogenities on a scale of 100–1000 Å3. The interior densities range from less than 0.5 g/cm3 to over 3 g/cm3. The low local densities are primarily associated with clusters of nonpolar sidechains while the high local density regions arise from the protein backbone secondary structures: helices and beta sheets. We show a rough correlation between local density and local polarity.
1H AND 13C NUCLEAR MAGNETIC RESONANCE SPECTRA OF SOME PEPTIDES WITH FIBRINOGEN‐LIKE REACTIVITY
Authors: RAE I.D. , SCHERAGA H.A.
Published: August 2010

The 1H and 13C spectra of four peptides, l‐Phe‐Val‐Arg‐pNA, d‐Phe‐Val‐Arg‐pNA, l‐Phe‐Pip‐Arg‐pNA and d‐Phe‐Pip‐Arg‐pNA (pNA = p‐nitroaniline, Pip = pipecolic acid residue), have been examined, and deductions made about their conformation in solution. The d‐Phe peptides, which are cleaved especially rapidly by thrombin in water, have structures (in deuterated DMSO) in which the aromatic ring of the d‐Phe residue is folded back over the Val or Pip residue. This arrangement is not found in the l‐Phe peptides. It is proposed that this feature (in which Phe could be situated near Val and near the Arg‐Gly bond of the Aα chain in the three‐dimensional structure of fibrinogen) may be specially advantageous for binding to the enzyme.
STEREOCHEMICAL STUDIES ON CYCLIC PEPTIDES
Authors: MANJULA G. , RAMAKRISHNAN C.
Published: August 2010

Conformational aspects of 4 → 1 hydrogen bonded cyclic pentapeptides are considered in this paper from the point of view of “contact criteria” and potential energy calculations. Three types of such hydrogen bonded conformations, designated A1, A2and B, are possible, involving some amount of strain on the bond angles. The energy of hydrogen bonded cyclopentaglycyl is somewhat less than that of the five‐fold symmetrical conformation. The stereochemical feasibility of introducingl‐ andd‐alanyl residues in these structures has also been studied and the possible types for different sequences of alanyl residues have been determined. The results are discussed further in the light of the limited data available from crystal structure and nuclear magnetic resonance studies on cyclic pentapeptides.
THEORETICAL CONFORMATIONAL ANALYSIS OF OXYTOCIN MOLECULE
Authors: NIKIFOROVICH G.V. , LEONOVA V.I. , GALAKTIONOV S.G. , CHIPENS G.I.
Published: August 2010

The total semi‐empirical conformational analysis of the oxytocin molecule has been carried out. It has been revealed the two main types of stable structures of cyclic moiety backbone and the great lability of the tail. The optimal spacing of cyclic moiety side chains has been found for every backbone structure. The calculation results are in good agreement with the data of physico‐chemical investigations. Among the set of stable molecule structures reported in the present study are structures with β‐turn conformation of the cyclic moiety backbone and without closer spacing of the cyclic moiety and the tail, as well as structures with closely spaced N‐ and C‐terminal parts which, however, lack β‐turn in the cyclic moiety.
ANTIBODIES AGAINST HAPTENS IN THE STUDY OF STRUCTURE AND BIOLOGICAL ACTIVITY OF GROWTH HORMONE
Authors: NOWICKI CRISTINA , SANTOMÉ JOSÉ A.
Published: August 2010

The α‐amino group of bovine Growth Hormone was selectively modified with TNBS with no detectable changes in growth promoting activity. TNP was used as hapten for the production of antibodies against the end terminal region of bGH. The region near the α‐amino group is not involved in the binding of bGH to rat liver cells, and it seems to be away from the part of the molecule that interacts with the cell binding sites.
A SERIES OF LYSYLDIPEPTIDE DERIVATIVES FOR RACEMIZATION STUDIES IN PEPTIDE SYNTHESIS
Authors: BENOITON N. LEO , KURODA KEIJI , CHEN FRANCIS M. F.
Published: August 2010

The series of diastereomeric peptide derivatives N‐benzoyl‐d,l‐X‐N‐benzyl‐oxycarbonyl‐L‐lysine methyl ester where X = alanyl, valyl, leucyl, phenylalanyl and isoleucyl are submitted as model systems for studying racemization in peptide synthesis. The diastereomers can be analyzed by quantitation of the separated ester methyl proton peaks of their nuclear magnetic resonance spectra. Data on the tendency to racemize of the different residues are presented. In polar solvents, valyl and isoleucyl residues racemize more readily than the other residues.
STUDIES ON PROTEIN FOLDING, UNFOLDING AND FLUCTUATIONS BY COMPUTER SIMULATION IV. Hydrophobic Interactions
Authors: GO NOBUHIRO , TAKETOMI HIROSHI
Published: August 2010

The theoretical model of proteins on the two‐dimensional square lattice, introduced previously, is extended to include the hydrophobic interactions. Two proteins, whose native conformations have different folded patterns, are studied. Units in the protein chains are classified into polar units and nonpolar units. If there is a vacant lattice point next to a nonpolar unit, it is interpreted as being occupied by solvent water and the entropy of the system is assumed to decrease by a certain amount. Besides these hydrophobic free energies, the specific longrange interactions studied in previous papers are assumed to be operative in a protein chain. Equilibrium properties of the folding and unfolding transitions of the two proteins are found to be similar, even though one of them was predicted, based on the one globule model of the transitions, to unfold through a significant intermediate state (or at least to show a tendency toward such a behavior), when the hydrophobic interactions are strongly weighted. The failure of this prediction led to the development of a more refined model of transitions; a non‐interacting local structure model. The hydrophobic interactions assumed here have a character of non‐specific long‐range interactions. Because of this character the hydrophobic interactions have the effect of decelerating the folding kinetics. The deceleration effect is less pronounced in one of the two proteins, whose native conformation is stabilized by many pairs of medium‐range interactions. It is therefore inferred that the medium‐range interactions have the power to cope with the decelerating effect of the non‐specific hydrophobic interactions.
SOLID PHASE SYNTHESIS OF THE PROTECTED 27 – 42 HEXADECAPEPTIDE OF THE HEAVY CHAIN FROM MYELOMA IMMUNOGLOBULIN M603 Elimination of Side Reactions Associated with Glycyl‐2‐oxypropionyl‐resin
Authors: TJOENG FOE SIONG , TAM JAMES P. , MERRIFIELD R.B.
Published: August 2010

A fully protected 27–42 hexadecapeptide of the variable region of myeloma immunoglobulin M603 was synthesized on a 2‐bromopropionyl‐resin by the solid phase method. Side reactions due to cyclization of glycyl‐2‐oxypropionylresin were studied under different reaction conditions. The loss of peptide chains at the dipeptide and tripeptide stages due to diketopiperazine formation was also examined. These side reactions were circumvented by using a combination of fragment and stepwise coupling methods. The synthesized protected peptide was removed from the resin in 85% yield by photolysis, and purified by crystallization and by chromatography on a Sephadex LH‐60 column.
HYDROGEN BONDS IN CRYSTAL STRUCTURES OF AMINO ACIDS, PEPTIDES AND RELATED MOLECULES
Authors: VINOGRADOV SERGE N.
Published: August 2010

The results of a survey of 439 hydrogen bonds in 95 recently determined crystal structures of amino acids, peptides and related molecules suggest that the following generalizations hold true for linear (angle X–H—Y > 150°) hydrogen bonds. (1) The charge on the acceptor group does not influence the length of a hydrogen bond. (2) For a given acceptor group, the hydrogen bond lengths increase in the order imidazolium N–H < ammonium N–H < guanidinium N–H; this order holds true for oxygen anion acceptor groups. Cl‐ions and the uncharged oxygen of water molecules. (3) The uncharged imidazole N–H group forms shorter hydrogen than the amide N–H group. (4) The carboxyl O–H groups form shorter hydrogen bonds than other hydroxyl groups. (5) The hydrogen bonds involving a halogen ion are longer than hydrogen bonds with other acceptors when corrected for their longer vander Waals radii. The observed differences between the lengths of hydrogen bonds formed by different donor and acceptor groups in amino acids and peptides, imply differences in the energetics of their formation.
INTRAMOLECULAR CROSS‐LINKING OF PROTEINS BY FORMATION OF LYSINOALANINE OR LANTHIONINE Modification of Disulfides in Ovomucoids
Authors: WALSH ROBERT G. , NASHEF AWS S. , FEENEY ROBERT E.
Published: August 2010

The disulfide bonds of ovomucoids were cleaved and new sulfur‐containing cross‐links were introduced by two separate chemical modification methods: (1) alkali treatment, and (2) cyanolysis. Alkali and cyanolytic treatments were used to cleave disulfide bonds and to introduce new synthetic nonreducible cross‐links consisting of residues of lysinoalanine (N‐(dl‐2‐amino‐2‐carboxyethyl)‐l‐lysine) and lanthionine (bis(2‐amino‐2‐carboxyethyl)sulfide). The two ovomucoids studied were turkey and penguin ovomucoids, which are “double‐headed” inhibitors of proteolytic enzymes with one inhibitory site for bovine trypsin and another for bovine α‐chymotrypsin or subtilisin. Trypsin does not compete with either α‐chymotrypsin or subtilisin, but the latter compete with one another, apparently for the same inhibitory site. The stability of inhibitory activities as a function of disulfide bond scission and the formation of new nondisulfide cross‐links was studied. In both methods of disulfide modification of turkey ovomucoid, inhibitory activity against trypsin was more stable with respect to the extent of modification than was inhibitory activity against chymotrypsin or subtilisin. With penguin ovomucoid, inhibitory activity against subtilisin was always more stable than activity against trypsin or chymotrypsin with both methods. With both ovomucoids it was thus possible to produce single‐headed inhibitors from the double‐headed inhibitors. The formation of the nonreducible cross‐links of lanthionine from cystines, and of lysinoalanines from cystines and lysines, with retention of a biochemical activity, suggests that such a procedure may have at least limited use as a cross‐linking method.
STUDIES ON TRYPSIN INHIBITORS Part IX. Synthesis and Trypsin Inhibitory Activity of the Duopentacontapeptide Corresponding to the Amino Acid Sequence of Porcine Pancreatic Secretory Trypsin Inhibitor II (Kazal)*
Authors: TOMATIS ROBERTO , GUARNERI MARIO , GUGGI AUGUSTO , SALVADORI SEVERO , ROCCHI RANIERO
Published: August 2010

The synthesis of the protected duopentacontapeptide corresponding to the entire amino acid sequence 1–52 of porcine pancreatic secretory trypsin inhibitor II (Kazal type) is described.

The benzyloxycarbonyltetradecapeptide tert‐butyloxycarbonylhydrazide (sequence 1–14) was selectively deblocked with trifluoroacetic acid and used to acylate, by the azide procedure, the peptide free base corresponding to the sequence 15–52. The isolated material was purified by ion exchange chromatography and the protecting groups were removed by successive treatments with anhydrous hydrogen fluoride, 1M piperidine and mercuric acetate.

Folding and formation of the disulfide bonds was accomplished by air oxidation in 0.02M phosphate buffer, pH8.

Determination of the inhibitory capacity indicated that the synthetic material is about 50% effective, at 30:1 inhibitor:trypsin molar ratio, in inhibiting the tryptic hydrolysis of Nα‐benzoyl‐dl‐arginine‐4‐nitroanilide. Full inhibition was achieved at a higher inhibitor:trypsin molar ratio. The stability constants and the standard free energy of binding of the complex between trypsin and the synthetic inhibitor have been determined.
COMPARATIVE THEORETICAL CONFORMATIONAL ANALYSIS OF THE INSULIN A6‐A11 PEPTIDES
Authors: RENNEBOOG‐SQUILBIN C.
Published: August 2010

The insulins of pig, ox, horse and goat differ only by the cyclic A6‐A11 peptide which is thought to be an antigenic determinant of the molecule. The structure of the four peptides is investigated by conformational energy calculations in order to verify whether a common backbone conformation can be found for all four species, the antigenic difference being consequently due only to the difference in the side chains exposed to the solvent, or whether each sequence gives rise to a preferential backbone conformation, which would lead to the conclusion that the antigenic difference is conveyed by a more pronounced difference in the molecular structure. From the results of the study on the isolated peptides, it appears that an energetically favourable backbone conformation common to all four species can be found. This conformation is compared with the structure deduced from the X‐ray diffraction data available for pig insulin.
REVERSIBLE GELATION OF ARACHIN
Authors: KUMAR K.D. NAVIN , NANDI P.K. , RAO M.S. NARASINGA
Published: August 2010

Arachin forms a gel at acidic pH (pH < 3.8) which is thermolabile. The factors governing the gelation seem to be the concentration of the protein, heating temperature, heating interval, cooling temperature of the heated solution, pH, ionic strength and dielectric constant of the medium. Urea decreases gel strength. The cross‐links involved in the gelation of arachin seem to be noncovalent in nature.
STEREOCHEMICAL STUDIES ON CYCLIC PEPTIDES
Authors: RAMAKRISHNAN C. , RAO B. N. NARASINGA
Published: August 2010

Conformational analysis of cyclic pentapeptides having two intra‐ring 3 1 hydrogen bonds has been carried out. It is found that the structure can easily be formed with trans planar peptide units without causing significant angular strain at the α‐carbon atoms. Four different types of conformations designated Types I‐IV are possible for the backbone structure. Details of these four types of conformations and also the accommodating possibility of these types for all‐glycyl and all‐alanyl residues are presented. Three of the four types have relatively low energies for glycyl residues whereas the other one has a slightly higher energy. When alanyl residues are introduced at the five α‐carbon atoms, the types that are energetically favourable depend upon the sequence of isomers. Energy calculations have also been carried out for the combinations of glycyl, L‐ and D‐alanyl residues. The theoretical results are compared with available experimental observations both from solution and solid state studies.
SYNTHESIS OF α‐ AND β‐MELANOCYTE STIMULATING HORMONES*
Authors: YANG YOUNG C.S. , HRUBY VICTOR J. , HEWARD CHRISTOPHER B. , HADLEY MAC E.
Published: August 2010

The solid phase synthesis of α‐melanocyte stimulating hormone (α‐MSH) using the benzhydrylamine resin and a number of recently described side chain protecting groups is given. The carboxamide terminal peptide was obtained directly by treatment of the peptide resin with liquid hydrogen fluoride at 0 in the presence of carbonium ion scavengers. The solid phase synthesis of the C‐terminal carboxylate hormone, porcine β‐melanocyte stimulating hormone (βp‐MSH), using a 1% cross‐linked Merrifield resin and the same side chain protecting groups as in the α‐MSH synthesis also is presented. Purification of both peptides was carried out by conventional chromatographic techniques. Both hormones were fully active and βp‐MSH was slightly more potent than previously reported in the literature.
MODIFICATION OF THE PROPERTIES OF BOVINE PANCREATIC RIBONUCLEASE A BY COVALENT ATTACHMENT OF D‐GLUCONYL‐GLYCINE RESIDUES*
Authors: BIONDI LAURA , FILIRA FERNANDO , GIORMANI VIRGILIO , ROCCHI RANIERO
Published: August 2010

Bovine pancreatic ribonuclease A was reacted with D‐gluconyl‐glycine azide in aqueous solution at pH 8.9, in absence of phosphates. Five out of 11 amino groups can be reproducibly modified and the penta D‐gluconyl‐glycinated ribonuclease A had greater than 70% of the enzymic activity of the unmodified enzyme toward cytidine 2′, 3′‐cyclic phosphate as well as uridine 2′, 3′‐cyclic phosphate and yeast RNA. The kinetic parameters Km and k2 of the modified enzyme were calculated from double‐reciprocal Lineweaver‐Burk plots, using cytidine 2, 3′‐cyclic phosphate as the substrate. The native and chemically modified protein exhibited identity in their reversible thermal transitions at neutral pH, with midpoint at about 60°. Circular dichroism measurements indicated that the overall conformation of the D‐gluconyl‐glycinated enzyme is not significantly different from that of the unglycosylated parent enzyme. The modified protein was less sensitive than the native ribonuclease A to attack by chymotrypsin, pepsin and elastase, indicating a protecting effect of the D‐gluconyl‐glycine units. Similar properties are shown by the glycosylated bovine pancreatic ribonuclease B.
DETERMINATION OF THE AVERAGE END‐TO‐END DISTANCE OF TWO ANGIOTENSIN II ANALOGS BY RESONANCE ENERGY TRANSFER
Authors: SCHILLER PETER W.
Published: August 2010

The angiotensin II analogs H. Tyr‐Arg‐Val‐Phe‐Val‐His‐Pro‐Trp. OH (I) and H. Tyr‐Arg‐Val‐Phe‐Val‐His‐Pro‐Trp. OH (II) were synthesized and their conformations in dilute aqueous solution (3 × 10‐5M) were studied by fluorescence techniques. Evaluation of singlet‐singlet energy transfer between tyrosine (donor) and tryptophan (acceptor) in the biologically active analog I resulted in a low transfer efficiency (E ˜ 0.1) Since transposition of the tyrosyl and tryptophanyl residues (analog II) produced a transfer efficiency similar to that observed in compound I, the orientation factor did not present a serious problem for the determination of the intramolecular Tyr‐Trp distances in these peptides on the basis of the Förster equation. Similar average Tyr‐Trp separations above 15 Å were obtained for analogs I and II at pH 5.2 and no drastic titration effects on the distance were observed with compound I in the pH range 1.5–8.5. The observed end‐to‐end distances indicate that the conformations of analogs I and II are not quite as compact as some of the models which have been proposed for angiotensin II. Furthermore, the results exclude an electrostatic head‐to‐tail interaction between the terminal NH+3‐ and COO‐groups as well as several proposed β‐ and γ‐turn models.
THERMOLYSIN AND BACILLUS SUBTILIS NEUTRAL PROTEASE
Authors: GRANDI CLAUDIO , VITA CLAUDIO , DALZOPPO DANIELE , FONTANA ANGELO
Published: August 2010

A comparative study on thermolysin from Bacillus thermoproteolyticus and neutral protease from Bacillus subtilis involving far‐and near‐ultraviolet circular dichroism (CD) and immunological techniques is reported. These enzymes are homologous metalloendopeptidases, having similar size, kinetic behaviour, substrate specificity and susceptibility to inhibitors. The far‐ultraviolet CD spectrum of each protein shows a minimum at 208 and a shoulder near 220 nm; differences in the extent of ellipticity, however, have been observed. Estimates of secondary structure obtained by quantitation of the far‐ultraviolet CD spectra indicated a higher helicity of neutral protease relative to thermolysin. In the presence of ethylenediaminetetraacetic acid, which removes calcium and the functional zinc ion from the metalloenzymes, neutral protease is immediately denatured, whereas thermolysin maintains a globular structure, although thermolabile. On the other hand, the zinc‐specific chelating agent tetraethylenepentamine does not have measurable effects on the conformation and conformational stability of either protein. Marked higher stability to temperature and guanidine hydrochloride were observed for thermolysin as compared with neutral protease, as indicated by monitoring conformational transitions with CD measurements at 220 nm. Antisera prepared in rabbits using thermolysin as immunogen do not cross‐react with neutral protease, indicating differences of surface structure between the two proteins. On the basis and limitations of the techniques employed, it is proposed that the two sequentially and functionally homologous metalloendopeptidases may have similar conformations at specific regions (active and binding sites, at least) of the polypeptide chain essential for biological function, while some variability in the structure of other regions may be tolerated.
SYNTHESIS OF p‐AMINO‐L‐PHENYLALANINE DERIVATIVES WITH PROTECTED p‐AMINO GROUP FOR PREPARATION OF p‐AZIDO‐L‐PHENYLALANINE PEPTIDES
Authors: FAHRENHOLZ FALK , THIERAUCH KARL‐HEINZ
Published: August 2010

For the synthesis of p‐azidophenylalanine peptides, the p‐amino group of p‐amino‐L‐phenylalanine is protected with the Z‐ or Boc residue via the copper complex or by specific acylation at pH 4.6. The α‐amino or α‐carboxy group is blocked by a protecting group (Boc, Ddz, OMe respectively Z, Nps, Ddz), which can be removed selectively. The synthesis of nine derivatives of p‐amino‐L‐phenylalanine for incorporation into the peptide chain is described. The p‐amino‐phenylalanine is converted to p‐azidophenylalanine without affecting disulfide bridges.
LIQUID‐LIQUID EXTRACTION IN PEPTIDE SYNTHESIS
Authors: SCHNEIDER CONRAD H. , ROLLI HANSPETER , BLASER KURT
Published: August 2010

An efficient procedure of peptide synthesis in solution based on liquid‐liquid extraction for the purification of intermediates (two‐phase method) is described. Generally, peptide segments of 10 and in favorable cases 15 amino acids can be prepared by using conventional blocking groups. Special blocking groups adapted for optimal performance are discussed. Simple equipment enabling rapid synthesis is also described.
PREDICTION OF THE SURFACE‐INTERIOR DIAGRAM OF GLOBULAR PROTEINS BY AN EMPIRICAL METHOD
Authors: NISHIKAWA KEN , OOI TATSUO
Published: August 2010

The number of amino acid residues in contact with a residue in a globular protein is a simple and good measure to show the relative location of the residue on the surface or in the interior of the protein. The contact number is estimated as the number of Cα atoms within a sphere of radius r (8 A) centered at the Cα atom of a given residue. The predictor: of a diagram (the plot of the contact number against the residue number) from a given amino acid sequence may be meaningful as an alternative to the secondary‐structure prediction currently performed. Parameter values are determined empirically using the observed contact numbers calculated from known structures of 39 proteins. In order to assess the real efficiency of the method, the prediction has been performed in the following way; all the proteins are divided into two groups; one group is used to derive parameter sets and the other serves to test the prediction accuracy. The test reveals that the parameter sets empirically determined are biased significantly towards the data base, the extent of which is roughly proportional to the number of parameter terms included. The results show that an adequate smoothing of a parameter set is the best way to reduce the extent of biasing towards the data base and to give the best prediction for ‘unknown’ proteins. The prediction accuracy finally obtained is about 0.4 (or roughly 70%), on the average, measured by the correlation coefficient between the predicted and observed diagrams. This value is of the same order as the accuracy in the current predictions of secondary structures.