Formation of 2′-5′ Phosphodiester Linkages in Polyribonucleotides

Unlike technical grade yeast RNA, which was confirmed to contain several per cent of 2′–5′ phosphodiester linkages, RNA prepared from different kinds of commercial yeast in a cold room consisted exclusively of 3′–5′ phosphodiester linkages. Heat treatment of the 3′–5′ linked RNA solution resulted in partial isomerization of the internucleotide linkage of the polynucleotide chain (C₃′-C₅′->C₂′-C₅′). The isomerization of RNA occurred in the presence of water, at high temperature, and under acidic conditions. Treatment of dry RNA at 100°C for 2hr did not result in any detectable isomerization. The isomerization was actually observed in yeast RNA when yeast cells suspended in sodium chloride solution were heated. It is concluded therefore that 2′-5′ phosphodiester linkages found in technical grade RNA had been formed neither at a step of precipitating RNA with acid nor at a step of drying RNA, but had been formed at a step of heat extraction of RNA from yeast. When 0.1 % poly (A) solution, pH 4.8, was heated for 20 hr in a boiling water bath, the isomerization proceeded during the first 6hr, and finally reached about 37%, irrespective of chain length.     

Spatial configurations of polynucleotide chains. 3. Polydeoxyribonucleotides

The virtual bond scheme set forth in preceding papers for treating the average properties of polyriboadenylic acid (poly rA) is here applied to the calculation of the unperturbed mean-square end-to-end distance of polydeoxyriboadenylic acid (poly dA). The modifications in structure and in charge distribution resulting from the replacement of the hydroxyl group at C_2′ in the ribose residue by hydrogen in deoxyribose produce only minor modifications in the conformational energies associated with the poly dA chain as compared to those found for poly rA. The main difference is manifested in the energy associated with rotations about the C_3′–O_3′ bond of the deoxyribose residue in the C_2′-endo conformation; accessible rotations are confined to the range between 0° and 30° relative to the trans conformation, whereas in the ribose unit the accessible regions comprise two ranges centered at approximately 35° and 85°. The characteristic ratio 〈r²〉0/nl² calculated on the basis of the conformational energy estimates is ≈9 for the poly dA chain with all deoxyribose residues in the C_3′-endo conformation and ≈21 with all residues in the C_2′-endo form. Satisfactory agreement is achieved between the theoretical values and experimental results on apurinic acid by treating the poly dA chain as a random copolymer of C_3′-endo and C_2′-endo conformational isomers present in a ratio of ～1 to 9.     

Theoretical drug design: 6-azauridine-5'-phosphate--its X-ray crystal structure, potential energy maps, and mechanism of inhibition of orotidine-5'-phosphate decarboxylase.

The cytostatic drug 6-azauridine is converted in vivo to 6-azauridine-5′-phosphate (z⁶Urd-5′-P), which blocks the enzyme orotidine-5′-phosphate decarboxylase (Ord-5′-Pdecase) and therefore inhibits the de novo production of uridine-5′-phosphate (Urd-5′-P). In order to relate the structure and function of z⁶Urd-5′-P, it was crystallized as trihydrate, space group P2₁2₁2₁ with a = 20.615 Å, b = 6.265 Å, c = 11.881 Å, and the structure established by Patterson methods. Atomic parameters were refined by full-matrix least-squares methods to R = 0.066 using 1638 counter measured x-ray data. The ribose of z⁶Urd-5′-P is in a twisted C(2′)-exo, C(3′)endo conformation, the heterocycle is in extreme anti position with angle N(6)-N(1)-C(1′)-O(4′) at 86.3°, and the orientation about the C(4′)-C(5′) bond is gauche, trans in contrast to gauche, gauche found for all the other 5′-ribonucleotides. Conformational energy calculations show that z⁶Urd-5′-P may adopt an extreme anti conformation not allowed to Urd-5′-P, and they also predict the same unusual trans, gauche conformation about the C(4′)-C(5′) bond in orotidine-5′-phosphate (Ord-5′-P) and in z⁶Urd-5′-P, which renders the distances O(2)…O(5′) in z⁶Urd-5′-P and O(7)…O(5′) in Ord-5′-P comparable. On this basis the function of z⁶Urd-5′-P as an Ord-5′-Pdecase inhibitor can be explained as being due to its structural similarity with the substrate Ord-5′-P and further clarifies the inhibitory action of 5′-nucleotides bearing the heterocycles oxipurinol, xanthine, or allopurinol [J. A. Fyfe, R. L. Miller, and T. A. Krenitsky, J. Biol. Chem. 248 , 3801 (1973)]. With this in mind, new inhibitors for Ord-5′-Pdecase may be designed.     

Haloalkyl complexes of the transition metals. Part 5. The synthesis and reactions of some new pentamethylcyclopentadienyl halomethyl and methoxymethyl complexes of molybdenum(II) and tungsten(II) and the X-ray crystal structure of the cationic ylide complex [η-C5Me5W(CO)3CH2PPh3]I

Synthetic routes are described for the new halo- methyl complexes of the type [η-C₅Me₅M(CO)₃- CH₂X]. The complexes where M = Mo, X = Cl or OMe and M = W, X = Cl, I, OMe have been fully characterized. Reaction of [η-C₅Me₅Mo(CO)₃CH₂Cl] with PPh₃ in methanol under reflux or acetonitrile at room temperature gives [η-C₅Me₅Mo(CO)₂(PPh₃)- Cl], whereas reaction of [η-C₅Me₅W(CO)₃CH₂I] with PPh₃ under similar conditions gives the cationic phosphorus ylide complex [η-C₅Me₅W(CO)₃CH₂- PPh₃]I. The structure of this ylide complex has been determined by X-ray crystallography. The complex crystallizes with half a molecule of CH₂Cl₂ in the monoclinic space group P2₁/n with a = 16.616- (8), b = 11.738(6), c = 18.126(9) Å, β = 101.74(2)° and Z = 4. The structure was solved and refined to R = 0.076. It confirms the formulation of the compound and the presence of the ylide ligand, WC_ylide 2.34(2) Å, PC_ylide 1.82(2) Å and the WC_ylideP angle of 119(1)°.     

Authigenic mineralization and detrital clay binding by freshwater biofilms: The Brahmani river,India

This study sought to understand the origin and fate of one of the bitumen mounds found on the bottom of Lake Baikal. These mounds are located at a depth of 900 m beneath oil spots detected on the surface of Lake Baikal (53° 18′24^″, 108° 23′20^″). The two mounds were sampled with a manipulator from a “MIR” deep-water manned submersible. Mature mound No. 8 was subjected to chemical and microbiological studies. Mound No. 3 was subjected only to chemical studies; we failed to perform microbiological analyses of this mound for logistic reasons. Oil spots collected from the water surface, samples of mound No. 3 and No. 8, were subjected to GC/MS analysis. The water contained aliphatic hydrocarbons with chains between C₈ and C₂₃, with the most abundant chain length being C₁₈. Mound No. 3 with the most abundant chain length being C₁₈ actively released oil droplets into the water. It contained 770 mg/g of C₁₃-C₃₂ n-alkanes, with a maximum at C₂₃ (160 mg/g). Mound No. 8 was inactive and contained 148 mg/g of aliphatic C₂₂-C₃₄ n-alkanes, with a maximum at C₂₅. Mound No. 8 also consisted of 3% inorganic matter, 48% unresolved complex mixture (UCM) and less than 1% other compounds (polyaromatic hydrocarbons, isoprenoids, carotenoids, and hopanes). The core of this sample used as inoculate, yielded Rhodococci when cultivated on oil as the only source of carbon. Cultivation of the sample on agar-containing Raymond inorganic medium with crude West Siberian oil as the only source of carbon revealed colonies of these bacteria, which all appeared identical. PCR was performed with DNA isolated from 5 colonies, using primers for 16S rRNA genes. Comparison of the sequences of the 5 PCR products over a length of 714 bp revealed that they were almost identical. Phylogenetic analysis of these homologous sequences showed that they were similar to the corresponding sequences of the genus Rhodococcus. Substrate demands, the morphology of the colonies, and SEM and TEM data confirmed that the isolates obtained could indeed be Rhodococci. All of the isolates could grow in bulk cultures with inorganic medium supplemented with crude oil. Moreover, all of the isolates degraded aliphatic hydrocarbons with lengths between C₁₁ and C₂₉. C₂₃-C₂₉ hydrocarbons were degraded completely. The isolates could grow at 4–37°C. The most unexpected finding was that of the many microorganisms capable of consuming oil, only Rhodococci exhibited this ability in the inactive bitumen mound. The possible mechanisms of how crude oil is transformed into bitumen mounds and mature bitumen are discussed.     

31P n.m.r. studies of complexes of NADPH and NADP+ with Escherichia coli dihydrofolate reductase

We have measured the ³¹P n.m.r. spectra of NADP⁺ and NADPH in their binary complexes with Escherichia coli dihydrofolate reductase and in ternary complexes with the enzyme and folate or methotrexate. The ³¹P chemical shift of the 2′ phosphate group is the same in all complexes; its value indicates that it is binding in the dianionic state and its pH independence suggests that it is interacting strongly with cationic residue(s) on the enzyme. Similar behaviour has been noted previously for the complexes with the Lactobacillus casei enzyme although the ³¹P shift is somewhat different in this complex, possibly due to an interaction between the 2′ phosphate group and His 64 which is not conserved in the E. coli enzyme. For the coenzyme complexes with both enzymes ³¹POC₂¹H_2′ spin-spin interactions were detected (7.5–7.8 Hz) on the 2′ phosphate resonances, indicating a POC₂H_2′ dihedral angle of 30 or 330 : this is in good agreement with the value of 330° measured in crystallographic studies¹ (Matthews et al., 1978) on the L. casei enzyme. NADPH-MTX complex. The pyrophosphate resonances are shifted to different extents in the various complexes and there is evidence that there is more OPO bond angle distortion in the E. coli enzyme complexes than in those with the L. casei enzyme. The effects of ³¹POC₅¹H_5′ spin coupling were detected on one pyrophosphate resonance and indicate that the POC₅H_5′ torsion angle has changed by at least ～30° on binding to the E. coli enzyme: this is considerably less than the distortion (～50°) observed previously in the L. casei enzyme complex.     

Structural and Conformational Studies on Deoxyguanosyl-3′,5′-Deoxyadenosine Monophosphate and Its Ethyl Phosphotriester Analogs - Left-Handed Dimers

Abstract

The mode of base-base stacking, the handedness and the sugar(dGpA)phosphate backbone conformation of deoxyguanosyl 3′-5′ deoxyadenosine and its diastereomeric ethyl phosphotriester analogs were studied by ¹H NMR, UV and CD spectroscopy. The results indicate the three dimers are left-handed, while the sugar phosphate backbone is comprised predominantly of C_2′-endo, gg (C_4′-C_5′) and g′g′ (C_5′-O) conformers. The two bases are extensively stacked and interact about 90° along the dyad axes. The extent of base overlap in dGpA is slightly greater than in either ethyl phosphotriester analog. The absolute configurations of the two ethyl phosphotriester diastereoisomers of dGpA can be assigned by one-dimensional and two-dimensional ¹H NMR nuclear Overhauser enhancement experiments.     

Organogold(I) complexes of a C2-symmetric diacetylide ligand derived from 1,1′-bi-2-naphthol

Alkynylgold(I) complexes incorporating a chiral binaphthyl group have been prepared. Bis(alkyne) reagents [rac-1,1′-C₂₀H₁₂-2,2′-(OCH₂CCH)₂] (1) and [rac-1,1′-C₂₀H₁₂-2,2′-(OC(O)CH₂CCH)₂] (2), react with [AuCl(SMe₂)] and base to give insoluble oligomeric alkynylgold(I) complexes [rac-1,1′-C₂₀H₁₂-2,2′-(OCH₂CCAu)₂]_n (3) and [rac-1,1′-C₂₀H₁₂-2,2′-(OC(O)CH₂CCAu)₂]_n (4), which react with phosphine or diphosphine ligands to give soluble complexes [rac-1,1′-C₂₀H₁₂-2,2′-(OCH₂CCAuPR₃)₂] (5), R = Ph or Cy, [rac-1,1′-C₂₀H₁₂-2,2′-(OCH₂CCAu)₂(Ph₂P(CH₂)_nPPh₂)] (6), or [rac-1,1′-C₂₀H₁₂-2,2′-(OC(O)CH₂CCAu)₂(Ph₂P(CH₂)_nPPh₂)] (7), with n = 3–5. Several of the complexes 6 and 7 are shown to exist as mixtures of isomeric forms in solution.     

Insertion reactions of carbonyl sulfide and carbon disulfide with [HRu(η5-C5H5)(EPh3)(E′Ph3)] (E,E′  P,As, Sb)

Monthioformate and dithioformate complexes of [HRu(η⁵-C₅H₅)(EPh₃)(E′Ph₃)] (E, E′  P, As, Sb) have been synthesized as a result of the insertion reactions of [HRu(η⁵-C₅H₅)(EPh₃)(E′Ph₃)] with carbonyl sulfide and carbon disulfide. The complexes were characterized by microanalytical, infra red, ¹H NMR, ¹³C NMR spectral data, molecular weight determination along with other studies.     

Surface wax of Andreaea and Pogonatum species

The mosses Andreaea rupestris, Pogonatum aloides and P. urnigerum contain surface waxes in amounts of 0.05–0.12% dry wt. The waxes consisted of esters (C₃₈-C₅₄), primary alcohols (C₂₀-C₃₂), free fatty acids (C₁₆-C₃₀), and alkanes (C₂₁-C₃₁). Additionally, aldehydes (C₂₂-C₃₀) were major constituents in the wax of P. urnigerum. The classes and their chain length distributions in the surface waxes of these mosses are comparable to those of epicuticular waxes of higher plants.     

An examination of the advantages of C3-C4 intermediate photosynthesis in warm environments

Abstract. The photosynthetic responses to temperature in C₃, C₃-C₄ intermediate, and C₄ species in the genus Flaveria were examined in an effort to identify whether the reduced photorespiration rates characteristic of C₃-C₄ intermediate photosynthesis result in adaptive advantages at warm leaf temperatures. Reduced photorespiration rates were reflected in lower CO₂ compensation points at all temperatures examined in the C₃-C₄ intermediate, Flaveria floridana, compared to the C₃ species, F. cronquistii. The C₃-C₄ intermediate, F. floridana, exhibited a C₃-like photosynthetic temperature dependence, except for relatively higher photosynthesis rates at warm leaf temperatures compared to the C₃ species, F. cronquistii. Using models of C₃ and C₃-C₄ intermediate photosynthesis, it was predicted that by recycling photorespired CO₂ in bundle-sheath cells, as occurs in many C₃-C₄ intermediates, photosynthesis rates at 35°C could be increased by 28%, compared to a C₃ plant. Without recycling photorespired CO₂, it was calculated that in order to improve photosynthesis rates at 35°C by this amount in C₃ plants, (1) intercellular CO₂ partial pressures would have to be increased from 25 to 31 Pa, resulting in a 57% decrease in water-use efficiency, or (2) the activity of RuBP carboxylase would have to be increased by 32%, resulting in a 22% decrease in nitrogen-use efficiency. In addition to the recycling of photorespired CO₂, leaves of F. floridana appear to effectively concentrate CO₂ at the active site of RuBP carboxylase, increasing the apparent carboxylation efficiency per unit of in vitro RuBP carboxylase activity. The CO₂-concentrating activity also appears to reduce the temperature sensitivity of the carboxylation efficiency in F. floridana compared to F. cronquistii. The carboxylation efficiency per unit of RuBP carboxylase activity decreased by only 38% in F. floridana, compared to 50% in F. cronquistii, as leaf temperature was raised from 25 to 35°C. The C₃-C₄ intermediate, F. ramosissima, exhibited a photosynthetic temperature temperature response curve that was more similar to the C₄ species, F. trinervia, than the C₃ species, F. cronquistii. The C₄-like pattern is probably related to the advanced nature of C₄-like biochemical traits in F. ramosissima The results demonstrate that reductions in photorespiration rates in C₃-C₄ intermediate plants create photosynthetic advantages at warm leaf temperatures that in C₃ plants could only be achieved through substantial costs to water-use efficiency and/or nitrogen-use efficiency.     

Phosphoenolpyruvate Carboxylase Purified from Leaves of C3, C4, and C3-C4 intermediate species of Alternanthera: Properties at Limiting and Saturating Bicarbonate

Phosphoenolpyruvate carboxylase (PEPC) was purified from leaves of four species of Alternanthera differing in their photosynthetic carbon metabolism: Alternanthera sessilis (C₃), A. pungens (C₄), A. ficoides and A. tenella (C₃-C₄ intermediates or C₃-C₄). The activity and properties of PEPC were examined at limiting (0.05 mM) or saturating (10 mM) bicarbonate concentrations. The V_max as well as K_m values (for Mg²⁺ or PEP) of PEPC from A. ficoides and A. tenella (C₃-C₄ intermediates) were in between those of C₃ (A. sessilis) and C₄ species (A. pungens). Similarly, the sensitivity of PEPC to malate (an inhibitor) or G-6-P (an activator) of A. ficoides and A. tenella (C₃-C₄) was also of intermediate status between those of C₃ and C₄ species of A. sessilis and A. pungens, respectively. In all the four species, the maximal activity (V_max), affinity for PEP (K_m), and the sensitivity to malate (K_I) or G-6-P (K_A) of PEPC were higher at 10 mM bicarbonate than at 0.05 mM bicarbonate. Again, the sensitivity to bicarbonate of PEPC from C₃-C₄ intermediates was in between those of C₃- and C₄-species. Thus the characteristics of PEPC of C₃-C₄ intermediate species of Alternanthera are intermediate between C₃- and C₄-type, in both their kinetic and regulatory properties. Bicarbonate could be an important modulator of PEPC, particularly in C₄ plants. This revised version was published online in August 2006 with corrections to the Cover Date.     

Studies on the Metabolites of Aspergillus versicolor (Vuillemin) Tiraboschi

Three new pigments, named versicolorins A, Band C, as metabolites from the mycelium of Aspergillus versicolor have been isolated. Versicolorin A, C₁₈H₁₀O₇, is fine orange yellow needles, m.p. 289°C (decomp.), [α]_D^-354°. It is an anthraquinoid pigment having three hydroxyl groups and a vinyl ether system contained in a five-membered ring. Versicolorin A trimethyl ether was hydrogenated to a dihydro-derivative, and by oxidation gave 3,5-dimethoxyphthalic acid and a hydroxy acid which may be 1,6,8-trirnethoxy-3-hydroxy anthraquinone-2-carboxylic acid. These chemical behavior and NMR data show that versicolorin A probably has the structure of (I). Versicolorin B, C₁₈H₁₂O₇, is fine orange yellow needles, m.p., 298°C (decomp.), [α]_D^-223° Its trimethyl ether is identical with that of dihydroversicolorin A. Therefore, the structure (II) could be assigned to versicolorin B. Versicolorin C, C₁₈H₁₂O₇, is orange red needles, m.p.>310°C, [α]_D O° Comparison of optical properties, IR and NMR spectra of versicolorin B and its methyl ether with those of versicolorin C and its methyl ether indicates that versicolorin C is very probably a racemate of versicolorin B.     

Crystal structure of dehydromonopetide, (Z)-N-acetyl-α,β-dehydrophenylalanine methylamide

The crystal structure of (Z)-acetyl-α,β-dehydrophenylalanine methylamide (monoclinic Cc, a = 10.241(1), b = 15.252(1), c = 8.643(1) Å, β = 120.98(1)°, Z = 4) has been solved by x-ray diffraction to an R-factor = 0.148, and compared to that of the homologous L -phenylalanine dervative. Molecules are intermolecularly hydrogen-bonded to four neighboring molecules in a three-dimensional network with alternating layers of interacting amide bonds and orthogonally arranged phenyl rings. The existence of the C^α = C^β double bond results in a phenyl orientation that is forbidden for phenylananine (χ¹ = ?7,8°), and in shorter C^α ? C^β and C^β ? C^γ distances. The geometrical paramenters of the peptide backbone are not drastically modified by α,β-unsaturation. However, the N-C^α-C′ angle is increased by nearly 5°, and the dimensions, and therefore probably the electronic conjugation, of the N-terminal amide group to be affected by the occurrence of the vicinal C^α = C^β double bond.     

Predictions of protein backbone bond distances and angles from first principles

A procedure is described, based on a spline-function representation of ab initio peptide conformational geometry maps, that allows one to predict backbone bond distances and angles of proteins as functions of the peptide ?(N-C^α)/Ψ(C^α-C′) torsions with an accuracy comparable to that of high-resolution protein crystallography. For example, for the more than 40 residues of crambin, the rms deviation between predicted and crystallographic values of N-C^α-C′ is 1.9° for the 1.5 Å resolution structure and 1.9° for the 0.83 Å resolution structure, compared with angle variations of < 10°. Accurate information on protein backbone geometries is important for establishing dictionaries of flexible geometry functions for use in empirical peptide and protein modeling. © 1995 John Wiley & Sons, Inc.     

Amidino-complexes of iron(II) and (III)

Lithioamidines {R′N(Li)C(R)NR′, I; R = CH₃, R′ = C₆H₅, p-CH₃,C₆H₄} react with iron(III) chloride

in monoglyme to produce navy-blue, high spin Fe{R′NC(R)NR′}₃ complexes which are extremely air and moisture sensitive. The corresponding reaction when R = R′ = C₆H₅ produces a soluble red complex and an air-stable green complex, whereas when R = H, R′ = C₆H₅ and R = R′ = C₆H₅ and the reaction is started at ca. ?20°, red and green complexes respectively are formed. Though all the complexes are formulated Fe{R′NC(R)NR′}₃, their properties reflect association through bridging amidino-groups. Iron(II) chloride reacts with I(R = CH₃, R′ = p-CH₃C₆H₄) to form two complexes, one crimson and soluble in organic solvents, and one brown and insoluble, which are fomulated [Fe{R′NC(R)NR′}₂]_n. The iron(III) complexes failed to react with, or were decomposed by, a variety of reducing, electrophilic and nucleophilic reagents, though blue Fe{p-CH₃C₆H₄NC(CH₃)N-p-CH₃C₆H₄}₃ reacts readily with nitric oxide to form a purple addition complex from which the N-nitroso-compound p-CH₃C₆H₄NC(CH₃)N(NO)-p-CH₃C₆H₄ was obtained in high yield. Treatment of the corresponding brown iron(II) complex with nitric oxide gave no reaction.     

Expression and localization of epitope-tagged protein kinase CK2

Protein kinase CK2, formerly known as casein kinase II, is a ubiquitous protein serine/threonine kinase. The enzyme exists in tetrameric complexes composed of two catalytic (CK2α and/or CK2α′) subunits and two subunits (CK2β) that appear to have a role in modulating the activity of the catalytic subunits. With the exception of their unrelated carboxy-terminal domains, the two isozymic forms of mammalian CK2 display extensive sequence identity. Furthermore, CK2α and CK2α′ exhibit remarkable conservation between species, suggesting that they may have unique functions. In the present study, the cDNAs encoding CK2α and CK2α′ were modified by addition of the hemagglutinin tag of the influenza virus at the amino terminus of the respective proteins. The epitope-tagged proteins were transfected into Cos-7 cells and the localization of the expressed proteins determined by indirect immunofluorescence using monoclonal antibodies specific for the epitope tag. The use of transfection favors the formation of homotetrameric complexes (i.e., α₂β₂, α′₂β₂) instead of heterotetrameric complexes (i.e., αα′β₂) that are present in many cells. Epitope-tagged CK2α and CK2α′ displayed kinase activity and the ability to form complexes with CK2β. The results of these studies also indicate definitively that CK2α and CK2α′ are both localized predominantly within the nucleus. Mutation of conserved lysine residues within the ATP binding domains of CK2α and CK2α′ resulted in loss of kinase activity. However, examination of these mutants indicates that kinase activity is not essential for formation of complexes between subunits of CK2 and is not required for nuclear localization of CK2. J. Cell. Biochem. 64: 525–537. © 1997 Wiley-Liss, Inc.     

Evidence for Deuterium Retention in the Products after Enzymatic C-C and Ether Bond Cleavages of Deuterated Lignin Model Compounds

The mechanism of C-C and ether bond cleavages of C_α-or C_β-deuterated β-O-4 and β-l lignin substructure models and the vicinal diol compounds catalyzed by the enzyme system from Phanerochaete chrysosporium culture was investigated. The enzymatic oxidation of β-O-4 lignin model compounds in the presence of H₂O₂ and O₂ yielded C₆-C_α-derived benzaldehyde, and C_β-C_γ-derived product together with the arylglycerol product. Likewise, the β-l models and the diol compounds also underwent the C-C bond cleavage, yielding C₆-C_β-derived benzaldehyde and the arylglycol product. The results demonstrated that the d-labels at C_α and C_β of the substrates were retained in the products after the C_α-C_β and ether bond cleavages.     

The Structural Basis of a Conserved P2 Threonine in Canonical Serine Proteinase Inhibitors

Abstract

Bowman-Birk inhibitors (BBIs) are a well-studied family of canonical inhibitor proteins of serine proteinases. In nature, the active region of BBIs possesses a highly conserved Thr at the P2 position. The importance of this residue has been reemphasized by synthetic BBI reactive site loop proteinomimetics. In particular, this residue was exclusively identified for active chymotrypsin inhibitors selected from a BBI template-assisted combinatorial peptide library. A further kinetic analysis of 26 P2 variant peptides revealed that Thr provides both optimal binding affinity and optimal resistance against enzymatic turnover by chymotrypsin.

Herein, we report the H-NMR spectroscopic study of a 5-membered sub-set of these reactive site loop peptides representing a stepwise elimination of the Thr side-chain functionalities and inversion of its side-chain chirality. The P2 Thr variant adopts a three-dimensional structure that closely mimics the one of the corresponding region of the complete protein. This validates the use of this template for the investigation of structure-function relationships. While the overall backbone geometry is similar in all studied variants, conformational changes induced by the modification of the P2 side chain have now been identified and provide a rational explanation of the kinetically observed functional differences. Eliminating the γ-methyl group has little structural effect, whereas the elimination of the γ-oxygen atom or the inversion of the side-chain chirality results in characteristic changes to the intramolecular hydrogen bond network. We conclude that the transannular hydrogen bond between the P2 Thr side-chain hydroxyl and the P5′ backbone amide is an important conformational constraint and directs the hydrophobic contact of the P2 Thr side chain with the enzyme surface in a functionally optimal geometry, both in the proteinomimetic and the native protein.

In at least four canonical inhibitor protein families similar structural arrangements for a conserved P2 Thr have been observed, which suggests an analogous functional role. Substitutions at P2 of the proteinomimetic also affect the conformational balance between cis and trans isomers at a distant Pro-Pro motif (P3′-P4′). Presented with a mixture of cis/trans isomers chymotrypsin appears to interact preferably with the conformer that retains the cis-P3′ Pro-trans-P4′ Pro geometry found in the parent BBI protein.