Proton transfer in and polarizability of hydrogen bonds coupled with conformational changes in proteins. II. IR investigation of polyhistidine with various carboxylic acids

Polyhistidine-carboxylic acid systems are studied by ir spectroscopy. It is shown that OH ?N ? O^?…H⁺N bonds formed between carboxylic groups and histidine residues are easily polarizable proton-transfer hydrogen bonds when the pK_a of the protonated histidine residues is about 2.8 units larger than that of the carboxylic groups. From these results it bis concluded that OH ?N ? O^? ?H⁺N bonds between glutamic or aspartic acid histidine residues in proteins may be easily polarizable proton-transfer bonds. Furthermore, it is demonstrated that water molecules shift the proton-transfer equilibria in these hydrogen bonds in favor of the polar structure, i.e., due to water or polar environments OH ?N ? O^? ?H⁺N bonds with smaller ΔpK_a values become easily polarizable proton-transfer hydrogen bonds. A consideration of the amide bands of polyhistidine shows that it can be present in five different conformations. It is shown that these conformational changes are strongly related to the degree of proton transfer. Hence, the degree of proton transfer, the degree of hydration, and conformation are not independent of each other, but are strongly coupled. Further proof for the interdependence of proton transfer and conformational changes are hysteresis effects, which are observed with studies of polyhistidine dependent on carboxylic acid, adsorption and desorption. OH ?N ? O^? ?H⁺N bonds between aspartic and glutamic acid and histidine residues are present in hemoglobin, in ribonucleases, and in proteases, whereby this type of bond is preferentially found in the active centers of these enzymes. It is pointed out that hydrogen bonds with such interaction properties should be of great significance for structure and especially functions of proteins in which they are present.     

Proton polarizability and proton transfer in histidine-phosphate hydrogen bonds as a function of cations present: ir investigations

(L -His)_n- dihydrogen phosphate systems are studied by ir spectroscopy in the presence of various cations and as a function of the degree of hydration. Ir continua indicate that (I) OH … N ? O^?…H⁺N (IIR) hydrogen bonds are formed and that these bonds show high proton polarizability, which increases from the Li⁺ to the K⁺ system. In the K⁺?system, His-P_i-P_i chains are formed, showing particularly high proton polarizability due to collective proton motion within both hydrogen bonds. The OH N ? O^?…H^?N equilibria are determined from ir bands. With the Li⁺ system, 55% of the protons are present at the histidine residues; this percentage is smaller with the Na⁺ system (41%), and amounts to only 32% with the K⁺ system. With the increasing degree of hydration the removal of the degeneracy of ν_as?PO^2?₃ vanishes, indicating loosening of the cations from the phosphates. Nevertheless, the hydrogen bond acceptor O atom becomes more negative; a shift of the equilibrium to the right is observed in the OH… N ? O^?…H⁺N bond. This is explained by the strong interaction of the dipole of the hydrogen bonds with the water molecules. All these results show that protons can be shifted easily in these hydrogen bonds due to their high proton polarizability. The transfer equilibria can be controlled easily by local electrical fields. In addition, these results may be of significance when phosphates interact with proteins.     

Proton translocation in hydrogen bonds with large proton polarizability formed between a Schiff base and phenols

OH…N ? O^?…H⁺N hydrogen bonds formed between N-all-transretinylidene butylamine (Schiff base) and phenols (1:1) are studied by IR spectroscopy. It is shown that both proton limiting structures of these hydrogen bonds have the same weight with Δ pK_a (50%) = (pK_a protonated Schiff base minus pK_a phenol) = 5.5. With the largely symmetrical systems, continua demonstrate that these hydrogen bonds show great proton polarizability. In the Schiff base + tyrosine system in a non-polar solvent the residence time of the proton at the tyrosine residue is much larger than that at the Schiff base. In CH₂CCl₂ these hydrogen bonds show, however, still proton polarizability, i.e., the position of the proton transfer equilibrium OH…N ? O^?…H⁺N is shifted to and fro as function of the nature of the environment of this hydrogen bond. Consequences regarding bacteriorhodopsin are discussed.     

Easily polarizable proton transfer hydrogen bonds between the side chains of histidine and the carboxylic acid groups of glutamic and aspartic acid residues in proteins

The nature of the hydrogen bonds formed between glutamic acid and histidine residues between aspartic acid and histidine residues is studied by i.r. spectroscopy. These studies were performed with $\text{(}\text{l}\text{-Glu}\text{)}{}_{\mathrm{n}}\text{+(}\text{l}\text{-His}\text{)}{}_{\mathrm{n}}$ and with associates of monomeric Glu + His and Asp + His systems in solutions whereby these amino acids had protected α-amino and α-carboxylic groups. It is shown that the OH …N?^?O?H⁺N bonds are easily polarizable proton transfer hydrogen bonds. The residence time of the proton at the His is a little larger in the case of the Asp + His than in the case of the Glu + His systems. Polar environments shift this proton transfer equilibrium in favour of the proton limiting structure ^?O?H⁺N, and less polar ones in favour of the structure OH?N. These results demonstrate that the large proton polarizability of the hydrogen bonded system in the active centre of chymotrypsin is responsible for the charge shift caused by the substrate, and thus for the increase in reactivity of the serine residue and the catalytic activity of the enzyme.     

Structurally symmetrical,easily polarizable hydrogen bonds between side chains in proteins and proton-conducting mechanisms. III

(L -Cys)_n, (L -Lys)_n, and (L -Glu)_n were studied by ir spectroscopy in terms of their degree of deprotonation or protonation. It is shown that structurally symmetrical, easily polarizable SH ?S^? ? ^?S ?HS, N⁺H ?N ? N ?H⁺N, and OH ?O^? ? ^?O ?HO hydrogen bonds are formed between the side chains. The different wave number distributions of the ir continua caused by these hydrogen bonds show that the barrier in the double-minimum proton potential decreases in the series of these hydrogen bonds. The stability of these hydrogen bonds against hydration increases in this series. The OH ?O^? ? ^?O ?HO bonds are not broken by small amounts of water. With (L -Cys)_n the formation of easily polarizable hydrogen bonds and a β-structure–coil transition are strongly interdependent. As a result of this coupling effect, the β-structure–coil transition becomes cooperative. With (L -Glu)_n, the formation of the polarizable hydrogen bonds and the observed conformational change are independent processes. The (L -Glu)_n conformation changes from α-helix to coil only if more than 80% of the residues are deprotonated. Finally, on the basis of the various types of easily polarizable hydrogen bonds, charge shifts in active centers of enzymes and the proton-conducting mechanism through hydrophobic regions of biological membranes are discussed.     

Proton transfer and polarizability of hydrogen bonds formed between cysteine and lysine residues

(L -Cys)_n + N-base systems and (L -Cys)_n + (L -Lys)_n systems were studied by ir spectroscopy. It is shown that in the water-free systems, SH ?N ? S^? ?H⁺N hydrogen bonds are formed. With the (L -Cys)_n + N-base systems, both proton-limiting structures in the SH ?N ? S^? ?H⁺N bonds have equal weight when the pK_a of the protonated N-base is 2 pK_a units larger than that of (L -Cys)_n. The same is true with the water-free (L -Cys)_n + (L -Lys)_n system. Thus, with regard to the type of proton potentials present, these hydrogen bonds are proton-transfer hydrogen bonds showing very large proton polarizabilities. This is confirmed by the occurrence of continua in the ir spectra. Small amounts of water open these hydrogen bonds and increase the transfer of the proton to (L -Lys)_n. In the (L -Lys)_n + N-base systems, with increasing proton transfer the backbone of (L -Cys)_n changes from antiparallel β-structure to coil. In (L -Cys)_n + (L -Lys)_n, the conformation is determined by the (L -Lys)_n conformation and changes depending on the chain length of (L -Lys)_n. Finally, the reactivity increase in the active center of fatty acid synthetase, which should be caused by the shift of a proton, is discussed on the basis of the great proton polarizability of the cysteine–lysine hydrogen bonds.     

Proton transfer in and polarizability of hydrogen bonds in proteins. Tyrosine-lysine and glutamic acid-lysine hydrogen bonds — IR investigations

The OH N O^– H⁺N hydrogen bonds formed between tyrosine and lysine, and between glutamic acid and lysine residues are studied by infrared spectroscopy considering the following systems: (l-lys)_n + phenol, copoly (l-lys, l-tyr)_n, (l-lys)_n + (l-tyr)_n and (l-lys)_n + (l-glu)_n. The phenol-lysine hydrogen bonds are largely symmetrical in the average if the pK_a of the protonated lysine is 2.2 units larger than that of the phenols. In the case of the hydrogen bonds between tyrosine and lysine residues in copoly (l-lys, l-tyr)_n and (l-lys)_n + (l-tyr)_n, the weight of the proton limiting structure OH N is 80–90%, and that of the polar O^– H⁺N structure 10–20%. Double minimum proton potentials occur but the proton is preferentially present at the tyrosine residues. In the (l-lys)_n + (l-glu)_n system, the protons are present at the lysine residues. Thus, these hydrogen bonds have very large dipole moments (about 10 D). With the lysine-phenole hydrogen bonds, hydration shifts the proton transfer equilibrium a little in favour of the polar proton limiting structure O^– H⁺N. These hydrogen bonds are broken to a large extent, however, when only about 3 water molecules are present per lysine residue. When less water is present, as in the copoly (l-lys, l-tyr)_n and (l-lys)_n + (l-tyr)_n systems, these hydrogen bonds are, however, formed quantitatively. Thus — as discussed in this paper — the tyrosine-lysine hydrogen bonds can participate in proton conducting hydrogen bonded systems — as, for instance, present in bacteriorhodopsin — performing the proton transport through hydrophobic regions of biological membranes.     

Proton polarizability of poly(L-tyrosine)–hydrogen phosphate hydrogen bonds as a function of alkali cations

We studied films of poly(L -tyrosine) with hydrogen phosphate (residue/phosphate, 1:1) by ir spectroscopy. The influences of the alkali cations (Li⁺, Na⁺, K⁺) and of the degree of hydration were clarified. If Li⁺ ions are present, the OH ?^?OP hydrogen bonds formed in the dried films between the tyrosine OH groups and hydrogen phosphate are asymmetrical. The formation of hydrogen phosphate–hydrogen phosphate hydrogen bonds is prevented by the presence of the Li⁺ ions. With an increase in the degree of hydration, the tyrosine–phosphate bonds are not broken but become slightly stronger. Completely different behaviour is found if K⁺ ions are present. In dry films, the OH ?^?OP ? O^? ?HOP hydrogen bonds formed between tyrosine and hydrogen phosphate show large proton polarizability. The tyrosine proton has a noticeable residence time at the acceptor O atom of the phosphate. The difference in the behaviour of the system with K⁺ ions when compared to the system with Li⁺ ions can be explained, since the hydrogen acceptor O atom of phosphate ions is more negatively charged due to the weaker influence of the K⁺ ions. Furthermore, POH ?^?OP hydrogen bonds between hydrogen phosphate molecules are formed. With an increase in the degree of hydration, the tyrosine–hydrogen phosphate hydrogen bonds are broken, all tyrosine protons are found at the tyrosine residues, and the -PO₃^? groupings are in a symmetrical environment, indicating that the K⁺ ions are removed from these groupings. If the degree of hydration increases further, hydrogen-bonded systems such as hydrogen phosphate–water–hydrogen phosphate are formed that show large proton polarizability due to collective proton motion. When Na⁺ ions are present, the OH ?^?OP ? O^? ?HOP hydrogen bonds formed in dry films still show proton polarizability, but the residence time of the tyrosine proton at the phosphate is very short.     

A high-resolution 13C-nmr study of collagenlike polypeptides and collagen fibrils in solid state studied by the cross-polarization–magic angle-spinning method. Manifestation of conformation-dependent 13C chemical shifts and application to conformational characterization

We have recorded high-resolution ¹³C-nmr spectra of collagen fibrils in the solid state by the cross-polarization–magic-angle-spinning(CP–MAS)method and analyzed the spectra with reference to those of collagenlike polypeptides. We used two kinds of model polypeptides to obtain reference ¹³C chemical shifts of major amino acid residues of collagen (Gly, Pro, Ala, and Hyp): the 3₁-helical polypeptides [(Gly)_nII, (Pro)_nII, (Hyp)_n, and (Ala? Gly? Gly)_nII], and the triple-helical polypeptides [(Pro? Gly? Pro)_n and (Pro? Ala? Gly)_n]. Examination of the ¹³C chemical shifts of these polypeptides, together with our previous data, showed that the ¹³C chemical shifts of individual amino acid residues are the same, within experimental error (±0.5 ppm), among different polypeptides with different primary sequences, if the conformations are the same. We found that the ¹³C chemical shifts of Ala residues of the 3₁-helical (Ala? Gly? Gly)_n and triple-helical (Pro? Ala? Gly)_n are significantly displaced, compared with those of the α-helix, β-sheet, and silk I form, and can be utilized as excellent probes to examine conformational features of collagen-like polypeptides. Further, the ¹³C chemical shifts of Gly and Pro residues in the triple-helical polypeptides are substantially displaced from those found in (Gly)_nII and (Pro)_nII of the 3₁-helix, reflecting further conformational change from the 3₁-helix to the supercoiled triple helix. In particular, the ¹³C chemical shifts of Gly C ? O carbons of the triple-helical polypeptides are substantially displaced upfield (4.1–5.1 ppm), with respect to those of the 3₁-helical polypeptides. These displacements are interpreted by that Gly C ? O of the former is not involved in NH …? O ? C hydrogen bonds, while this carbon of the latter is linked by these kinds of hydrogen bonds. On the basis of these ¹³C chemical shifts, as reference data for the collagenlike structure, we were able to assign the ¹³C-nmr peaks of Gly, Ala, Pro, and Hyp residues of collagen fibrils, which are in good agreement with the values expected from the model polypeptides mentioned above. We also discuss a plausible conformational change of collagen fibrils during denaturation.     

Easily polarizable N+H…N hydrogen bonds between histidine side chains and proton translocation in proteins

Histidinium perchlorate having protecting groups at the α-amino and α-carboxylate group is studied by IR spectroscopy as function of the addition of protected histidine molecules. An intense continuous absorption arises, indicating that the N⁺H…N ? N…H⁺N formed are easily polarizable hydrogen bonds. From the integral absorbance of a band the concentration of the histidine-histidinium complex, i.e. the concentration of the easily polarizable hydrogen bonds is determined. It is shown that the absorbance of the continuum increases in proportion to the concentration of the easily polarizable N⁺H…N ? N…H⁺N bonds. Finally, it is discussed that via such an easily polarizable histidine-histidinium hydrogen bond a proton translocation in the active center of ribonuclease A may occur.     

Prototropic tautomerism and basic molecular principles of hypoxanthine mutagenicity: an exhaustive quantum-chemical analysis

The molecular structures, relative stability order, and dipole moments of a complete family of 21 planar hypoxanthine (Hyp) prototropic molecular–zwitterionic tautomers including ylidic forms were computationally investigated at the MP2/6–311++G(2df,pd)//B3LYP/6–311++G(d,p) level of theory in vacuum and in three different surrounding environments: continuum with a low dielectric constant (??=?4) corresponding to a hydrophobic interface of protein–nucleic acid interactions, dimethylsulfoxide (DMSO), and water. The keto-N1HN7H tautomer was established to be the global minimum in vacuum and in continuum with ??=?4, while Hyp molecule exists as a mixture of the keto-N1HN9H and keto-N1HN7H tautomers in approximately equal amounts in DMSO and in water at T?=?298.15?K. We found out that neither intramolecular tautomerization by single proton transfer in the Hyp base, nor intermolecular tautomerization by double proton transfer in the most energetically favorable Hyp·Hyp homodimer (symmetry C _2h ), stabilized by two equivalent N1H…O6 H-bonds, induces the formation of the enol tautomer (marked with an asterisk) of Hyp with cis-oriented O6H hydroxyl group relative to neighboring N1C6 bond. We first discovered a new scenario of the keto–enol tautomerization of Hyp?·?Hyp homodimer (C _2h ) via zwitterionic near-orthogonal transition state (TS), stabilized by N1⁺H…N1^? and O6⁺H…N1^? H-bonds, to heterodimer Hyp^??·?Hyp (C _s ), stabilized by O6H…O6 and N1H…N1 H-bonds. We first showed that Hyp^??·?Thy mispair (C _s ), stabilized by O6H…O4, N3H…N1, and C2H…O2 H-bonds, mimicking Watson–Crick base pairing, converts to the wobble Hyp?·?Thy base pair (C _s ), stabilized by N3H…O6 and N1H…O2 H-bonds, via high- and low-energy TSs and intermediate Hyp?·?Thy^?, stabilized by O4H…O6, N1H…N3, and C2H…O2 H-bonds. The most energetically favorable TS is the zwitterionic pair Hyp⁺?·?Thy^? (C _s ), stabilized by O6⁺H…O4^?, O6⁺H…N3^?, N1⁺H…N3^?, and N1⁺H…O2^? H-bonds. The authors expressed and substantiated the hypothesis, that the keto tautomer of Hyp is a mutagenic compound, while enol tautomer Hyp^? does not possess mutagenic properties. The lifetime of the nonmutagenic tautomer Hyp^? exceeds by many orders the time needed to complete a round of DNA replication in the cell. For the first time purine–purine planar H-bonded mispairs containing Hyp in the anti-orientation with respect to the sugar moiety – Hyp?·?Ade _syn , Hyp?·?Gua^? _syn , and Hyp?·?Gua _syn , that closely resembles the geometry of the Watson–Crick base pairs, have been suggested as the source of transversions. An influence of the surrounding environment (??=?4) on the stability of studied complexes and corresponding TSs was estimated by means of the conductor-like polarizable continuum model. Electron-topological, structural, vibrational, and energetic characterictics of all conventional and nonconventional H-bonds in the investigated structures are presented. Presented data are key to understanding elementary molecular mechanisms of mutagenic action of Hyp as a product of the adenine deamination in DNA.     

Defect peptide chemistry: Perturbations in the structure of a homopentapeptide induced by a guest residue interrupting side-chain regularity

The fully blocked pentapeptide Tfa-(Deg)₂-L -Abu-(Deg)₂-OtBu (Tfa:triflouroacetyl; Deg: C^α,α-diethylglycine; OtBu: tert-butoxy) adopts in the crystal state a regular, right-handed 3₁₀-helical structure stabilized by three N ? H …? O ? C intramolecular 1 ← 4 (or C₁₀) H bonds, as determined by an x-ray diffraction analysis. However, a Fourier transform ir absorption and ¹H-nmr study strongly supports the view that in deuterochloroform solution the four Deg residues at both termini of the peptide main chain are involved in successive, fully extended C₅ forms. A comparison with the stable, fully developed, multiple C₅ conformation of Tfa-(Deg)₅-OtBu indicates that incorporation of an Abu guest residue, interrupting the side-chain uniformity of the host (Deg)₅ homopeptide, while altering only marginally the conformation in a solvent of low polarity, is responsible for a dramatic perturbation of the crystal-state structure. © 1994 John Wiley & Sons, Inc.     

Phosphate- N base hydrogen bonds involving proton transfer with reference to the non-enzymic hydrolysis of ATP

IR spectra of aqueous solutions of 1:1 mixtures of H₂PO₄^? and various N bases have been studied as models for (POH?N) → (P^?O?H⁺N) hydrogen bonds. 50% proton transfer is observed when the pKa of the protonated N base is 1.1 smaller than that of the phosphate group. The hydrogen bonds are easily polarizable near this equilibrium. These results strongly support the conclusion that such bonds contribute 1) to the self-association of ATP and ADP and 2) to the association of the hydrolysis products ADP and inorganic phosphate.     

Rigidity of α-helical polypeptides. A new method of obtaining the persistence length from viscosimetric data

The hydrodynamic properties of α-helical poly(L -glutamic acid), (Glu)_n in aqueous solutions and in mixtures of water with organic solvents have been interpreted in terms of the persistence length of the macromolecule. A modification of the method of Vitovskaya and Tsvetkov has been proposed in order to allow a more accurate determination of this parameter. The addition of an organic solvent increases strongly the rigidity of the helical conformation of (Glu)_n. A comparison is made with some data of the literature of poly[N⁵-(3-hydroxy propyl)L -glutamine], [Gln(CH₂)₃OH]_n, and poly(γ-benzyl-L -glutamate), [Glu(OBzl)]_n.     

Asparagine and glutamine differ in their propensities to form specific side chain-backbone hydrogen bonded motifs in proteins

Short range side chain‐backbone hydrogen bonded motifs involving Asn and Gln residues have been identified from a data set of 1370 protein crystal structures (resolution ≤ 1.5 Å). Hydrogen bonds involving residues i ? 5 to i + 5 have been considered. Out of 12,901 Asn residues, 3403 residues (26.4%) participate in such interactions, while out of 10,934 Gln residues, 1780 Gln residues (16.3%) are involved in these motifs. Hydrogen bonded ring sizes (C_n, where n is the number of atoms involved), directionality and internal torsion angles are used to classify motifs. The occurrence of the various motifs in the contexts of protein structure is illustrated. Distinct differences are established between the nature of motifs formed by Asn and Gln residues. For Asn, the most highly populated motifs are the C₁₀ (CO^δ_i …NH_{i + 2}), C₁₃ (CO^δ_i …NH_{i + 3}) and C₁₇ (N^δH_i …CO_{i ? 4}) structures. In contrast, Gln predominantly forms C₁₆ (CO^ε_i …NH_{i ? 3}), C₁₂ (N^εH_i …CO_{i ? 2}), C₁₅ (N^εH_i …CO_{i ? 3}) and C₁₈ (N^εH_i …CO_{i ? 4}) motifs, with only the C₁₈motif being analogous to the Asn C₁₇structure. Specific conformational types are established for the Asn containing motifs, which mimic backbone β‐turns and α‐turns. Histidine residues are shown to serve as a mimic for Asn residues in side chain‐backbone hydrogen bonded ring motifs. Illustrative examples from protein structures are considered. Proteins 2012; © 2011 Wiley Periodicals, Inc.     

Chain length dependent transition of 310- to α-helix of Boc-(Ala-Aib)n-OMe

An apolar synthetic octapeptide, Boc-(Ala-Aib)₄-OMe, was crystallized in the triclinic space group P1 with cell dimensions a = 11.558 Å, b = 11.643 Å, c = 9.650 Å, α = 120.220°, β = 107.000°, γ = 90.430°, V = 1055.889 ų, Z = 1, C₃₄H₆₀O₁₁N₈·H₂O. The calculated crystal density was 1.217 g/cm³ and the absorption coefficient ? was 6.1. All the intrahelical hydrogen bonds are of the 3₁₀ type, but the torsion angles, ? and ψ, of Ala(5) and Ala(7) deviate from the standard values. The distortion of the 3₁₀-helix at the C-terminal half is due to accommodation of the bulky Boc group of an adjacent peptide in the nacking. A water molecule is held between the N-terminal of one peptide and the C-terminal of the other. The oxygen atom of water forms hydrogen bonds with N (1) -H and N (2) -H, which are not involved in the intrahelical hydrogen bonds. The hydrogen atoms of water also formed hydrogen bonds with carbonyl oxygens of the adjacent peptide molecule. On the other hand, ¹H-nmr analysis revealed that the octapeptide took an α-helical structure in a CD₃CN solution. The longer peptides, Boc-(Ala-Aib)₆-OMe and Boc-(Ala-Aib)₈-OMe, were also shown to take an α-helical structure in a CD₃CN solution. An α-helical conformation of the hexadecapeptide in the solid state was suggested by x-ray analysis of the crystalline structure. Thus, the critical length for transition from the 3₁₀- to α-helix of Boc-(Ala-Aib)_n-OMe is 8. © 1993 John Wiley & Sons, Inc.     

β-Turn conformations in crystal structures of model peptides containing α,α-Di-n-propylglycine and α,α-Di-n-butylglycine

The crystal state conformations of three peptides containing the α,α-dialkylated residues. α,α-di-n-propylglycine (Dpg) and α,α-di-n-butylglycine (Dbg), have been established by x-ray diffraction. Boc-Ala-Dpg-Alu-OMe (I) and Boc-Ala-Dbg-Ala-OMe (III) adopt distorted type II β-turn conformations with Ala (1) and Dpg/Dbg (2) as the corner residues. In both peptides the conformational angles at the Dxg residue (I: ? = 66.2°, ψ = 19.3°; III: ? = 66.5°. ψ = 21.1°) deviate appreciably from ideal values for the i + 2 residue in a type II β-turn. In both peptides the observed (N…O) distances between the Boc CO and Ala (3) NH groups are far too long (1: 3.44 Å: III: 3.63 Å) for an intramolecular 4 → 1 hydrogen bond. Boc-Ala-Dpg-Ata-NHMe (II) crystallizes with two independent molecules in the asymmetric unit. Both molecules HA and HB adopt consecutive β-turn (type III-III in HA and type III-I in IIB) or incipient 3₁₀-helical structures, stabilized by two intramolecular 4 → 1 hydrogen bonds. In all four molecules the bond angle N-C^α-C′ (τ) at the Dxg residues are ≥ 110°. The observation of conformational angles in the helical region of ?,ψ space at these residues is consistent with theoretical predictions. © 1995 John Wiley & Sons, Inc.     

Accommodation of a D-Phe residue into a right-handed 310-helix: Structure of Boc-D-Phe-(Aib)4-Gly-L-Leu-(Aib)2-Ome,an analogue of the amino terminal segment of antiamoebins and emerimicins

The crystal structure of the nonapeptide Boc-D -Phe-Aib-Aib-Aib-Aib-Gly-Leu-Aib-AibOMe (I), which is an analogue of the N-terminal sequence of antiamoebins and emerimicins, establishes a completely 3₁₀-helical conformation with seven successive intramolecular 4 → 1 hydrogen bonds. The average, ?, ψ values for residues 1–8 are ?59° and ?32°, respectively. Crystal parameters are C₄₇H₇₇N₉O₁₂, space group P1, a = 10.636(4) Å, b = 11.239(4) Å, c = 12.227(6) Å, α = 101.17(4)°, β = 97.22(4)°, γ = 89.80(3)°, Z = 1, R = 5.95% for 3018 data with |F₀| > 3α(F), resolution 0.93 Å. The use of the torsion angle κ = C(i ? 1)N(i)C^α(i)C^β(i), where κ = 68° for D -Phe and κ = 164° for L -Leu, confirms the opposite configurations of these residues. The ?, ψ values of ?62° and ?32° at D -Phe are unusual, since this region is characteristic of residues with L configurations. Peptide I possesses only two chiral residues of opposing configuration. The observed right-handed 3₁₀-helical structure suggests that helix sense has probably been determined by the stereo-chemical preferences of the Leu residue. © 1993 John Wiley & Sons, Inc.     

Peptide design 310-helical conformation of a linear pentapeptide containing two dehydrophenylalanines,Boc-Gly-ΔZPhe-Leu-ΔZPhe-Ala-NHCH3

α, β-Dehydroamino acids are expected to provide conformational constraint to the peptide backbone. A pentapeptide containing two dehydrophenylalanines (Δ^ZPhe) separated by one L -amino acid has been synthesized and its solid state conformation determined. The pentapeptide, Boc-Gly-Δ^ZPhe-Leu-Δ^ZPhe-Ala-NHCH₃, crystallizes from aqueous methanol in the orthorhombic space group P2₁2₁2₁. There are four formula units, C₃₅H₄₆N₆O₇, in a unit cell of dimensions a = 10.155(3), b = 15.175(1), and c = 23.447(2) Å, at room temperature. The structure was solved by direct methods program, SIR88, and refined to a final R = 0.038 based on 3049 reflections with I > 2σ(I). All the peptide links are trans and the backbone conformation of the pentapeptide can be described as a 3₁₀-helix, with mean ?, ψ values of ?65.1° and ?22.8° (the value is averaged over the first four residues). There are four intramolecular 4 → 1 type hydrogen bonds characteristic of 3₁₀-type helices. In the crystal, the helices are held together by intermolecular N? H…?O?C head-to-tail and lateral hydrogen bonding between symmetry related molecules. This mode of packing is similar to the packing motifs observed so often in other oligopeptides that adopt a 3₁₀-helical structure. © 1993 John Wiley & Sons, Inc.     

Investigation of protonatable residues in Rhodothermus marinus caa 3 haem-copper oxygen reductase: comparison with Paracoccus denitrificans aa 3 haem-copper oxygen reductase

The Rhodothermus marinus caa ₃ haem-copper oxygen reductase contains all the residues of the so-called D- and K-proton channels, with the notable exception of the helix VI glutamate residue (Glu278^I in Paracoccus denitrificans aa ₃), being nevertheless a true oxygen reductase reducing O₂ to water, and an efficient proton pump. Instead, in the same helix, but one turn below, it has a tyrosine residue (Tyr256^I, R. marinus caa ₃ numbering), whose hydroxyl group occupies the same spatial position as the carboxylate group of Glu278^I, as deduced by comparative modelling techniques. Therefore, we proposed previously that this tyrosine residue could play an important role in the proton pathway. In this article we further study this hypothesis, by investigating the equilibrium thermodynamics of protonation in R. marinus caa ₃, using theoretical methodologies based on the structural model previously obtained. Control calculations are also performed for the P. denitrificans aa ₃ oxygen reductase. In both oxygen reductases we find several residues that are proton active (i.e., that display partial protonation) at physiological pH, some of them being redox sensitive (i.e., sensitive to the protein redox state). However, the caa ₃ Tyr256^I is not proton active at physiological pH, in contrast to the aa ₃ Glu278^I which is both proton active at physiological pH and shows a high redox sensitivity. In R. marinus caa ₃ we do not find any other residues in the same protein zone that can have this property. Therefore, there are no putative D-channel residues that are proton active in this oxidase. The protonatable residues of the K-channel are much more functionally conserved in both oxygen reductases than the same type of residues in the D-channel. Two (Tyr262^I and Lys336^I, caa ₃ numbering) out of three protonatable K-channel residues are proton active and redox sensitive in both proteins.