Non-protein amino acids in peptide design

An overview of the use of non-protein amino acids in the design of conformationally well-defined peptides, based on work from the author’s laboratory, is discussed. The crystal structures of several designed oligopeptides illustrate the useα-aminoisobutyric acid (Aib) in the construction of helices, D-amino acids in the design of helix termination segments and^DPro-Xxx segments for nucleating ofβ-hairpin structures.β- andγ-amino acid residues have been used to expand the range of designed polypeptide structures. Dedicated to Professor C N R Rao on his 70th birthday     

Aromatic-aromatic interactions in crystal structures of helical peptide scaffolds containing projecting phenylalanine residues

Aromatic-aromatic interactions between phenylalanine side chains in peptides have been probed by the structure determination in crystals of three peptides: Boc-Val-Ala-Phe-Aib-Val-Ala-Phe-Aib-OMe, I; Boc-Val-Ala-Phe-Aib-Val-Ala-Phe-Aib-Val-Ala-Phe-Aib-OMe, II; Boc-Aib-Ala-Phe-Aib-Phe-Ala-Val-Aib-OMe, III. X-ray diffraction studies reveal that all three peptides adopt helical conformations in the solid state with the Phe side chains projecting outward. Interhelix association in the crystals is promoted by Phe-Phe interactions. A total of 15 unique aromatic pairs have been characterized in the three independent crystal structures. In peptides I and II, the aromatic side chains lie on the same face of the helix at i/i + 4 positions resulting in both intrahelix and interhelix aromatic interactions. In peptide III, the Phe side chains are placed on the opposite faces of the helix, resulting in exclusive intermolecular aromatic interactions. The distances between the centroids of aromatic pair ranges from 5.11 to 6.86 A, while the distance of closest approach of ring carbon atoms ranges from 3.27 to 4.59 A. Examples of T-shaped and parallel-displaced arrangements of aromatic pairs are observed, in addition to several examples of inclined arrangements. The results support the view that the interaction potential for a pair of aromatic rings is relatively broad and rugged with several minima of similar energies, separated by small activation barriers.     

Electrodeposition of monodispersed Fe nanocrystals from an ionic liquid

Monodispersed Fe nanocrystals up to approximately 2 nm thick, approximately 50 nm wide and approximately 120 nm long have been electrodeposited from the ionic melt AlCl(3)-1-methyl-3-butylimidazolium chloride [AlCl3-[MBIm](+)Cl(-)] at room temperature on Au(111) and have been characterized in-situ by electrochemical scanning tunneling microscopy.     

Kinetics of lamellar-to-cubic and intercubic phase transitions of pure and cytochrome c containing monoolein dispersions monitored by time-resolved small-angle X-ray diffraction

We investigated the effect of incorporation of a small aqueous peripheral membrane protein (cyt c) into the three-dimensional periodic nanochannel structures formed by the lipid monoolein (MO) on its rich phase behavior as a function of temperature, pressure, and protein concentration using synchrotron X-ray small-angle diffraction. By simultaneous use of the pressure-jump relaxation technique and time-resolved synchrotron X-ray diffraction, we also studied the kinetics of various lipid mesophase transformations of the system for understanding the mechanistic pathways of their formation influenced by the protein-lipid interactions. Cyt c incorporated into the bicontinuous cubic phase Ia3d of MO has a significant effect on the lipid structure and the pressure stability of the system already at low protein concentrations. Concentrations higher than 0.2 wt % of cyt c led to an increase in interfacial curvature due to interaction of the protein with the lipid headgroups. This promotes the formation of a new, probably partially micellar cubic phase of crystallographic space group P4(3)32. Upon pressurization, the P4(3)32 phase undergoes a phase transition to a cubic Pn3m phase with smaller partial specific volume. Increase in protein concentration increases the pressure stability of the P4(3)32 phase. The formation of this phase from the cubic phase Pn3m is a slow process taking many seconds and having a time lag in the beginning. It seems to occur as a two-state process without ordered intermediate states. At temperatures above 60 degrees C, the P4(3)32 phase is unable to accommodate the unfolded protein and transforms to a bicontinuous cubic Ia3d phase. Time-resolved small-angle X-ray scattering studies show that the L(alpha) --> Ia3d transition in pure MO dispersions under limited hydration conditions occurs within a time interval of 1 s at 35 degrees C preceded by a lag phase of 1.5 s. The Ia3d cubic phase initially forms with a much larger lattice constant due to hydration and experiences an initially lower curvature that relaxes within about 1 s. Interestingly, no other cubic phases are involved as intermediates in the transition, i.e., the gyroid cubic phase is able to form directly from the L(alpha) phase. The mechanism behind the L(alpha) --> Ia3d transition in pure MO dispersions has been discussed within the framework of recent stalk models for membrane fusion. In the presence of cyt c, the L(alpha) --> Ia3d transition is much slower. The rather long relaxation times of the order of seconds are probably due to a kinetic trapping of the system and limitation by the transport and redistribution of water and lipid in the evolving new lipid phases. We also studied the transition from the pure lamellar L(alpha) phase to the Ia3d-P4(3)32 two phase region and observed a rather complex transition behavior with transient lamellar and cubic intermediate states.     

Synthesis of Quinoline-Based Thieno-Seleno-Phenylquinazolinones

The synthesis of quinoline-substituted phenylquinazolinones containing sulfur and selenium is described. These molecules were isolated from a series of reactions of 2-phenyl-4H-3,1-benzoxazin-4-one with 2-chloro, 2-thieno, and 2-selenoquinoline-3-carbaldehyde hydrazones. The structure of the isolated compounds has been elucidated on the basis of IR, ¹ H NMR, mass spectral, and elemental analysis data.     

An unusual conformation of gabapentin (Gpn) in Pyr‐Gpn‐NH‐NH‐Pyr stabilized by weak interactions

The crystal structure of N‐[(1‐{2‐oxo‐2‐[2‐(pyrazin‐2‐ylcarbonyl)hydrazin‐1‐yl]ethyl}cyclohexyl)methyl]pyrazine‐2‐carboxamide monohydrate (Pyr‐Gpn‐NN‐NH‐Pyr·H₂O), C₁₉H₂₃N₇O₃·H₂O, reveals an unusual trans–gauche (tg⁻) conformation for the gabapentin (Gpn) residue around the C^γ—C^β (θ₁) and C^β—C^α (θ₂) bonds. The molecular conformation is stabilized by intramolecular N—H...N hydrogen bonds and weak C—H...O interactions. The packing of the molecules in the crystal lattice shows a network of strong N—H...O and O—H...O hydrogen bonds together with weak C—H...O and π–π inteactions.     

Seven new hindered isomeric rhodopsins: A reexamination of the stereospecificity of the binding site of bovine opsin

Results of interaction of seven new geometric isomers of retinal (7-cis, 7,9-dicis; 7,11-dicis, 7,13-dicis; 9,11-dicis 7,9,11-tricis 7,9,13-tricis) with bovine opsin are reported. All of them form pigments with absorption maxima varying between 450 and 480 nm. The rates of pigment formation were generally considerably lower than those of 11-cis-retinal and the yields were less than quantitative. Implications of these results for the stereospecificity of the binding site of opsin are discussed.     

Microscopic and electronic structure of semimetallic Sb and Semiconducting AlSb fabricated by nanoscale electrodeposition: An in situ scanning probe investigation

The nanoscale electrocrystallization of pure Sb and the compound semiconductor AlSb on Au(111) has been studied by in situ scanning probe techniques (STM and STS) employing an ionic liquid electrolyte, {AlCl3-[C4mim]+Cl-} (1:1) containing SbCl3. The characteristic changes of the electronic structures with varying potentials have been probed for the first time by normalized differential conductance spectra, (dI/dU)/(I/U). In the underpotential deposition range of Sb the formation of two layers is observed. For the first monolayer a (square root 3 x square root 3)R30 degrees structure is determined from atomically resolved STM images. During the deposition and dissolution of the Sb monolayers characteristic wormlike or spinodal structures appear indicating surface alloying of antimony with the gold substrate. Under overpotential conditions two different Sb structures have been observed. If the deposition potential is continuously stepped to -0.1 V, Sb nanostripes form. On the other hand, randomly dispersed small clusters occur if the potential is jumped from 0.0 to -0.3 V vs Al/Al(III). Both modifications exhibit typical semimetallic behavior as shown by the STS spectra. At -1.1 V the cyclic voltammogram shows a clear reduction wave that is assigned to AlSb compound formation. Deposits in this potential range are characterized by a homogeneous distribution of clusters with diameters of approximately 20 nm. Conductance spectra of these clusters exhibit the main features of the electronic structure of the bulk semiconductor AlSb, with a band gap of 2.0 +/- 0.2 eV. Electrodeposition experiments on both sides of the compound deposition potential show a strong doping effect that is manifest in the corresponding conductance spectra.     

Diproline templates as folding nuclei in designed peptides. Conformational analysis of synthetic peptide helices containing amino terminal Pro-Pro segments

The effect of N-terminal diproline segments in nucleating helical folding in designed peptides has been studied in two model sequences Piv-Pro-Pro-Aib-Leu-Aib-Phe-OMe (1) and Boc-Aib-Pro-Pro-Aib-Val-Ala-Phe-OMe (2). The structure of 1 in crystals, determined by X-ray diffraction, reveals a helical (alphaR) conformation for the segment residues 2 to 5, stabilized by one 4-->1 hydrogen bond and two 5-->1 interactions. The N-terminus residue, Pro(1) adopts a polyproline II (P(II)) conformation. NMR studies in three different solvent systems support a conformation similar to that observed in crystals. In the apolar solvent CDCl3, NOE data favor the population of both completely helical and partially unfolded structures. In the former, the Pro-Pro segment adopts an alphaR-alphaR conformation, whereas in the latter, a P(II)-alphaR structure is established. The conformational equilibrium shifts in favor of the P(II)-alphaR structure in solvents like methanol and DMSO. A significant population of the Pro(1)-Pro(2) cis conformer is also observed. The NMR results are consistent with the population of at least three conformational states about Pro-Pro segment: trans alphaR-alphaR, trans P(II)-alphaR and cis P(II)-alphaR. Of these, the two trans conformers are in rapid dynamic exchange on the NMR time scale, whereas the interconversion between cis and trans form is slow. Similar results are obtained with peptide 2. Analysis of 462 diproline segments in protein crystal structures reveals 25 examples of the alphaR-alphaR conformation followed by a helix. Modeling and energy minimization studies suggest that both P(II)-alphaR and alphaR-alphaR conformations have very similar energies in the model hexapeptide 1.