Side-chain effect on conformation of ionizable polypeptides in aqueous solution

In order to study the effect of side-chain length on the conformation of polypeptides, conformational changes of various ionic polypeptides with various lengths of side chain, poly-N^ε-glutaryl-L -lysine (PGL), poly-N^δ-glutaryl-L -ornithine (PGO), poly-N^ε-succinyl-L -lysine (PSL), and poly-N^δ-succinyl-L -ornithine (PGO), were investigated by ORD, potentiometric titration, and dilatometric measurements in aqueous solution. The results of optical rotation and potentiometric titration measurements indicate strongly that the α-helix stability increases in the sequence PSO < PSL ～ PGO < PGL, which corresponds to increased side-chain length. The volume change associated with the helix–coil transition also increased in the above sequence. This series of polymers seems to be more hydrophobic compared with poly-L -glutamic acid or poly-L -lysine, as suggested from the values of enthalpy and entropy changes for coil–helix transitions.     

Ordered conformation of polypeptides and proteins in acidic dodecyl sulfate solution

The conformation of some polypeptides and proteins in sodium dodecyl sulfate (NaDodSO4) solutions was studied by circular dichroism. The type and extent of induced structure depend on their helix- and beta-forming potential. Anionic side groups in segments of helix or beta form tend to destabilize the ordered structure unless they are protonated. beta-Endorphin has one Glu inside a predicted helical segment; its helicity in a NaDodSO4 solution is enhanced at pH below 4. alpha-Melanocyte-stimulating hormone having a Glu in a beta segment undergoes a pH-induced coil to beta transition in 1.25 mM NaDodSO4 (excess surfactant will disrupt the beta form). Reduced somatostatin assumes a beta form in 2 mM NaDodSO4 and a partial helix in 25 mM NaDodSO4, both of which are unchanged in acidic pH because it lacks -COOH groups. The unordered gastrin with five consecutive Glu's becomes helical in a NaDodSO4 solution at pH 4. Neurotensin with one Glu has no structure-forming potential and is unordered in both neutral and acidic NaDodSO4 solutions. This charge effect also manifests in segments of ordered structure for polypeptides and proteins such as glucagon, cytochrome c, parvalbumin, ribonuclease A, and lysozyme. The effect is especially predominant in tropomyosin that is rich in clusters of anionic side groups. Its more than 90% helicity is reduced to about one-half in a neutral NaDodSO4 solution, but most of it can be restored by lowering the pH to 2.4.     

Unsaturated amino-acid residues as probes for the conformation of polypeptides in solution

Acetyl-(dehydro-Phe) and acetyl-bis(dehydro-Phe) groups have been attached to the ε-amino group of the lysine residues of the copolymer poly(Glu⁹²Lys⁸) by reacting this last with acetyl-(dehydro-Phe)-azlactone and acetyl-bis(dehydro-Phe)-azlactone, respectively. In the latter case induced CD is observed between 250 and 330 nm, due to the relative dissymmetric disposition of the two dehydro-Phe groups under the chiral field of the polypeptide chain. pH dependence of the induced CD, observed for the copolymer and lacking in the lowmolecular-weight structural model, is related to the α-helical and random coiled conformation of the polypeptide chain.     

Crystal structure and conformation of polypeptides: L-leucylglycylglycylglycine

Crystals of L-leucylglycylglycylglycine, LGGG (C12H22N4O5), grown from an ethanol-water solution, are orthorhombic, space groups P2(1)2(1)2(1), with unit cell dimensions (at 22 +/- 3 degrees) a = 9.337(1), b = 10.995(1), c = 15.235(1)A, v = 1563.4 A3, Z = 4 with a density of Dobs = 1.29 g.cm-3 and Dcalc = 1.279 g.cm-3. The crystal structure was solved by the application of direct methods and refined to an R value of 0.029 for 1018 reflections with I greater than or equal to 2 sigma. The molecule exists as a zwitterion in the crystal. The trans peptide backbone takes up a folded conformation at the middle glycylglycyl link accompanied by a significant nonplanarity up to delta omega of 8 degrees at the middle peptide and is relatively more extended at the two ends. The molecules are linked together intermolecularly in an infinite sequence of head to tail 1-4' hydrogen bonds, as is typical of charged peptides. It is interesting to note that while glycylglycylglycine takes up an extended beta-sheet conformation, addition of Leu to the N-terminal results in a bent conformation.     

Induced helical conformation of ionic polypeptides by phospholipids solubilized in a nonionic surfactant solution.

Phosphatidylcholine that has been solubilized in hexadecylpoly (oxyethylene) ether can induce a coil-to-helix transformation for poly (L-glutamic acid) in neutral solution. Similarly, solubilized phosphatidylserine promotes a helical conformation of poly (L-lysine) at neutral pH through complex formation. The mixed micelles of a phospholipid and a nonionic surfactant are thermodynamically stable and do not separate on standing. The nonionic surfactant here has no effect on the conformation of the two polypeptides.     

Effect of phospholipid bilayers on solution conformation of branched polymeric polypeptides and peptide-polymer conjugates

This report provides a detailed analysis on the influence of phosholipid bilayers on the conformation of poly[Lys(X(i)-DL-Ala(m))] (XAK, where X = Ser, Orn, Glu, or AcGlu) type branched polypeptides and their peptide conjugates. CD spectra of polycationic (SAK, OAK), amphoteric (EAK), or polyanionic (Ac-EAK) polylysine derivatives were recorded in 0.25M acetate buffer at pH 7.4 as well as in the presence of DPPC or DPPC/PG (95/5, 80/20 mol/mol) liposomes. Based on these data, two groups of polypeptides are described. Group one contains polypeptides with significantly ordered conformation even in buffer solution (SAK, AcEAK), which is essentially not altered by phospholipids. Group two, branched polypeptides (OAK, EAK), with only partially ordered conformation in aqueous solution in the presence of phospholipid bilayers with high PG content, could adopt more (EAK) or less (OAK) ordered alpha-helical structure depending on their charge properties. In addition, we report on the synthesis of two new sets of oligopeptide-branched polypeptide conjugates. Studies with selected conjugates suggest that these compounds are highly ordered in buffer solution almost regardless from the helix-forming ability of the carrier (AK, SAK, EAK) and from the hydrophilic/hydrophobic character of peptides attached (AVKDEL vs FWRGDLVFDFQV). Addition of phospholipid bilayers with different composition essentially had no modifying effect on conformation of conjugates. From this we can conclude that the covalently coupled oligopeptides has a predominant effect of the conformational properties of conjugates.     

Solid-state conformation of some basic sequential polypeptides

We have studied the structure of solid films obtained by x-ray diffraction, from several basic polypeptides with a defined sequence. The alterating polypeptides poly(Ala-Lys), poly(Leu-Lys), poly(Val-Lys), and poly(Arg-Leu) all show a cross-β-structure in which layers of hydrophilic side chains alternate with layers containing hydrophobic side chains. The other polypeptides studied are not in the β-conformation and appear to be in the α-helical conformation. The helices obtained from poly(Lys-Ala-Ala) and poly(Lys-Ala-Ala-Lys) appear to be packed in an unusual fashion, which favors interaction between alanine side chains. Such behavior is not found in poly(Lys-Leu-Ala).     

The beta conformation of polypeptides of valine, isoleucine, and threonine in solution and solid-state: optical and infrared studies.

Water-soluble polypeptides of L -valyl and L -isoleucyl residues flanked with DL -lysyl blocks [poly(DL Lys · HCl)_x–poly(L Val)_y–poly(DL Lys · HCl)_x, poly(DL Lys · HCl)_x–poly-(L Ile)_y–poly(DL Lys · HCl)_x] and homopoly(L -threonine) were prepared. The β conformation of these polymers in water, as well as in aqueous methanol, was confirmed by infrared spectroscopy and circular dichroism studies. The optical properties of these valyl and isoleucyl polypeptides were quite different from those of previously reported synthetic homopolypeptides in the β structure. Their differences could be explained by the presence of a “single extended β chain” without either intra- or interchain association.     

Vibrational analysis of conformation in peptides,polypeptides, and proteins

A vibrational force field for the polypeptide chain has been developed for normal-mode analysis of such molecules. It can reproduce observed frequencies of known structures to within about 5 cm^?1. We review the application of this technique to conformational problems in peptides (β-turns and their model compounds), polypeptides [the α_II-helix and crystalline poly(glycine II)], and proteins (bacteriorhodopsin and glucagon).     

Photoregulation in prokaryotes

The spectroscopic identification of sensory rhodopsin I by Bogomolni and Spudich in 1982 provided a molecular link between the light environment and phototaxis in Halobacterium salinarum, and thus laid the foundation for the study of signal transducing photosensors in prokaryotes. In recent years, a number of new prokaryotic photosensory receptors have been discovered across a broad range of taxa, including dozens in chemotrophic species. Among these photoreceptors are new classes of rhodopsins, BLUF-domain proteins, bacteriophytochromes, cryptochromes, and LOV-family photosensors. Genetic and biochemical analyses of these receptors have demonstrated that they can regulate processes ranging from photosynthetic pigment biosynthesis to virulence.     

Preferential conformation of substance P in solution

The three-dimensional structure of substance P has been studied by 1H-NMR, (500 MHz), and by circular dichroism (CD) in different solvents. The analysis of the different NMR parameters suggest that substance P adopts a rather extended structure in dimethylsulfoxide and pyridine. In water, besides the aggregation phenomenon, the monomeric substance P presents a complex conformational equilibrium. The addition of sodium dodecylsulfate to the aqueous solution induces, as shown by CD spectroscopy, a preferential alpha-helical conformation. And in methanol three structural conclusions may be drawn: the flexibility of the N-terminal Arg-Pro-Lys, the alpha-helical structure of Pro4-Gln5-Gln6-Phe7-Phe8 and the interaction of the C-terminal carboxamide with the primary amides from both glutamines.     

The conformation of echinomycin in DMSO solution

The conformation of the antibiotic echinomycin in DMSO solution has been determined from two-dimensional NMR and distance geometry calculation with distance constraints. Five converged conformations were calculated with NOE distance constraints followed by restraint energy minimization.     

The conformation of adenovirus VAI-RNA in solution

The secondary structure of an adenovirus associated low molecular weight RNA (VAI-RNA) has been studied by partial digestion with T1-RNase and S1-endonuclease followed by T1-fingerprint analysis. The empirical secondary structure has been compared with two computer generated models based on minimal free energy of the structure. The results suggest that VAI-RNA in solution has a compact structure with a free energy of around -60 kcal with two stems and four bulge regions. The implication of this structure for the function of VAI-RNA is discussed.     

The solution conformation of malformin A

Solution conformations of the cyclic pentapeptide plant-hormone malformin A, whose conformational freedom is constrained by an intramolecular disulfide bridge, are derived and presented here. The nmr and CD data of Ptak are used to place restrictions on the search for possible malformin A solution conformers of low energy. Only two distinct conformers were found to be consistent with Ptak's data. Both structures are characterized by an internally buried (solvent-shielded) D -Cys² amide proton, a seven-membered (1–3)hydrogen bond between (N–H) and (O?C), and a disulfide bridge conformation with a P chirality as manifested in the nmr study by the temperature independence of the amide proton chemical shifts for the D -Cys² and D -Leu⁴ residues and the negative sign of the long wavelength maximum in the CD spectrum, respectively. Inspection of space-filling molecular models of both structures indicates severe steric barriers to their rapid interconversion. Thus, it appears that only one of the two conformers may be present in solution. The difference in their calculated dipole moments (4.6 and 6.9D) suggests an experimental method for distinguishing between the two proposed solution structures.