Behavior of amphipathic helices on analysis via matrix methods, with application to glucagon, secretin, and vasoactive intestinal peptide

New Fourier transform infrared based computational method for peptide secondary structure determination. I. Description of method

Fourier transform infrared (FTIR) experiments in dimethylsulfoxide, a solvent incapable of H donation, demonstrate that H --> D isotopic replacement on the amide side of peptide bonds involves modifications of both the position and intensity of the amide I band. The effect of the isotopic substitution is particularly significant in the 1710-1670 and 1670-1650 cm(-1) regions, which are generally associated with beta-turns and alpha-helices. This behavior, attributed to the existence of intramolecular H-bonds in the polypeptide chain, is directly correlated to the presence of different secondary structures. Utilizing the effects induced by isotopic substitution, a method for the quantitative determination of the percentage of intramolecular H-bonds and the correlated secondary structures is proposed. The method consists of three principal steps: resolution of the fine structure of the amide I band with the determination of the number and position of the different components; reconstruction of the experimentally measured amide I band as a combination of Gaussian and Lorentzian functions, centered on the wave numbers set by band-narrowing methods, through a curve-fitting program; and quantitative determination of the population of the H-bonded carbonyls and the correlated secondary structures by comparison of the integrated intensities pertaining to the components with homologous wave numbers before and after isotopic exchange. The method is tested on a synthetic fragment of proocytocin that was previously analyzed by NMR techniques using the same solvent systems.

Structural studies of a baboon (Papio sp.) plasma protein inhibitor of cholesteryl ester transferase

A 38-residue protein associated with cholesteryl ester transfer inhibition has been identified in baboons (Papio sp.). The cholesteryl ester transfer inhibitor protein (CETIP) corresponds to the N-terminus of baboon apoC-I. Relative to CETIP, baboon apoC-I is a weak inhibitor of baboon cholesteryl ester transferase (CET). To study the structural features responsible for CET inhibition, CETIP was synthesized by solid-phase methods. Using sodium dodecyl sulfate (SDS) to model the lipoprotein environment, the solution structure of CETIP was probed by optical and 1H NMR spectroscopy. Circular dichroism data show that the protein lacks a well-defined structure in water but, upon the addition of SDS, becomes helical (56%). A small blue shift of 8 nm was observed in the intrinsic tryptophan fluorescence of CETIP in the presence of saturating amounts of SDS, suggesting that tryptophan-23 is not buried deeply in the lipid environment. The helical nature of CETIP in the presence of SDS was confirmed by upfield 1Halpha secondary shifts and an average solution structure determined by distance geometry/simulated annealing calculations using 476 NOE-based distance restraints. The backbone (N-Calpha-C=O) root-mean-square deviation of an ensemble of 17 out of 25 calculated structures superimposed on the average structure was 1.06+0.30 A using residues V4-P35 and 0.51+/-0.17 A using residues A7-S32. Although the side-chain orientations fit the basic description of a class A amphipathic helix, both intramolecular salt bridge formation and "snorkeling" of basic side chains toward the polar face play minor, if any, roles in stabilizing the lipid-bound amphipathic structure. Conformational features of the calculated structures for CETIP are discussed relative to models of CETIP inhibition of cholesteryl ester transferase.

Structural aspects of the interaction of peptidyl-glycylleucine-carboxyamide, a highly potent antimicrobial peptide from frog skin, with lipids

The interaction of PGLa (peptidyl-glycylleucine-carboxyamide), a 21-amino-acid residue cationic peptide, isolated from the skin of the South African clawed frog, Xenopus laevis, with model membrane systems was investigated. Our studies focussed on the importance of the difference in the phospholipid composition of bacterial and erythrocyte membranes. This is of particular interest to gain information on the specificity of membranolysis exhibited by this peptide against bacteria but not against erythrocytes. In phosphate buffer at physiological pH, as well as in the presence of the zwitterionic phosphatidylcholine and sphingomyelin. the peptide had a random structure but it adopted an alpha-helical conformation in the presence of negatively charged lipids. Furthermore, calorimetric experiments showed that PGLa had no effects on the thermotropic phase behavior of liposomes composed of the choline phosphatides, while separation of a distinct peptide-rich domain was observed for phosphatidylglycerol liposomes. In addition to the main transition of pure 1,2-dipalmitoylglycerophosphoglycerol at 40 degrees C a second transition owing to the peptide-perturbed lipid domains was found at 41 degrees C. This conclusion is supported by X-ray diffraction experiments which indicated that PGLa penetrates into the hydrophobic core of the bilayer inducing an untilting of the hydrocarbon chains as observed in the gel phase of the pure lipid. These results demonstrate that this antibacterial peptide specifically interacts with negatively charged lipid membranes, which are characteristic of bacterial membranes. This can be explained based on the structural features of PGLa.

Conformational studies of an amphipathic peptide corresponding to human apolipoprotein A-II residues 18-30 with a C-terminal lipid binding motif EWLNS

A peptide was designed and synthesized to enhance the lipid binding properties of a 13-residue fragment of apolipoprotein A-II. The peptide, VTDYGKDLMEKVKEWLNS [apoA-II(18-30)+], contains a five-residue amphipathic motif, EWLNS, at the C-terminus of apolipoprotein A-II residues 18-30. The lipid binding properties of apoA-II(18-30)+ were assessed using optical spectroscopy in the presence of sodium dodecyl sulfate (SDS), dodecylphosphocholine (DPC), tetradecyltrimethyl ammonium chloride (TMA) and dimyristoylphosphatidylcholine (DMPC). The fluorescence emission spectra and the circular dichroism data suggested that apoA-II(18-30)+ interacted most strongly with SDS and most weakly with DMPC. An ensemble of structures for apoA-II(18-30)+ in aqueous solution containing SDS was calculated using distance geometry/simulated annealing methods from 308 NOE-based distance restraints. The backbone (N-C-C = O) RMSD from the average structure of an ensemble of 15 out of 20 calculated structures was 0.54 +/- 0.16 A. Apart from some dynamic fraying at both termini, the distance geometry and simulated annealing calculations showed that apoA-II(18-30)+ adopted a well defined amphipathic helix with distinct hydrophobic and hydrophilic faces.

Molecular dynamics simulation of a leucine zipper motif predicted for the integrase of human immunodeficiency virus type 1

We have used the molecular dynamics (MD) simulation package AMBER4 to search the conformation of a peptide predicted as a leucine zipper motif for the human immunodeficiency virus type 1 integrase protein (HIV IN-LZM). The peptide is composed of 22 amino acid residues and its location is from Val 151 to Leu 172. The searching procedure also includes two known alpha-helices that served as positive controls--namely, a 22-residue GCN4-p1 (LZM) and a 20-residue poly (L-alanine) (PLA). A 21-residue peptide extracted from a cytochrome C crystal (CCC-t) with determined conformation as a beta-turn is also included as a negative control. At the beginning of the search, two starting conformations--namely, the standard right-handed alpha-helix and the fully stretched conformations--are generated for each peptide. Structures generated as standard alpha-helix are equilibrated at room temperature for 90 ps while structures generated as a fully stretched one are equilibrated at 600 K for 120 ps. The CCC-t and PLA helices are nearly destroyed from the beginning of equilibration. However, for both the HIV IN-LZM and the GCN4-p1 LZM structures, there is substantial helicity being retained throughout the entire course of equilibration. Although helix propagation profiles calculated indicate that both peptides possess about the same propensity to form an alpha-helix, the HIV IN-LZM helix appears to be more stable than the GCN4-p1 one as judged by a variety of analyses on both structures generated during the equilibration course. The fact that predicted HIV IN-LZM can exist as an alpha-helix is also supported by the results of high temperature equilibration run on the fully stretched structures generated. In this run, the RMS deviations between the backbone atoms of the structures with the lowest potential energy (PE) identified within every 2 ps and the structure with the lowest PE searched in the same course of simulation are calculated. For both the HIV IN-LZM and the GCN4-p1 LZM, these rms values decrease with the decrease of PE, which indicates that both structures are closer in conformations as their PEs are moved deeper into the PE well.

Partitioning of vasoactive intestinal polypeptide into lipid bilayers

Incubation of radiolabeled vasoactive intestinal polypeptide (VIP) with preformed lipid vesicles composed of phosphatidylcholine, phosphatidylglycerol and cholesterol resulted in reversible and saturable association of the peptide with the lipid bilayer. The pH-optimum for the reaction was in the physiological range. The vesicle-associated peptide displayed enhanced stability to proteolytic digestion, it was efficiently released into the supernatant by detergent-solubilization of the vesicles but remained vesicle-associated during treatment with agents that disrupt ionic interactions. Peptide binding by electrically neutral vesicles was lower than that by negative vesicles. Electron spin resonance studies with 5-doxylstearic acid or 16-doxylstearic acid labeled vesicles suggested that VIP decreased the fluidity close to the surface of the bilayer and increased the fluidity in its hydrophobic core. These observations suggest that VIP can bind and penetrate lipid bilayers.

Stabilization of helical structure in two 17-residue amphipathic analogues of the C-terminal peptide of cytochrome C

The conformations of two 17-residue peptide analogues derived from the C-terminal sequence of pigeon cytochrome c (native sequence = KAERADLIAYLKQATAK) were examined in aqueous and lipid environments by CD spectroscopy. The two analogues, KKLLKKLIAYLKQATAK (K peptide) and EELLEELIAYLKQATAK (E peptide), were made amphipathic with respect to helical segregation by substituting a 6-residue sequence at the N-terminus of the native peptide. Their structures were compared to the native peptide under aqueous conditions of varying pH and temperature, and in the presence of liposomes composed of phosphatidylcholine and phosphatidylserine in the ratio of 9:1. The results indicated that the native peptide remains unstructured under all the conditions examined even though this region of the native molecule is surface exposed and helical. The E peptide, however, was helical under aqueous conditions at 25 degrees C from pH 2-10 with a maximum helicity at pH 4 (54% helix from analysis of CD data). The ellipticity of the E peptide at pH 4 and 8 was concentration dependent, indicating an aggregation phenomenon. In studies in which the CD spectrum was measured at different temperatures, the E peptide became more helical at lower temperatures at pH 4 but not at pH 8. Upon interaction with a lipid membrane in the form of liposomes, there appeared to be a slight destabilization in the structure of the E peptide. The K peptide in an aqueous environment behaved like the native peptide in that it was structureless at all pHs and temperatures examined. In the presence of liposomes, however, this peptide had a high helical content (75% helix from analysis of CD data). These findings suggest that while stabilization of the helix dipole with negative charges at the N-terminus are important in inducing helical conformation in the E peptide, hydrophobic interactions created during aggregation appear to provide the principal stabilizing force. The results with the K peptide demonstrate that the positive N-terminal sequence of this peptide is able to interact with the negatively charged head groups in the phospholipid membrane in such a fashion as to stabilize a helical structure that is not apparent in an aqueous environment alone.

Identification of peptide hormones of the amphipathic helix class using the helical hydrophobic moment algorithm

Eisenberg's helical hydrophobic moment (less than mu H greater than) algorithm was applied to the analysis of the primary structure of amphipathic alpha-helical peptide hormones and an optimal method for identifying other peptides of this class determined. We quantitate and compare known amphipathic helical peptide hormones with a second group of peptides with proven nonamphipathic properties and determine the best method of distinguishing between them. The respective means of the maximum 11 residue less than mu H greater than for the amphipathic helical and control peptides were 0.46 (+/-/-0.07) and 0.33 (0.07) (P + 0.004). To better reflect the amphipathic potential of the entire peptide, the percent of 11 residue segments in each peptide above a particular less than mu H greater than was plotted vs less than mu H greater than. The resulting curves are referred to as HM-C. The mean HM-C (of the two groups) was highly significantly different such that the HM-C method was superior to others in its ability to distinguish amphipathic from nonamphipathic peptides. Several potential new members of this structural class were identified using this approach. Molecular modeling of a portion of one of these, prolactin inhibitory factor, reveals a strongly amphipathic alpha helix at residues 4-21. This computer-based method may enable rapid identification of peptides of the amphipathic alpha-helix class.

Importance of the C-terminal alpha-helical structure for glucagon's biological activity

The synthetic glucagon analogues [Glu21]glucagon, 2, and [Lys17,18,Glu21]glucagon, 3, were designed using Chou-Fasman calculations for the purpose of enhancing the probability for the formation of a C-terminal amphipathic alpha-helical conformation. Circular dichroism indicates increased alpha-helical content for these analogues in solution relative to glucagon. Analogues 2 and 3 also exhibit a 3-fold and 5-fold increase in receptor binding potency, respectively. The adenylate cyclase stimulating potencies of 2 and 3 relative to glucagon are 2.1 and 7 times greater, respectively. Attempts were made at further alpha-helical enhancement by further substitutions in the 10-13 region of glucagon, as represented by the glucagon analogues [Phe13,Lys17,18 Glu21]glucagon, 4, and [Phe10,13,Lys17,18,Glu21]glucagon, 5. These latter substitutions resulted in lowered receptor binding and adenylate cyclase potencies for 4 and 5 relative to 3 despite increased alpha-helical content in solution as observed by circular dichroism spectroscopy.

Conformational determinants in receptor recognition of peptide hormones: interaction of parathyroid hormone with the glucagon receptor

Receptor binding assays demonstrate that bovine parathyroid hormone (PTH) and human PTH(1-34) can displace [125I]iodoglucagon from binding to its receptor in rat liver plasma membranes. The displacement of [125I]iodoglucagon requires several thousand-fold more bovine PTH or human PTH(1-34) than glucagon. However, the PTH peptides are more effective than secretin, which up to a concentration of 10(-5) M exhibits no ability to displace [125I]iodoglucagon. The greater potency of PTH compared with secretin occurs despite the fact that secretin shows a great deal of sequence homology with glucagon while PTH shows none. We demonstrate by circular dichroism that in the presence of 3 mM SDS glucagon and hPTH(1-34) have similar secondary structure contents, while secretin is more helical. Our results suggest that receptors can recognize gross conformational features of a peptide hormone in addition to interacting with a specific amino acid sequence. The ability of PTH to interact with glucagon receptors can be modulated by incorporation of charged amphiphiles into the plasma membrane. Negatively charged taurodeoxycholic acid increases the binding of the more cationic PTH while positively charged myristyltrimethylammonium bromide decreases this interaction. These effects demonstrate that receptor specificity can be modulated by its lipid environment and that electrostatic interactions between the hormone and the membrane surface can contribute to receptor binding.

Interaction of atriopeptin III with lipids and detergents

Atriopeptin III, a potent natural hypotensive agent, contains little alpha-helical structure but substantial amounts of beta-structure. The peptide can self-associate at millimolar concentrations or can associate with the anionic phospholipid, dimyristoylphosphatidylglycerol. Both of these processes are accompanied by a conformational change suggesting the formation of an increased amount of beta-structure. The peptide can broaden the transition and lower the transition enthalpy of dimyristoylphosphatidylglycerol. The results demonstrate that a peptide hormone can associate with lipid largely in the form of a beta-structure.

Conformational study of two synthetic peptides with sequence analogies to the N-terminal fragment of RNase A

The conformational properties of two synthetic model peptides, AEAAHAAEAAHMG (PA) and AEAAHAFEAAHMG (PF), have been studied using CD and 1H-NMR methods. In both peptides, glutamate and histidine residues are situated in such a way that two salt bridges between Glu- (i) and His+ (i + 3) can be formed. A salt bridge of this type (Glu- 9-His+ 12) was postulated previously to stabilize, to a great extent, the alpha-helical conformation of isolated N-terminal fragments of RNase A: C-peptide and S-peptide (A. Bierzyński, P.S. Kim and R.L. Baldwin, Proc. Natl. Acad. Sci. U.S.A. 79 (1982) 2470). Although in both PA and PF salt bridges between glutamates and histidines are formed, as demonstrated by the pH-titration curves of the glutamate gamma-proton signals, no traces of helical conformation have been detected. Evidently, the Glu- (i)-His+ (i + 3) salt bridges do not stabilize the alpha-helical conformation. A comparative analysis of PA and PF NMR spectra provides strong evidence that the phenylalanyl ring in PF interacts not only with the hydrophobic methyl groups of almost all alanine residues but also with the histidine rings and the glutamate side chains in their protonated as well as deprotonated forms. Similar interactions, involving Phe 8, can be expected in the N-terminal fragments of RNase and should be taken into account as an important factor determining the conformational properties of C- and S-peptides.

The hydrophobic moment of the amphipathic helix of salmon calcitonin and biological potency

The formation of an amphipathic helix in the central portion of calcitonin contributes to the potency of this hormone. We have synthesized a number of analogs of salmon calcitonin, containing deletions in the region of the peptide which is thought to form an amphipathic helix. There is no direct relationship between the hydrophobic moment of the helix and the biological activity of the peptide. For example, salmon des-Leu19-calcitonin and des-Ser13-calcitonin both have lower helical hydrophobic moments but have greater or equal biological potency compared with the native hormone. We suggest that other conformational features, such as flexibility and helix-forming potential, are also important in determining biological potency.

Conformation of peptides of the secretin-VIP-glucagon family in solution

The significance of a well defined molecular architecture in hormone receptor interaction and the methods available for the study of preferred conformations are discussed. The conformational freedom in glucagon is a major obstacle in the determination of its biologically relevant geometry. In the secretin molecule intramolecular forces generate a folded, partially helical conformation. In respect of long range cooperative interactions resulting in a compact molecule with secondary-tertiary structure secretin is similar to globular proteins. In VIP some characteristics of secretin and also of glucagon can be recognized. Further progress in conformation analysis can be expected from the study of rigid, cyclic analogs in which the biological activities of the parent hormones are retained or even enhanced. Such analogs have well defined conformations without external stabilization from membrane mimicking lipids. Therefore, they provide information on the biologically relevant geometry of the hormones and contribute also to our knowledge of receptor sites.

Secretin receptor activity in rat gastric glands. Binding studies, cAMP generation and pharmacology

We measured 125I-secretin binding to membranes prepared from rat fundic glands and compared the abilities of natural and synthetic secretin (SN) analogs to inhibit 125I-secretin binding and to activate the cAMP generating system in glandular and subcellular preparations from the fundus and antrum. The natural peptides structurally related to porcine secretin (pSN) included: chicken secretin (cSN), vasoactive intestinal peptide (VIP), porcine peptide with N-terminal histidine and C-terminal isoleucine amide (PHI), helodermin, growth hormone releasing factors isolated from the rat hypothalamus (rhGRF-43, rhGRF-29) or from a human pancreatic tumour (hpGRF-40). These peptides inhibited the binding of 125I-secretin to rat fundic membranes: pSN greater than cSN greater than PHI, VIP and activated the cAMP generating system in fundic glands, according to the following order of potency; pSN greater than cSN greater than PHI, VIP greater than rhGRF-29 greater than rhGRF-43. Porcine peptide with N-terminal tyrosine and C-terminal tyrosine (PYY), GIP, SOM and hpGRF-40 were inactive. Structural requirements for secretin receptor activity were evaluated with four synthetic secretin analogs corresponding to porcine secretin substituted at the N-terminal end by sequence portion of VIP, GIP, GLU and SOM: Ala4-Val5-SN(VIP-SN); Tyr1-Ala2-Glu3-SN (GIP-SN); Gln3-SN (GLU-SN) and Phe1-Phe1-Trp3-Lys4-SN (SOM-SN). The relative potencies of the analogs in fundic and antral preparations were: pSN greater than VIP-SN greater than VIP, GIP-SN greater than GLU-SN greater than SOM-SN for 125I-secretin displacement and cAMP production (glandular cAMP generation and adenylate cyclase activation).(ABSTRACT TRUNCATED AT 250 WORDS)

The functional nature of calcium binding units in calmodulin, troponin C and parvalbumin

Examination of the interaction of major tranquilizers with calmodulin results in the generalization that the functional nature of calcium binding helix-loop-helix regions found in several calcium binding proteins including calmodulin, troponin C and parvalbumin is dependent upon the topography of the hydrophobic and hydrophilic regions on the amphiphilic N-terminal alpha-helix of the helix-loop-helix conformation formed by the binding of the calcium cation to these proteins. The relation of the topography of this amphiphilic alpha-helix to drug binding is delineated at the molecular level and the results obtained are used to describe the interaction of beta-endorphin, dynorphin, alpha-MSH and other peptides with calmodulin. The utility of this hypothesis is further demonstrated by the description of a possible interaction between troponin C, troponin I and troponin T of the troponin complex in skeletal muscle.