Influence Of Amino Acid Sequence Research Articles

Influence of amino acid sequence in a peptidic Cu+-responsive luminescent probe inspired by the copper chaperone CusF.

Copper(i) is a soft metal ion that plays an essential role in living organisms and Cu+-responsive probes are required to detect Cu+ ions in physiological conditions and understand its homeostasis as well as the diseases associated with its misregulation. In this article, we describe a series of cyclic peptides, which are structurally related to the copper chaperone CusF, and that behave as Cu+-repsonsive probes. These peptide probes comprise the 16-amino acid loop of CusF cyclized by a β-turn inducer dipeptide and functionalized by a Tb3+ complex for its luminescence properties. The mechanism of luminescence enhancement relies on the modulation of the antenna effect between a tryptophan residue and the Tb3+ ion within the probe when Cu+ forms a cation-π interaction with the tryptophan. Here, we investigate the influence of the amino acid sequence of these cyclic peptides on the copper-induced modulation of Tb3+ emission and show that the rigid β-turn inducer Aib-d-Pro and insertion of the Tb3+ complex close to its tryptophan antenna are required to obtain turn-on Cu+ responsive probes. We also show that the amino acid sequence, especially the number and position of proline residues has a significant impact on metal-induced luminescence enhancement and metal-binding constant of the probes.

The influence of amino acid sequence on structure and morphology of polydiacetylene containing peptide fibres.

A systematic study was performed on the influence of charge and steric hindrance on the assembly into fibres of a series of pentameric peptides based on the well-known β-sheet forming sequence Gly-Ala-Gly-Ala-Gly, which were N-terminally acylated with pentacosadiynoic acid. To investigate the effect of steric hindrance and charge repulsion on the fibre structure, either the N-terminal or the C-terminal amino acid in the sequence was replaced by a glutamic acid or lysine residue. Furthermore, peptide amphiphiles (PAs) with an amide or a free acid group at the C-terminus were compared. Steric hindrance and charge repulsion were addressed individually by varying the pH during and after fibre preparation. The self-assembled structures were examined with circular dichroism (CD) spectroscopy and transmission electron microscopy (TEM). UV spectroscopy was used to probe the diacetylene packing in the hydrophobic tail, both by polymerisation behaviour and chromatic properties of the polymers. In brief, the assembly was hindered more if the modification was close to the alkyl tail, and glutamic acid brought about a larger effect than lysine. PAs with two charges yielded assemblies which after polymerisation were found to be the most susceptible towards changes in pH, behaving as a colour-based pH sensor. Typically, TEM and UV showed the same trends, indicating that a distorted morphology as observed with TEM is indicative of a poorer molecular packing of the peptide amphiphile fibres, probed via the changes in absorption of the polydiacetylene backbone.

Molecular dynamics simulation of β-sheet formation in self-assembled peptide amphiphile fibers

The influence of amino acid sequence on the secondary structure of peptide amphiphile (PAs) cylindrical micelles and fibers that are self-assembled in solution is studied using molecular dynamics simulations. Simulations for two choices of PAs were performed, starting with structures that have the correct overall shape, but which restructure considerably during the simulation, with one fiber being composed of valine rich PAs and the other of alanine rich PAs. Self-assembly is similar in both simulations, with stable fibers (diameter is 7.7–8 nm) obtained after 40 ns. We find that the valine rich PA fiber has a higher β-sheet population than the alanine rich fiber, and that the number of hydrogen bonds is higher. This behavior of the valine rich fiber is consistent with experimental measurements of higher stiffness, and it shows that stiffness can be varied while still maintaining self-assembly.

The Influence of Amino Acid Sequence and Functionality on the Binding Process of Peptides onto Gold Surfaces

We present a molecular dynamics study of the binding process of peptide A3 (AYSSGAPPMPPF) and other similar peptides onto gold surfaces, and identify the functions of many amino acids. Our results provide a clear picture of the separate regimes present in the binding process: diffusion, anchoring, crawling and binding. Moreover, we explored the roles of individual residues. We found that tyrosine, methionine, and phenylalanine are strong binding residues; serine serves as an effective anchoring residue; proline acts as a dynamic anchoring point, while glycine and alanine give flexibility to the peptide backbone. We then show that our findings apply to unrelated phage-derived sequences that have been reported recently to facilitate AuNP synthesis. This new knowledge may aid in the design of new peptides for the synthesis of gold nanostructures with novel morphologies.

Influence of amino acid sequence on the interaction of short peptides containing 3-[2-(9-anthryl)benzoxazol-5-yl]-alanine with β-cyclodextrin

AbstractThe influence of peptide sequence and Leu chirality in linear and cyclic peptides containing 3-[2-(9-anthryl)benzoxazol-5-yl]alanine on interaction with β-cyclodextrin were studied using fluorescence and NMR spectroscopy. The analysis of enthalpy-entropy compensation effect (α=1.05±0.02 and TΔS00=15.1±0.5 kJ mol−1) indicates that the entropic contribution connected with the solvent reorganization is the major factor governing the peptides-β-cyclodextrin complexation. Moreover, spatial orientation of guest-host molecule depends more than association constant on Leu residue configuration. However, the cyclization of the peptide chain substantially decrease the association constant with β-CD. An analysis of 2D NMR spectra reveals that inclusion complex is formed by penetration of cyclodextrin cavity from wider and narrow rims by anthryl group in the case of Box(Ant)-SPKL or anthryl and Leu residues for Box(Ant)-SPK(D)L analogue.

Electron-capture induced dissociation of doubly charged dipeptides: on the neutral losses and N–Cα bond cleavages

Electron capture by doubly charged peptide cations leads to neutral losses in addition to N-C(α) bond cleavages that give c and z fragments. In this work we discuss the influence of amino acid sequence on hydrogen versus ammonia loss and the propensity for subsequent partial side-chain cleavage after ammonia loss to give w fragment ions. Experiments were done on two series of doubly protonated dipeptides, [XK+2H](2+) and [XR+2H](2+), where X is one of the twenty common amino acid residues, excluding aspartic acid (D), and K and R are lysine and arginine, respectively. While it was previously established that NH(3) is lost exclusively from the N-terminal ammonium group and not from side-chain ammonium groups, we find here that ammonia can be lost from guanidinium radicals as well. The ratio between H loss and NH(3) loss reveals some information on internal ionic hydrogen bonds and peptide conformation since proton sharing between the N-terminal ammonium group and a basic side chain decreases the probability for NH(3) loss due to a lower recombination energy and as a result reduced capture probability. The abundance of w ions was found to correlate with the reaction energy for their formation; highest yield was found for CK and lowest for AK and HK. The survival rate of charge-reduced species was higher for XR than for XK, which is likely linked to the formation of long-lived C(α) radicals in the latter case. The probability for N-C(α) bond cleavage is smaller on average for XR than for XK which indicates that hydrogen transfer from the ε-ammonium radical to the amide group triggers some of the cleavages, or is a result of the different distances between the amide group and the charges in XR and XK. Finally, our data support the previous concept that charge partitioning between c and z fragments can be explained by competition between the two fragments for the proton.

FRET-based assay of the processing reaction kinetics of stimulus-responsive peptides: influence of amino acid sequence on reaction kinetics

In the field of chemical biology, methods for controlling peptidyl function by a stimulus are attracting increasing attention. Recently, we reported a stimulus-responsive peptide, which can be cleaved after exposure to a stimulus. In this study, we developed a FRET-based assay system to estimate the kinetics of the stimulus-induced processing (peptide bond cleavage) reaction. Based on the FRET system, it was clarified that introduction of a sterically less-hindered or polar residue at the position adjacent to the stimulus-responsive amino acid accelerates the processing reaction.

Formation of [b(n) + 17 + Ag]+ product ions from Ag+ cationized native and acetylated peptides.

We compared the tandem mass spectra of a range of native and acetylated Ag(+) cationized peptides to determine the influence of the derivatization step on the abundance of the [b(n) + 17 + Ag](+) product ions. Using tripeptides, the smallest for which the mechanisms to generate [b(2) - 1 + Ag](+) and [b(2) + 17 + Ag](+) products are both operative, we found that in most cases acetylation causes an increase in the abundance of the C-terminal rearrangement ion, [b(2) + 17 + Ag](+), relative to the rival N-terminal rearrangement ion, [b(2) - 1 + Ag](+). The presence of a free amino group to bind to the metal ion significantly influences the relative abundances of the product ions. We propose a mechanism for the formation of the [b(n) + 17 + Ag](+) that is based on the formation of a five-membered oxazolidin-5-one and tetrahedral carbon intermediate that may collapse to a peptide upon release of CO and an imine, aided by the fact that the ring formed during C-terminal rearrangement is both a hemiacylal and hemiaminal. We also identified an influence of amino acid sequence on the relative abundances of the [b(n) + 17 + Ag](+) and [b(n) - 1 + Ag](+) product ions, whereby bulky substituents located on the alpha-carbon of the amino acid to the C-terminal side of the cleavage site apparently promote the formation of the [b(n) + 17 + Ag](+) product over [b(n) - 1 + Ag](+) when the amino acid to the N-terminal side of the cleavage site is glycine. The latter ion is the favored product, however, when the bulky group is positioned on the alpha-carbon of the amino acid to the N-terminal side of the cleavage site.

The Influence of Amino Acid Sequence on the Fibrillogenicity and Amyloidogenicity of the Carboxy-Terminus of β-Amyloid Precursor Protein

C-APP, a synthetic peptide corresponding to the C-terminal 20 amino acids of β-amyloid precursor protein, forms amyloid fibrils in vitro. We investigated the effect of altering the C-APP sequence or deleting part of it on its ability to form amyloid fibrils. Substituting any single amino acid in the C-APP sequence with alanine did not prevent the formation of CAPP-like fibrils. Peptides with single or multiple substitutions that included T11, F14, F15, or Q19 showed reduced fibril-forming capacity while those with K1 and/or K13 replaced with alanine or glutamic acid showed enhanced capacity. When P10 or F14 was replaced with alanine, the fibrils were less congophilic than C-APP fibrils. All of the truncated peptides that were able to form fibrils contained at least 9 amino acids from the N-terminus of C-APP or amino acids 7-20 from the C-terminus. However, several peptides that met these criteria, but started at Q3 or contained only 2-4 amino acids C-terminal to P-l0, failed to form many or typical fibrils. Peptides that contained the C-APP sequence pIus 5-20 adjacent amino acids from the βamyloid precursor protein formed fibrils less readily than C-APP and most of the fibrils were not congophilic. The exception was CAPP-30, which formed moderate amounts of congophilic fibrils resembling C-APP fibrils morphologically. Therefore, proteolysis which releases C-APP from these peptides (except CAPP-30) would be predicted to enhance their amyloidogenicity. These results suggest that several features of C-APP peptide may be important in fibril formation. One of these features is the length of the peptide, with lengths of about 10, 20, or 30 amino acids, favoring fibril formation.

Probing the influence of sequence‐dependent interactions upon α‐helix stability in alanine‐based linear peptides

The observation that short, linear alanine-based polypeptides form stable alpha-helices in aqueous solution has allowed the development of well-defined experimental systems with which to study the influence of amino acid sequence upon the stability of secondary structure. We have performed detailed conformational searches upon six alanine-based peptides in order to rationalize the observed variation in the alpha-helical stability in terms of side-chain-backbone and side-chain-side-chain interactions. Although a simple, gas-phase, potential model was used to obtain the conformational energies for these peptides, good agreement was obtained with experiment regarding their relative alpha-helical stabilities. Our calculations clearly indicate that valine, isoleucine, and phenylalanine residues should destabilize the alpha-helical conformation when included within alanine-based peptides because of energetically unfavorable side-chain-backbone interactions, which tend to result in the formation of regions of 3(10)-helix. In the case of valine, the destabilization most probably arises from entropic effects as the isopropyl side chain can assume more orientations in the 3(10)-helical form of the peptide. A detailed examination of very short-range interactions in these peptides has also indicated that an interaction, involving fewer than five consecutive residues, whose stabilizing effect reinforces that of the (i, i + 4) hydrogen bond may be the basis of the requirement for increased nucleation (sigma) and propagation parameters (s) required by Zimm-Bragg theory to predict the alpha-helical content for compounds in this class of short peptides. Our calculations complement recent work using modified Zimm-Bragg and Lifson-Roig theories of the helix-coil transition, and are consistent with molecular dynamics simulations upon linear peptides in aqueous solution.

Influence of amino acid sequence on the formation and stability of cyclohepta-amylose (cyclomaltoheptaose) inclusion-complexes with phenylalanine-containing dipeptides

The formation and the molecular dynamics of the inclusion complexes of cyclohepta-amylose (cyclomaltoheptaose) with l-lysyl- l-phenylalanine, l-phenylalanyl- l-leucine, and l-leucyl- l-phenylalanine in aqueous solution have been studied by 1H- and 13C-n.m.r. spectroscopy. The displacements in 1H-chemical shift and the decrease in N T 1 η values for the guest carbons on addition of cyclohepta-amylose show that the inclusion complexes are formed by insertion of the guest's phenyl ring into the host's cavity, and the stability of the complexes depends on the types of amino acid residue adjoining the aromatic residue and on their sequence. Here, N is the number of protons directly bonded to a given carbon, T 1 is the 13C spin-lattice relaxation-time, and η is the viscosity of the solution.

Synthesis and Conformational Studies of Model Histones: II Sequential and Random Polypeptides with the Composition L‐Lysyl:L‐Alanyl:L‐Proline

AbstractThe sequential polytripeptide (Lys‐Ala‐Pro)n and the random polypeptide (Lys36.2 Ala32.5 Pro31.3)n were synthesized as model histones to be used in studying the structure and interactions of nucleohistone complexes. The CD spectra of (Lys‐Ala‐Pro)n in aqueous solutions, at both pH 7 and 11, as well as in HFIP, TFA, and 1 M SDS (pH 7), indicated that this polytripeptide only assumed the random coil conformation under all these conditions. In aqueous solution, the CD spectra of the random sequence polypeptide indicated that this polymer undergoes a pH‐dependent random coil‐helix transition as the pH is raised from 7 to 11. This polymer was also partially helical in TFE. The observation that the random polymer can assume a regular, asymmetric structure may be due to a clustering of lysyl and alanyl residues at one end of the polymer because of the faster incorporation of Pro than Lys or Ala, as indicated by their respective kinetics of polymerization. The random conformation of the sequential polypeptide, (Lys‐Ala‐Pro)n, is probably determined by the presence of Pro at regular intervals. It is concluded that the sequential polymer (Lys‐Ala‐Pro)n is a plausible model histone for use in studying the influence of amino acid sequence and composition on the structure and interactions of nucleohistone complexes.

The Influence of Amino Acid Sequence on Protein Structure

On the basis of the known sequences and structures of myoglobin, and alpha and beta hemoglobin, a possible correlation between certain amino acids in the sequence and the location of the helical and non-helical parts of the structure is suggested. The presence in the sequence of four critical groups; proline, aspartic acid, glutamic acid, or histidine appears to be necessary (although the last three are not sufficient) for a helical disruption to form. Additional support for this correlation is obtained from analyses of proline replacement in mutant and variant proteins. A mechanism based on hydrophobic bonding is proposed as a rationale for the apparent behavior of these groups. On the basis of these rules and correlations, secondary structures can be proposed for lysozyme and tobacco mosaic virus protein which are consistent with several pieces of evidence.