Oligopeptide Chains Research Articles

Chirality-Induced Spin Selectivity: Analysis of Density Functional Theory Calculations.

Chirality-induced spin selectivity (CISS), which was demonstrated in several molecular and material systems, has drawn much interest recently. The phenomenon, described in electron transport by the difference in the transport rate of electrons of opposite spins through a chiral system, is however not fully understood. Herein, we employed density functional theory in conjunction with spin-orbit coupling to evaluate the percent spin-polarization in a device setup with finite electrodes at zero bias, using an electron transport program developed in-house. To study the interface effects and the level of theory considered, we investigated a helical oligopeptide chain, an intrinsically chiral gold cluster, and a helicene model system that was previously studied (Zöllner et al. J. Chem. Theory Comput. 2020, 16, 7357-7371). We find that the magnitude of the spin-polarization depends on the chiral system-electrode interface that is modeled by varying the interface boundary between the system's regions, on the method of calculating spin-orbit coupling, and on the exchange-correlation functional, e.g., the amount of exact exchange in the hybrid functionals. In addition, to assess the effects of bias, we employ the nonequilibrium Green's function formalism in the Quantum Atomistix Toolkit program, showing that the spin-flip terms could be important in calculating the CISS effect. Although understanding CISS in comparison to experiment is still not resolved, our study provides intrinsic responses from first-principles calculations.

Positive Synergy between the Helical Poly(phenylacetylene) Backbones and the Helical L-Proline Oligopeptide Pendants for Enhanced Enantioseparation Properties.

A series of optically active helical poly(phenylacetylene)s (PPA-Pro1, PPA-Pro3, PPA-Pro6, PPA-Pro9, and PPA-Pro12) bearing different chain lengths of L-proline oligopeptide in the side chains were obtained by polymerizing the corresponding novel phenylacetylene monomers. The monomer adopted a trans-rich helix structure when the L-proline oligopeptide chain length was longer, according to the optical activities and 2D-NMR analysis. The helical structure could be maintained and significantly influenced the polymers' helical conformation by introducing the L-proline oligopeptide to the pendants. By the way, the morphology of PPA-Pro3 was observed by atomic force microscope (AFM) on highly oriented pyrolytic graphite (HOPG), and the information on the helix direction, pitch, and chain arrangement was obtained. Also, the chiral separation properties of these polymer-based chiral stationary phases (CSPs) were investigated using high-performance liquid chromatography (HPLC). The poly(phenylacetylene)s showed enhanced enantioseparation properties toward various racemates depending on the longer chain length of the L-proline oligopeptide in the pendants and the positive synergy between the helical backbone and helical side chains. Particularly, PPA-Pro9 showed comparable or even superior enantioseparation properties for racemates 2 and 9 to four commercial columns (Daicel Chiralpak or Chiralcel AD, AS, OD, and OT), indicating that these poly(phenylacetylene)-based CSPs have potential practical values. This work presented here provides inspiration for the further development of CSPs based on a new paradigm.

Revisiting the influence of pH on 1JCαH and chemical shifts of glycine and alanine short oligopeptides.

The pH dependence of several NMR parameters of glycine and alanine short oligopeptides has been reported previously in different studies. Here we have thoroughly examined, summarized and demonstrated the dependences of 1H, 13C and 15N chemical shifts and protonation states of amino acids using two-dimensional NMR experiments. Nevertheless, 1JCαH one bond spin-spin coupling constants are more informative and convenient for determination of the position and protonation state of glycine and alanine residue in the oligopeptide chain. In particular, for various oligopeptides (up to six residues), it was shown that the pH dependence of 1JCαH of N-terminal glycine and alanine residues is larger than that of C-terminal groups, and in backbone residues, it is not influenced by pH and only slightly depends on the position of the amino acid residue in the chain.

Poly(β-amino ester)s-Based Delivery Systems for Targeted Transdermal Vaccination.

Nucleic acid vaccines have become a transformative technology to fight emerging infectious diseases and cancer. Delivery of such via the transdermal route could boost their efficacy given the complex immune cell reservoir present in the skin that is capable of engendering robust immune responses. We have generated a novel library of vectors derived from poly(β-amino ester)s (PBAEs) including oligopeptide-termini and a natural ligand, mannose, for targeted transfection of antigen presenting cells (APCs) such as Langerhans cells and macrophages in the dermal milieu. Our results reaffirmed terminal decoration of PBAEs with oligopeptide chains as a powerful tool to induce cell-specific transfection, identifying an outstanding candidate with a ten-fold increased transfection efficiency over commercial controls in vitro. The inclusion of mannose in the PBAE backbone rendered an additive effect and increased transfection levels, achieving superior gene expression in human monocyte-derived dendritic cells and other accessory antigen presenting cells. Moreover, top performing candidates were capable of mediating surface gene transfer when deposited as polyelectrolyte films onto transdermal devices such as microneedles, offering alternatives to conventional hypodermic administration. We predict that the use of highly efficient delivery vectors derived from PBAEs could advance clinical translation of nucleic acid vaccination over protein- and peptide-based strategies.

Tug-of-War in a Dynamic Helical Peptide: Solvent-Induced Helix-Helix Transition of a Lactam-Bridged Peptide Composed of Point- and Axial Chiralities Remote from Each Other.

The dynamic axial chirality of oligopeptide-bound 2,2'-bipyridine (bpy) residues can be remote-controlled and diastereoselectively locked. A right-handed (P)-310 -helix is first induced in the dynamic helical oligopeptide by an l-valine (l-Val) far from the bpy moiety and the induced axial bpy chirality is diastereoselectively dioxidized. The resulting l-Val-containing linear oligopeptides at the 3,3'-positions retain their (P)-310 -helices independent of the axial chirality (aR or aS) of the N-terminal N,N'-dioxide-bpy unit, while a lactam-bridged dynamic helical oligopeptide exhibits a unique solvent-induced helix-helix transition as a result of competitive helix-inducing biases between the l-Val and (aR) or (aS)-N,N'-dioxide-bpy residues remote from each other along the entire oligopeptide chain in a tug-of-war like manner.

Biotechnology Based Process for Production of a Disulfide-Bridged Peptide.

A disulfide-bridged peptide drug development candidate contained two oligopeptide chains with 11 and 12 natural amino acids joined by a disulfide bond at the N-terminal end. An efficient biotechnology based process for the production of the disulfide-bridged peptide was developed. Initially, the two individual oligopeptide chains were prepared separately by designing different fusion proteins and expressing them in recombinant E. coli. Enzymatic or chemical cleavage of the two fusion proteins provided the two individual oligopeptide chains which could be conjugated via disulfide bond by conventional chemical reaction to the disulfide-bridged peptide. A novel heterodimeric system to bring the two oligopeptide chains closer and induce disulfide bond formation was designed by taking advantage of the self-assembly of a leucine zipper system. The heterodimeric approach involved designing fusion proteins with the acidic and basic components of the leucine zipper, additional amino acids to optimize interaction between the individual chains, specific cleavage sites, specific tag to ensure separation, and two individual oligopeptide chains. Computer modeling was used to identify the nature and number of amino acid residue to be inserted between the leucine zipper and oligopeptides for optimum interaction. Cloning and expression in rec E. coli, fermentation, followed by cell disruption resulted in the formation of heterodimeric protein with the interchain disulfide bond. Separation of the desired heterodimeric protein, followed by specific cleavage at methionine by cyanogen bromide provided the disulfide-bridged peptide.

Biochemical studies on dipeptidyl peptidase I (cathepsin C) from germinated Vigna radiata seeds

Dipeptidyl peptidases (DPPs) are widely distributed exopeptidases that hydrolyse the dipeptide moieties from the N-termini of oligopeptide chains. In the present study, DPP-I was purified from germinated moong bean seeds via acid and ammonium sulphate precipitation followed by successive chromatographies, that is, gel filtration (pH 7.4), cation exchange (pH 5.9) and anion exchange (pH 7.5). The purity of the enzyme was confirmed by native polyacrylamide gel electrophoresis (PAGE) and in situ gel assay. Purified plant DPP-I is a monomeric enzyme with a molecular weight of 38kDa. It works optimally at pH 7.0 and 40°C, and it exhibits stability at pH ranging from acidic to slightly alkaline. Plant DPP-I preferentially hydrolyses glycine–arginine–4-methoxy-β-naphthylamide and various other synthetic dipeptidyl substrates, but none of the studied endopeptidase and monopeptidase substrates. Inhibitory studies revealed the role of Cys and His amino acids in the catalytic mechanism. Functional studies of DPP-I revealed the significant role of this glycoproteinous enzyme in protein mobilization during germination.

Formation of oligopeptides in high yield under simple programmable conditions.

Many high-yielding reactions for forming peptide bonds have been developed but these are complex, requiring activated amino-acid precursors and heterogeneous supports. Herein we demonstrate the programmable one-pot dehydration–hydration condensation of amino acids forming oligopeptide chains in around 50% yield. A digital recursive reactor system was developed to investigate this process, performing these reactions with control over parameters such as temperature, number of cycles, cycle duration, initial monomer concentration and initial pH. Glycine oligopeptides up to 20 amino acids long were formed with very high monomer-to-oligomer conversion, and the majority of these products comprised three amino acid residues or more. Having established the formation of glycine homo-oligopeptides, we then demonstrated the co-condensation of glycine with eight other amino acids (Ala, Asp, Glu, His, Lys, Pro, Thr and Val), incorporating a range of side-chain functionality.

Polarization Effect and Electric Potential Changes in the Stimuli-Responsive Molecular Monolayers Under an External Electric Field

Under the exerted external electric field (Eex), significant polarization effects are demonstrated in the switching process of positively charged oligopeptide chains on the gold surface by using the polarizable force-field-based molecular dynamics (MD) simulations. The changes of electrostatic environment during the conformational switching are described by calling density functional theory (DFT) calculations of atomic charges or fragment-centered dipole moments. The charge-variable polarizable force field (Q-POL) model shows a good agreement with the experimental observations of both the open-circuit state (OC) without Eex and extended/bent conformation (ON/OFF) with upward/downward Eex, while the nonpolarizable force field (Non-POL) with the fixed atomic partial charges fails to reproduce experiments for the ON state. The charged oligopeptide chains (with each residue furnished with a positive charge) challenge the application of the coarse-graining polarizable force field based on the fragment dipoles (Dfrag-POL). Through tracing the dynamics of charge centers of both counterions and oligopeptide chains in the switching process, a qualitative picture is depicted for understanding the polarization phenomena in the dielectric monolayer in OC/ON/OFF states. With the applied electric field, the rearrangement of ions leads to the induced internal E-field, Ein, in the direction opposite to Eex. The values of total electric field, Etotal, and the interfacial potential Φx were evaluated. The relationship between the applied electric potential and the interfacial potential is built for the switching OC/ON/OFF states. The analysis of the induced internal E-field and interfacial potential may shed light on the further modification of theoretical models to better understand the electrical-induced switching mechanism.

Quantitative serine protease assays based on formation of copper(II)-oligopeptide complexes.

A quantitative protease assay based on the formation of a copper-oligopeptide complex is developed. In this assay, when a tripeptide GGH fragment is cleaved from an oligopeptide chain by serine proteases, the tripeptide quickly forms a pink GGH/Cu(2+) complex whose concentration can be determined quantitatively by using UV-Vis spectroscopy. Therefore, activities of serine proteases can be determined from the formation rate of the GGH/Cu(2+) complex. This principle can be used to detect the presence of serine protease in a real-time manner, or measure proteolytic activities of serine protease cleaving different oligopeptide substrates. For example, by using this assay, we demonstrate that trypsin, a model serine protease, is able to cleave two oligopeptides GGGGKGGH () and GGGGRGGH (). However, the specificity constant (kcat/Km) for is higher than that of (6.4 × 10(3) mM(-1) min(-1)vs. 1.3 × 10(3) mM(-1) min(-1)). This result shows that trypsin is more specific toward arginine (R) than lysine (K) in the oligopeptide sequence.

Electronic transport through oligopeptide chains: An artificial prototype of a molecular diode

Using an effective tight-binding model, together with a transfer matrix technique, we investigate the electronic transport through an oligopeptide chain composed by two amino acid pairs alanine–lysine (Ala–Lys) and threonine–alanine (Thr–Ala), respectively, sandwiched between two platinum electrodes. Our results show that factors such as the oligopeptide chain length and the possible combinations between the amino acids residues are crucial to the diode-like profile of the current–voltage (I–V) characteristics, whose asymmetric curves were analyzed using the inverted rectification ratio (IRR).

Modulation of Biointeractions by Electrically Switchable Oligopeptide Surfaces: Structural Requirements and Mechanism.

Understanding the dynamic behavior of switchable surfaces is of paramount importance for the development of controllable and tailor-made surface materials. Herein, electrically switchable mixed self-assembled monolayers based on oligopeptides have been investigated in order to elucidate their conformational mechanism and structural requirements for the regulation of biomolecular interactions between proteins and ligands appended to the end of surface tethered oligopeptides. The interaction of the neutravidin protein to a surface appended biotin ligand was chosen as a model system. All the considerable experimental data, taken together with detailed computational work, support a switching mechanism in which biomolecular interactions are controlled by conformational changes between fully extended (“ON” state) and collapsed (“OFF” state) oligopeptide conformer structures. In the fully extended conformation, the biotin appended to the oligopeptide is largely free from steric factors allowing it to efficiently bind to the neutravidin from solution. While under a collapsed conformation, the ligand presented at the surface is partially embedded in the second component of the mixed SAM, and thus sterically shielded and inaccessible for neutravidin binding. Steric hindrances aroused from the neighboring surface-confined oligopeptide chains exert a great influence over the conformational behaviour of the oligopeptides, and as a consequence, over the switching efficiency. Our results also highlight the role of oligopeptide length in controlling binding switching efficiency. This study lays the foundation for designing and constructing dynamic surface materials with novel biological functions and capabilities, enabling their utilization in a wide variety of biological and medical applications.

Theory study on glycine linear oligopeptide vibrational spectrum frequency shift

By using the density functional theory, glycine linear oligopeptide of different lengths was geometrically optimized on the 6-31G (d) basis set level, their growth processes were simulated, and the average binding energy and vibration frequency were calculated with geometry. The results showed that the average binding energies tend to change in a regular pattern and stabilize with the number of residues increasing; With the oligopeptide chain bond length analysis it was found that the chain to the radial direction there is a opposite trend for chain and radial direction, which is anisotropic. It was found by the IR spectrum analysis that red shifts and blue shifts occur respectively when the same group of peptide bond vibrate, which is anisotropic; These phenomena originate from that quasi one-dimensional nanostructures lead to the anisotropy of the bond length; the induced effects, coupling effects and hydrogen bonding etc. between the same groups lead to the vibration frequency red shifts and blue shifts. The authors conclude that the growth of glycine linear oligopeptide is conducive to stability of the structure, and the authors infer that the oligopeptide has the tendency of self-assembled growth; Through the conformation and spectrum, the authors infer that there is a size effect in physical and chemical properties. The physical and chemical properties of peptide chain end group are extremely stable and unaffected by the impact of the oligopeptide chain length The results are significant to measuring the length and the number of residue of peptide, and to manufacturing the special features oligopeptide chain.

Electronic structure analysis of glycine oligopeptides and glycine–tryptophan oligopeptides

Using the density functional theory (DFT), we have studied the energy gap, charge distribution, density of states and chemical activity of glycine (Gn) oligopeptides and glycine–tryptophan (GWn) oligopeptides. The results show that: (1) with the increasing of Gn residues, the chemical activity of Gn oligopeptides focuses on the terminal amino and carboxyl groups, which may be the main cause of self-assembly behaviors in Gn oligopeptide chains; (2) the chemical reaction activity has size effect. The size effect disappears when the residue number exceeds 7. The Gn oligopeptides with 7 residues is the shortest chain which has the same reaction activity as that of longer size peptide; (3) the activity of GWn oligopeptides presents size effect and odd-even effect. However, the size effect and odd-even effect both vanish when the chain of GWn oligopeptides is longer than 12 residues. (4) It is difficult in self-assembly for GWn oligopeptide chains, because its activity mainly focuses on the indole ring and the Gn residues at the end of oligopeptides. (5) The big side groups result in the very near energy level of LUMO and LUMO+1 of GWn oligopeptide chains. It shows that the electron-accepting ability of oligopeptide chainsis composed of two orbitals addition. The results in the paper may help us understand the changes of physical and chemical properties of peptide synthesis process.

Functional protease assay using liquid crystals as a signal reporter

We report a functional protease assay in which liquid crystals (LCs) are used as signal reporters to transduce the test results into optical signals. In this assay, an oligopeptide substrate (CLSELDDRADALQAGASQFESSAAKLKRKYWWKNLK) is used as a probe. This oligopeptide can be cleaved by α-chymotrypsin at multiple locations and become smaller fragments after the cleavage. When the original oligopeptide is immobilized on a solid surface, its long flexible oligopeptide chain is able to influence the orientation of a thin layer of LC supported on the surface, as is evident as a bright spot on the surface. In contrast, when the shorter oligopeptide fragments are immobilized on the same surface, their shorter, less flexible chains cannot disrupt the orientation of LC, and a dark spot is observed. On the basis of the dark or bright signal from LC, α-chymotrypsin in buffer solution or complex media such as chicken broth can be detected by using the naked eye. However, when the incubation time is 3h, the limit of detection (LOD) for α-chymotrypsin in buffer solution is 50ng/mL, whereas that in chicken broth is only 500ng/mL. Unlike traditional antibody-based assays which show little difference between active and inactive α-chymotrypsin, only active protease can be detected in this assay. This study shows the potential utility of LCs for detecting functional proteases with good specificity and sensitivity.

Temperature-cycle single-molecule FRET microscopy on polyprolines

Accessing the microsecond dynamics of a single fluorescent molecule in real time is difficult because molecular fluorescence rates usually limit the time resolution to milliseconds. We propose to apply single-molecule temperature-cycle microscopy to probe molecular dynamics at microsecond timescales. Here, we follow donor and acceptor signals of single FRET-labeled polyprolines in glycerol to investigate their conformational dynamics. We observe a steady-state FRET efficiency distribution which differs from theoretical distributions for isotropically orientated fluorescent labels. This may indicate that the orientation of fluorescent labels in glycerol is not isotropic and may reflect the influence of the dye linkers. With proper temperature-cycle parameters, we observed large FRET changes in long series of cycles of the same molecule. We attribute the main conformational changes to reorientations of the fluorescent labels with respect to the oligopeptide chain, which take place in less than a few microseconds at the highest temperature of the cycle (250 K). We were able to follow the FRET efficiency of a particular construct for more than 2000 cycles. This trajectory displays switching between two conformations, which give rise to maxima in the FRET efficiency histogram. Our experiments open the possibility to study biomolecular dynamics at a time scale of a few microseconds at the single-molecule level.

TioS T‐TE – a prototypical thioesterase responsible for cyclodimerization of the quinoline‐ and quinoxaline‐type class of chromodepsipeptides

The family of chromodepsipeptides constitutes a class of structurally related pseudosymmetrical peptidolactones and peptidothiolactones synthesized by nonribosomal peptide synthetases. The chromodepsipeptides, which are analogous to the extensively characterized echinomycin, attain their DNA-bisintercalating properties from chromophore moieties attached to the N-termini of the oligopeptide chain. Thiocoraline, a quinoline-substituted DNA-bisintercalator isolated from marine actinomycetes, is a two-fold symmetric octathiodepsipeptide currently undergoing preclinical trials phase II. In the present study, the excised peptide cyclase TioS T-TE (thiolation-thioesterase bidomain) was employed as a general catalyst for the in vitro generation of thiocoraline analogs. TioS T-TE is capable of catalyzing ligation and the subsequent cyclization of tetrapeptidyl-thioester substrates, circumventing the demanding synthesis of octapeptidyl substrates. The general importance of several amino acid residues within the tetrapeptide was evaluated and revealed new insights with respect to the iterative mechanism utilized by the thioesterase. Additionally, substrate tolerance towards the cyclizing nucleophile allows the formation of macrolactones instead of the native macrothiolactones. Several thiocoraline analogs were isolated and investigated for DNA-bisintercalation activity. Relaxed substrate specificity regarding the chromophore moiety enables the chemoenzymatic synthesis of the quinoxaline- and quinoline-type class of chromodepsipeptides. TioS T-TE is the first nonribosomal peptide synthetase-derived thioesterase, capable of macrothiolactonization and macrolactonization, working in an iterative manner.

Subdiffusion in Peptides Originates from the Fractal-Like Structure of Configuration Space

Molecular dynamics simulation of oligopeptide chains reveals configurational subdiffusion at equilibrium extending from 10(-12) to 10(-8) s. Trap models, involving a random walk with a distribution of waiting times, cannot account for the subdiffusion, which is found rather to arise from the fractal-like structure of the accessible configuration space.

Homochiral Oligopeptides Generated by Induced “Mirror Symmetry Breaking” Lattice‐Controlled Polymerizations in Racemic Crystals of Phenylalanine N‐Carboxyanhydride

The formation of diastereoisomeric libraries of oligopeptides through the heterogeneous polymerization of racemic crystals of phenylalanine N-carboxyanhydride (PheNCA) is reported. The diastereoisomeric compositions of the oligopeptides formed on polymerization of (R,S) crystals incorporating the deuterium-tagged S enantiomer were determined by MALDI-TOF mass spectrometry. The racemic mixtures of the oligopeptides longer than pentamers are represented primarily by diastereoisomers of homochiral sequence and with peptides containing only one heterochiral repeating unit. A mechanism comprising the following three sequential steps to account for this unusual observation is proposed: 1) formation of dimers and trimers at a partially damaged liquid/solid interface, 2) chain propagation that takes place within the bulk of the crystal through a lattice-controlled "zipper-like" mechanism between homochiral molecules arranged in a head-to-tail motif to yield crystalline antiparallel beta-sheets of alternating oligopeptide chains of homochiral sequence of opposite handedness, and 3) enantiomeric cross-inhibition that results in chain termination. Induced desymmetrization of the racemic mixtures of the formed peptides was achieved by the polymerization of the mixed quasi-racemic crystals of (R)-PheNCA, ((S)-PheNCA), and (S)-ThieNCA (3-(2-thienyl)-alanine N-carboxyanhydride) of various compositions. These experiments resulted in the formation of nonracemic libraries of oligopeptides composed of homochiral chains of (R)-Phe and copolymers of randomly distributed (S)-Phe and (S)-Thie sequences. From these findings, we propose a stochastic model for the generation of libraries of nonracemic mixtures of oligopeptides from the polymerization of host (R,S)-PheNCA with racemic mixtures of other guest NCA amino acids dissolved in limited quantities in the crystal.

Tertiary structure of Staphylococcus aureus cell wall murein.

The recently described scaffold model of murein architecture depicts the gram-negative bacterial cell wall as a gel-like matrix composed of cross-linked glycan strands oriented perpendicularly to the plasma membrane while peptide bridges adopt a parallel orientation (B. A. Dmitriev, F. V. Toukach, K. J. Schaper, O. Holst, E. T. Rietschel, and S. Ehlers, J. Bacteriol. 185:3458-3468, 2003). Based on the scaffold model, we now present computer simulation studies on the peptidoglycan arrangement of the gram-positive organism Staphylococcus aureus, which show that the orientation of peptide bridges is critical for the highly cross-linked murein architecture of this microorganism. According to the proposed refined model, staphylococcal murein is composed of glycan and oligopeptide chains, both running in a plane that is perpendicular to the plasma membrane, with oligopeptide chains adopting a zigzag conformation and zippering adjacent glycan strands along their lengths. In contrast to previous models of murein in gram-positive bacteria, this model reflects the high degree of cross-linking that is the hallmark of the staphylococcal cell wall and is compatible with distinguishing features of S. aureus cytokinesis such as the triple consecutive alteration of the division plane orientation and the strictly centripetal mode of septum closure.