Conformational Analysis Of Peptides Research Articles

Strategy for improving circular dichroism spectra deconvolution accuracy for macrocyclic peptides in drug discovery

Peptide therapeutics have emerged as an appealing modality in the pharmaceutical industry. Understanding peptide conformation in solution remains one of the most critical areas for peptide drug development. Circular dichroism (CD) spectroscopy is a useful technique to study the secondary structure of proteins and peptides, but the current approaches are limited to protein-focused models to predict high-order structures of peptides, and the models were built based on X-ray crystallography instead of solution-based technique, as a result, such models may have poor predictions for peptides. In this study, we present a novel CD deconvolution model to determine peptide conformation in solution. To quantitatively obtain secondary structure information using CD, a calibration model is needed beforehand to establish the relationship between each secondary structure feature and the corresponding CD response. A reference set containing the majority of cyclic peptides with known structures from solution-state NMR spectroscopy was used to build the calibration model for CD deconvolution. Improved prediction accuracy on the secondary structure determination for cyclic peptides was achieved by this model compared to the commercial standard model using commercially available platforms. This new CD deconvolution method is crucial for peptide conformational analysis in solution, and has the potential to greatly accelerate peptide drug candidate optimization in the pharmaceutical drug discovery field.

Porous organic cages as inhibitors of Aβ42 peptide aggregation: a simulation study.

The aggregation of Aβ monomers into oligomers with β-sheet structures is an important cause of Alzheimer's disease (AD), while the Aβ42 peptide is more toxic and prone to aggregate. It is of great significance to study the inhibition mechanism of Aβ42 monomer aggregation and find excellent inhibitors for the treatment of AD. Research in recent years has focused on small molecule compounds and nanoparticles, but they all have certain limitations. As a new type of porous material, a porous organic cage (POC) has potential application feasibility in the biomedical field due to its unique physicochemical properties. In this work, molecular dynamics simulations were used for the first time to explore the interaction and conformational transformation of the Aβ42 peptide in CC3 crystals with different morphologies (planar and spherical). The results show that the adsorption of the Aβ42 peptide on different CC3 crystals is mainly achieved through strong van der Waals forces. During the simulations, the Aβ42 peptide undergoes various degrees of structural changes. Compared to that in water, this binding induces more irregular structures, such as turns and 3-helices, and inhibits the production of β-sheets, while enhancing the overall backbone rigidity of the Aβ42 peptide. The transformation analysis of peptide conformation is further complemented by free energy landscape and cluster analysis. These findings provide a strong basis for CC3 crystals as novel inhibitors to inhibit the toxicity and aggregation of the Aβ42 peptide.

Tyrosyltyrosylcysteine-Directed Synthesis of Chiral Cobalt Oxide Nanoparticles and Peptide Conformation Analysis.

Chiral inorganic nanomaterials have revealed opportunities in various fields owing to their strong light-matter interactions. In particular, chiral metal oxide nanomaterials that can control light and biochemical reactions have been highlighted due to their catalytic activity and biocompatibility. In this study, we present the synthesis of chiral cobalt oxide nanoparticles with a g-factor of 0.01 in the UV-visible region using l- and d-Tyr-Tyr-Cys ligands. The conformation of the Tyr-Tyr-Cys peptide on the nanoparticle surfaces was identified by 2D NMR spectroscopy analysis. In addition, the sequence effect of Tyr-Tyr-Cys developing chiral nanoparticles was analyzed. The revealed peptide structure, along with the experimental results, demonstrate the important role of the thiol group and carboxyl group of the Tyr-Tyr-Cys ligand in chirality evolution. Importantly, due to the magnetic properties of chiral cobalt oxide nanoparticles and their strong absorption in the UV region, the circular dichroism (CD) responses can be dramatically modulated under an external magnetic field.

The Conformation and Aggregation of Proline-Rich Surfactant-Like Peptides.

The secondary structure of proline-rich surfactant-like peptides is examined for the first time and is found to be influenced by charged end groups in peptides P6K, P6E, and KP6E and an equimolar mixture of P6K and P6E. The peptides exhibit a conformational transition from unordered to polyproline II (PPII) above a critical concentration, detected from circular dichroism (CD) measurements and unexpectedly from fluorescence dye probe measurements. Isothermal titration calorimetry (ITC) measurements provided the Gibbs energies of hydration of P6K and P6E, which correspond essentially to the hydration energies of the terminal charged residues. A detailed analysis of peptide conformation for these peptides was performed using density functional theory calculations, and this was used as a basis for hybrid quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) simulations. Quantum mechanics simulations in implicit water show both peptides (and their 1:1 mixture) exhibit PPII conformations. However, hybrid QM/MM MD simulations suggest that some deviations from this conformation are present for P6K and P6E in peptide bonds close to the charged residue, whereas in the 1:1 mixture a PPII structure is observed. Finally, aggregation of the peptides was investigated using replica exchange molecular dynamics simulations. These reveal a tendency for the average aggregate size (as measured by the radius of gyration) to increase with increasing temperature, which is especially marked for P6K, although the fraction of the most populated clusters is larger for P6E.

Structure-Activity Relationship Studies, SPR Affinity Characterization, and Conformational Analysis of Peptides That Mimic the HNK-1 Carbohydrate Epitope.

The design of molecules that mimic biologically relevant glycans is a significant goal for understanding important biological processes and may lead to new therapeutic and diagnostic agents. In this study we focused our attention on the trisaccharide human natural killer cell-1 (HNK-1), considered the antigenic determinant of myelin-associated glycoprotein and the target of clinically relevant auto-antibodies in autoimmune neurological disorders such as IgM monoclonal gammopathy and demyelinating polyneuropathy. We describe a structure-activity relationship study based on surface plasmon resonance binding affinities aimed at the optimization of a peptide that mimics the HNK-1 minimal epitope. We developed a cyclic heptapeptide that shows an affinity of 1.09×10-7 m for a commercial anti-HNK1 mouse monoclonal antibody. Detailed conformational analysis gave possible explanations for the good affinity displayed by this novel analogue, which was subsequently used as an immunological probe. However, preliminary screening indicates that patients' sera do not specifically recognize this peptide, showing that murine monoclonal antibodies cannot be used as a guide to select immunological probes for the detection of clinically relevant human auto-antibodies.

Molecular dynamics simulations of conformation changes of HIV-1 regulatory protein on graphene

The fragment of viral protein R (Vpr), Vpr13-33, plays an important role in regulating nuclear importing of HIV genes through channel formation in which it adopts a leucine-zipper-like alpha-helical conformation. A recent experimental study reported that helical Vpr13-33 would transform to β-sheet or random coil structures and aggregate on the surface of graphene or graphene oxide through hydrophobic interactions. Due to experimental limitations, however, there is still a considerable lack of understanding on the adsorption dynamics at the early stage of the conformational transition at water-graphene interface and the underlying driving force at molecular level. In this study, atomistic molecular dynamics simulations were used to explore the conformation transition phenomena. Vpr13-33 kept α-helical structure in solution, but changed to β-sheet structure when strongly adsorbed onto graphene. Preferential adsorption of Vpr13-33 on graphene is dominated by hydrophobic interactions. The cluster analysis identified the most significant populated conformation and the early stage of structure conversion from α-helical to β-sheet was found, but the full β-sheet propagation was not observed. Free energy landscape analysis further complemented the transformation analysis of peptide conformations. These findings are consistent with experimental results, and give a molecular level interpretation for the reduced cytotoxicity of Vpr13-33 to some extent upon graphene exposure. Meanwhile, this study provides some significant insights into the detailed mechanism of graphene-induced protein conformation transition.

Conformational studies on peptides having dipropylglycine (Dpg) or 1-aminocycloheptanecarboxylic acid (Ac7 c) within the sequence of l-leucine (Leu) residues.

A conformational analysis of peptides having dipropylglycine (Dpg) or 1-aminocycloheptanecarboxylic acid (Ac7 c) within l-leucine (Leu) residues was conducted in solution and in a crystal state. Dpg and Ac7 c had similar structures with acyclic and cyclic side chains, respectively. FTIR, 1 H NMR, and CD spectra measurements revealed that the preferred conformations of Dpg- and Ac7 c-containing l-Leu peptides in solution were similar; both had a right-handed (P) 310 -helix. The Dpg-containing octapeptide adopted a right-handed (P) α-helix in the crystal state. Dpg and Ac7 c homopeptides had planar and helical structures as their preferred conformations, respectively; however, Dpg- and Ac7 c-containing l-Leu peptides adopted similar structures in solution. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 210-218, 2016.

Modeling of Platinum-Aryl Interaction with Amyloid-β Peptide.

Ligand field molecular mechanics (LFMM), density functional theory (DFT), and semiempirical PM7 methods are used to study the binding of two Pt(II)-L systems to an N-terminal fragment of the amyloid-β peptide, where L = 2,2-bipyridyl or 1,10-phenanthroline. Molecular dynamics simulations are used to explore the conformational freedom of the peptide using LFMM combined with AMBER molecular mechanics parameters. We establish a modeling protocol, allowing for identification and analysis of favorable platinum-binding modes and peptide conformations. Preferred binding modes are identified for each ligand investigated; metal coordination occurs via Nε in His residues for both ligands--His6ε-His13ε and His6ε-His14ε for the bipyridyl and phenanthroline ligands, respectively. The observed change in binding mode for the different ligands suggests that the binding mode of these platinum-based structures can be controlled by the choice of ligand. In the bipy systems, Boltzmann population at 310 K is dominated by a single conformer, while in the phenanthroline case, three conformations make significant contributions to the ensemble. The relative stability of these conformations is due to the inherent stability of binding platinum via Nε in addition to subtle H-bonding effects.

Conformational analysis of peptides and glycopeptides derived from the consensus sequence for β-O-glucosylation.

Cys-Xxx-Ser-Xxx-Pro-Cys (Xxx= any amino acid but Pro) is the most common sequence present in naturally occurring peptides and proteins glycosylated with β-O-glucose (β-O-Glc). Taking into account the lack of studies concerning the spatial disposition of this sequence, we have synthesized and analyzed, in aqueous solution, the conformational behavior of peptides and a glycopeptide derived from the particular fragment Cys-Ala-Ser-Ser-Pro-Cys. This sequence is found in the crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor. Our studies, based on the use of NOESY experiments in combination with molecular dynamics (MD) simulations, indicate that for this particular fragment, initially characterized by a type I β-turn motif, the glycosylation with β-O-Glc forces the peptide backbone into an extended conformation. This conformation is stabilized by the presence of both hydrogen bonds and water pockets between the peptide and the sugar moieties.

Peptide Conformation Analysis Using an Integrated Bayesian Approach.

Unlike native proteins that are amenable to structural analysis at atomic resolution, unfolded proteins occupy a manifold of dynamically interconverting structures. Defining the conformations of unfolded proteins is of significant interest and importance, for folding studies and for understanding the properties of intrinsically disordered proteins. Short chain protein fragments, i.e., oligopeptides, provide an excellent test-bed in efforts to define the conformational ensemble of unfolded chains. Oligomers of alanine in particular have been extensively studied as minimalist models of the intrinsic conformational preferences of the peptide backbone. Even short alanine peptides occupy an ensemble of substates that are distinguished by small free energy differences, so that the problem of quantifying the conformational preferences of the backbone remains a fundamental challenge in protein biophysics. Here, we demonstrate an integrated computational-experimental-Bayesian approach to quantify the conformational ensembles of the model trialanine peptide in water. In this approach, peptide conformational substates are first determined objectively by clustering molecular dynamics snapshots based on both structural and dynamic information. Next, a set of spectroscopic data for each conformational substate is computed. Finally, a Bayesian statistical analysis of both experimentally measured spectroscopic data and computational results is carried out to provide a current best estimate of the substate population ensemble together with corresponding confidence intervals. This distribution of substates can be further systematically refined with additional high-quality experimental data and more accurate computational modeling. Using an experimental data set of NMR coupling constants, we have also applied this approach to characterize the conformation ensemble of trivaline in water.

Vibrational spectral signatures of peptide secondary structures:N-methylation and side chain hydrogen bond in cyclosporin A

Molecular dynamics simulations are performed to explore important conformations of cyclosporin A, an immunosuppressive cyclic undecapeptide drug, in different media including gas-phase, chloroform, and acetonitrile. Density functional theory calculations are used to refine the low-lying conformers and to predict their infrared and vibrational circular dichroism spectra. Vibrational spectral signatures in the important amide II, I, and A regions are identified for typical peptide secondary structures including β-turn (type II' or I), antiparallel β-sheet (flat or twisted), inverse γ-turn, N-methylated peptide bond, and side chain H-bond. New insights into the spectral signatures of secondary structures especially with N-methylation and side chain hydrogen bond are provided, which can be very useful for further peptide conformation analysis in general.

Unambiguous Assignment of Vibrational Spectra of Cyclosporins A and H

Vibrational infrared and circular dichroism spectra of two cyclosporins A and H are predicted by density functional theory calculations using the nuclear magnetic resonance proposed structure in chloroform. Spectral signatures in the important amide II, I, and A regions are identified for typical peptide secondary structures including type II' beta-turn, antiparallel beta-sheet, inverse gamma-turn, N-methylated peptide bond, and side-chain H-bond. Our theoretical spectra agree very well with available experimental data in nonpolar media and unambiguously clarify their controversial vibrational assignment. The new insights into the spectral signatures of secondary structures can be very useful for peptide conformation analysis in general.

Transitions: From the Editor‐in‐Chief of Biopolymers‐Peptide Science

I write with mixed emotions: My five-year term as Editor-in-Chief of Biopolymers-Peptide Science, the official journal of the American Peptide Society, is ending. I will miss serving the peptide community in this way and striving to provide a journal that optimally showcases the broad spectrum of exciting science carried out by peptide scientists worldwide. To me, the value of Biopolymers-Peptide Science has been enhanced by the inclusion of topical reviews—called ‘Current Trends in Peptide Science’ (edited by Charles Deber) as well as original research articles. Additionally, we have had the luxury of offering theme issues based on meetings or organized by guest editors to provide a focused view of a significant research area in peptide science. In a recent issue, we gathered papers from Young Investigators in Peptide Science, and it is intended to continue to highlight the work of the coming generation of peptide researchers. This mixture of types of articles and themes makes this journal a true reflection of the science being done by our community. I believe it works and that it is unique. Over the period of my editorship, Peptide Science has honored the passing of major figures in our field whose careers have had great impact on peptide science, including Murray Goodman Arno Spatola, and most recently Bruce Merrifield. Putting these memorial issues together has been bittersweet: They serve as tributes and outpourings from our community to these friends and colleagues. But of course, they are concrete reminders of the losses. For me personally, I can't think about my tenure as Editor without remembering Arno Spatola's effective persuasion (as all who knew him will understand very well!); he was responsible for identifying candidates to be the next editor of the journal and was assigned to urge me to put my name up for the position—there was certainly no way I could say no. How painful to then find myself putting together an issue honoring Arno after his abrupt and tragic passing during my first year as Editor. On a bright and positive note: We happily announce that Biopolymers-Peptide Science will be in terrific hands starting in 2009: Joel Schneider of the University of Delaware will assume the helm. Joel has a wonderful background in peptide science, having trained with Jeff Kelly and Bill DeGrado. Moreover, he has creatively developed and spearheaded a research program exploiting the novel characteristics of designed peptides that enable them to possess desired materials properties. These peptides have a great deal of potential as novel biomaterials. Joel's expertise encompasses peptide synthesis, conformational analysis, chemical biology, and structure. He has creative ideas to catalyze growth and excitement in the next chapter of the journal's life. Thanks Joel, and may everyone send you their most significant papers!!!! Lastly, many have helped to make my term as Editor smoother and more rewarding: I would like to take this opportunity to publicly thank them: the Associate Editors who work tirelessly on behalf of the journal—Claudio Toniolo, Sylvie Blondelle, Yuji Kobayashi, Charles Deber, and most recently, Joel Schneider; the Editorial Board, who serve the journal in many ways; and the Wiley editors I've worked with—first Swapna Spadhye, then Elizabeth Cox, as well as those who have managed the review process and production—Lisa Brodsky, Matthew Hollender, Carol Ann McNelis, all of Wiley, and Karen Mann of Cadmus. It's been a fun ride, and couldn't have happened without you all! Lila M. Gierasch Editor-in-Chief*, * Biopolymers-Peptide Science.

3P-063 13C同位体置換赤外分光法を用いたペプチド構造解析法の開発(蛋白質・計測,解析の方法論,第46回日本生物物理学会年会)

3P-063 13C同位体置換赤外分光法を用いたペプチド構造解析法の開発(蛋白質・計測,解析の方法論,第46回日本生物物理学会年会)

Synthesis and structural studies of peptides containing a glucose-derived furanoid sugar amino acid

Conformational analysis of peptides containing a glucose-derived furanoid sugar amino acid (Gaa) by detailed NMR and constrained MD studies revealed that peptides with repeating Gaa-Leu-Val units had conformational signatures very similar to those of linear homooligomers of Gaa.

Conformational studies of peptides containing cis-3-hydroxy-D-proline.

Conformational analysis of peptides containing cis-3-hydroxy-d-proline (d-cis-3-Hyp) by NMR studies revealed that the 3-hydroxyl group in this amino acid plays a significant role in the overall three-dimensional structures of the peptides. When the d-cis-3-Hyp had its 3-hydroxyl group protected as the benzyl (Bn) ether, the peptide displayed a beta-hairpin structure in both CDCl(3) and DMSO-d(6). Even after the removal of the Bn group, the resulting deprotected compound retained the same structure as in the protected version in CDCl(3). However, in polar solvent DMSO-d(6), the C-terminal strand of the hydroxyl-deprotected peptide flipped to the side of the hydroxyl group, breaking the hairpin to form a pseudo beta-turn-like nine-membered ring structure involving an intramolecular hydrogen bond between LeuNH --> HypC3-OH.

Calix[8]arene-mediated self-assembly of tetrapeptide H-Leu-Leu-Ile-Leu-OMe.

Conformational analysis of peptide 1, H-Leu-Leu-Ile-Leu-OMe on complexing with macro cycle calix[8]arene has been carried out using (1)H-NMR and FTIR spectroscopic techniques. Stoichiometry of the complex formed in the 1:8 ratio was evidenced by a Job plot. NMR studies of the above peptide show a marked downfield shift and an increase in (3)J values for NH resonances on complexing with calix[8]arene. The characteristic NOE connectivity between N(i+1)H and C(ialpha)H confirm beta-sheet conformation in the complexed state. Both (1)H-NMR and FTIR results indicate that the alpha-amino group of Leu I is proximal to the macrocycle and is involved in hydrogen bond formation with phenolic hydrogen atom of the calix[8]arene. This suggests that calix[8]arene provides a suitable platform for peptide 1 to self-assemble in a parallel beta-sheet conformation. The nature of calix[8]arene interaction with peptide 1 has been studied using dynamic NMR studies, which concludes that a bifurcated hydrogen bonding interaction exists in the molecular interfaces of the assembly.

Synthesis of N‐[(tert‐Butoxy)carbonyl]‐3‐(9,10‐dihydro‐9‐oxoacridin‐2‐yl)‐L‐alanine, a New Fluorescent Amino Acid Derivative

AbstractA simple synthesis of a new, highly fluorescent amino acid and of its protected derivative useful in peptide studies is described. The obtained derivative, N‐[(tert‐butoxy)carbonyl]‐3‐(9,10‐dihydro‐9‐oxoacridin‐2‐yl)‐L‐alanine (6), shows intense long‐wave absorption (above 360 nm) and emission (above 400 nm). The quantum yield of fluorescence of the investigated compound is very high, so it can serve as a sensitive analytical probe useful, e.g., in analysis of peptide conformations.

Peptides with selective affinity for carbon nanotubes.

Because of their extraordinary electronic and mechanical properties, carbon nanotubes have great potential as materials for applications ranging from molecular electronics to ultrasensitive biosensors. Biological molecules interacting with carbon nanotubes provide them with specific chemical handles that would make several of these applications possible. Here we use phage display to identify peptides with selective affinity for carbon nanotubes. Binding specificity has been confirmed by demonstrating direct attachment of nanotubes to phage and free peptides immobilized on microspheres. Consensus binding sequences show a motif rich in histidine and tryptophan, at specific locations. Our analysis of peptide conformations shows that the binding sequence is flexible and folds into a structure matching the geometry of carbon nanotubes. The hydrophobic structure of the peptide chains suggests that they act as symmetric detergents.

Structure-Based Design of Potent Histatin Analogues

Conformational studies of human salivary peptide, histatin 3 (Hst3), were performed by nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy in a membrane-mimicking environment. The structural information that was obtained was used in the design of peptide analogues with improved antifungal activity. In the presence of increasing concentrations of L-alpha-dimyristoylphosphatidylcholine (L-alpha-DMPC) lipid vesicles, a dramatic increase in a minimum at 198 nm is observed in the CD spectra of Hst3. The NMR data of Hst3 in the presence of L-alpha-DMPC lipid vesicles reveal the proximity of residues Y(10) and S(20), indicating the existence of a more compact structure. Peptide analogues were designed on the basis of this observation, which incorporated a disulfide bond to stabilize an extended loop in this region of the sequence. One of these, peptide 4, was 100 times more potent than Hst5 against Saccharomyces cerevisiae cells. Conformational analysis of peptide 4 revealed a looped structure with charged residues protruding on the outside surface, while a combination of aromatic residues and histidines are packed into an internal core.