Local Chain Conformation Research Articles

Potent and Protease Resistant Azapeptide Agonists of the GLP‐1 and GIP Receptors

AbstractThe gut‐derived peptide hormones glucagon‐like peptide‐1 (GLP‐1) and glucose‐dependent insulinotropic polypeptide (GIP) play important physiological roles including glucose homeostasis and appetite suppression. Stabilized agonists of the GLP‐1 receptor (GLP‐1R) and dual agonists of GLP‐1R and GIP receptor (GIPR) for the management of type 2 diabetes and obesity have generated widespread enthusiasm and have become blockbuster drugs. These therapeutics are refractory to the action of dipeptidyl peptidase‐4 (DPP4), that catalyzes rapid removal of the two N‐terminal residues of the native peptides, in turn severely diminishing their activity profiles. Here we report that a single atom change from carbon to nitrogen in the backbone of the entire peptide makes them refractory to DPP4 action while still retaining full potency and efficacy at their respective receptors. This was accomplished by use of aza‐amino acids, that are bioisosteric replacements for α‐amino acids that perturb the structural backbone and local side chain conformations. Molecular dynamics simulations reveal that aza‐amino acid can populate the same conformational space that GLP‐1 adopts when bound to the GLP‐1R. The insertion of an aza‐amino acid at the second position from the N‐terminus in semaglutide and in a dual agonist of GLP‐1R and GIPR further demonstrates its capability as a viable alternative to current DPP4 resistance strategies while offering additional structural variation that may influence downstream signaling.

Potent and Protease Resistant Azapeptide Agonists of the GLP-1 and GIP Receptors.

The gut-derived peptide hormones glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP) play important physiological roles. Stabilized agonists of the GLP-1 receptor (GLP-1R) and the GIP receptor (GIPR) for the management of diabetes and obesity have generated widespread enthusiasm and have become blockbuster drugs. These therapeutics are refractory to the action of dipeptidyl peptidase-4 (DPP4), that catalyzes rapid removal of the two N-terminal residues of the native peptides, in turn severely diminishing their activity profiles. Here we report that a single atom change from carbon to nitrogen in the backbone of the entire peptide make them refractory to DPP4 action while still retaining full potency and efficacy at their respective receptors. This was accomplished by use of aza-amino acids, that are bioisosteric replacements for a-amino acids that perturb the structural backbone and local side chain conformations. Molecular dynamics simulations reveal that aza-amino acid can populate the same conformational space that GLP-1 adopts when bound to the GLP-1R. The insertion of an aza-amino acid at the second position from the N-terminus in semaglutide and in a dual agonist of GLP-1R and GIPR further demonstrates its capability as a viable alternative to current DPP4 resistance strategies while offering additional structural variety.

Distribution of Density of States in Organic Field–Effect Transistors Based on Polymer Dielectrics

AbstractThe distribution of density of states (DOS) holds fundamental importance in determining charge transport within organic field–effect transistors (OFETs). Herein, the modulation of DOS distribution in OFET devices is demonstrated by altering the chain conformation of the polymer dielectrics. A rapid film‐formation technique, specifically the spin‐casting method, is used to fabricate the dielectric layer using poly(methyl methacrylate) (PMMA). This method allows for the retention of some memory of the chain conformations from the solution to the resulting dry film. This memory effect is employed to prepare thin PMMA films with different local chain conformations by adjusting the quality of the solvent. Good solvent forms solidified films with a reduced amount of gauche conformer in the PMMA chain, resulting in a narrow DOS distribution width. Consequently, the device exhibited enhanced charge mobility and a reduced subthreshold swing. The observed change in the width of the DOS distribution can be attributed to the alteration of the local energy state of the semiconductor, induced by the local chain conformation of PMMA dielectrics through electrostatics and steric interactions.

Effect of interfacial local conformation of polymer chains on adhesion strength

The aggregation states of polymer chains at solid interfaces are strongly related to their adhesion properties.

Absolute local conformation of poly(methyl methacrylate) chains adsorbed on a quartz surface.

Polymer chains at a buried interface with an inorganic solid play a critical role in the performance of polymer nanocomposites and adhesives. Sum frequency generation (SFG) vibrational spectroscopy with a sub-nanometer depth resolution provides valuable information regarding the orientation angle of functional groups at interfaces. However, in the case of conventional SFG, since the signal intensity is proportional to the square of the second-order nonlinear optical susceptibility and thereby loses phase information, it cannot be unambiguously determined whether the functional groups face upward or downward. This problem can be solved by phase-sensitive SFG (ps-SFG). We here applied ps-SFG to poly(methyl methacrylate) (PMMA) chains in direct contact with a quartz surface, shedding light on the local conformation of chains adsorbed onto the solid surface. The measurements made it possible to determine the absolute orientation of the ester methyl groups of PMMA, which were oriented toward the quartz interface. Combining ps-SFG with all-atomistic molecular dynamics simulation, the distribution of the local conformation and the driving force are also discussed.

Crystal Polymorphism of Isodimorphic Polyesters Tuned by cis- and trans-C═C Comonomer Units.

Polymorphism is ubiquitous in polymer crystallization due to the diversified chain conformations and interchain packings in polymer crystals. Controlling chain conformation is effective in tailoring the crystal polymorphism of polymers, which, however, is challenging at the molecular level. Herein, we have synthesized poly(butylene adipate) (PBA)-based copolymers containing C═C units and demonstrated the important role of trans/cis-C═C units in tuning the chain conformation and crystal polymorphism of polymers. Both PBA-based trans- and cis-copolymers show isodimorphic crystallization behavior with the partial inclusion of C═C units in PBA crystals. The presence of trans-C═C units favors the formation of metastable β-crystals of PBA and retards the β-to-α crystal transition upon heating due to the highly conformational matching between trans-C═C units and β-crystals. Conversely, the incorporation of cis-C═C units destroys the regularity of the trans conformation and favors the growth of α-crystals of PBA. This work has elucidated the crucial role of local chain conformation in the crystal polymorphism of polymers.

Free-Energy Landscape Analysis of Protein-Ligand Binding: The Case of Human Glutathione Transferase A1

Glutathione transferases (GSTs) are a superfamily of enzymes which have in common the ability to catalyze the nucleophilic addition of the thiol group of reduced glutathione (GSH) onto electrophilic and hydrophobic substrates. This conjugation reaction, which occurs spontaneously but is dramatically accelerated by the enzyme, protects cells against damages caused by harmful molecules. With some exceptions, GSTs are catalytically active as homodimers, with monomers generally constituted of 200 to 250 residues organized into two subdomains. The first is the N-terminal subdomain, which contains an active site named G site, where GSH is hosted in catalytic conformation and which is generally highly conserved among GSTs. The second subdomain, hydrophobic, which binds the substrate counterpart (H site), can vary from one GST to another, resulting in structures able to recognize different substrates. In the present work, we performed all-atom molecular dynamics simulations in explicit solvent of human GSTA1 in its APO form, bound to GSH ligand and bound to GS-conjugated ligand. From MD, two probes were analyzed to (i) decipher the local conformational changes induced by the presence of the ligand and (ii) map the communication pathways involved in the ligand-binding process. These two local probes are, first, coarse-grained angles (θ,γ), representing the local conformation of the protein main chain and, second, dihedral angles χ representing the local conformation of the amino-acid side chains. From the local probes time series, effective free-energy landscapes along the amino-acid sequence were analyzed and compared between the three different forms of GSTA1. This methodology allowed us to extract a network of 33 key residues, some of them being located in the experimentally well-known binding sites G and H of GSTA1 and others being located as far as 30Å from the original binding sites. Finally, the collective motions associated with the network of key residues were established, showing a strong dynamical coupling between residues Gly14-Arg15 and Gln54-Val55, both in the same binding site (intrasite) but also between binding sites of each monomer (intersites).

Change in local conformation of polymer chains at film surface attached to solid surface.

Adhesion is a molecular event where polymer chains contact with a material surface to form an interfacial layer. To obtain a better understanding of the adhesion on a molecular scale, we herein examined the conformational change of polystyrene (PS) chains at the film surface after contacting with hydrophobic or hydrophilic surfaces using sum-frequency generation (SFG) spectroscopy. Chains altered their local conformations with a quartz surface more quickly than a hydrophobic alkyl-functionalized one. A full-atomistic molecular dynamics simulation showed that these results, which were coupled with the contact process of PS chains with the solid surface, could be explained in terms of the Coulomb interaction between them.

Effects of Glycine on the Local Conformation and Internal Backbone Dynamics of Polypeptides

The effects, that glycine (Gly) has on the local chain conformation and internal backbone dynamics (IBD) of polypeptides, were investigated by comparing the fluorescence response of a series of pyr...

Insight into morphological, physicochemical and spectroscopic properties of β-chitin nanocrystalline structures

We systematically investigated the effect of β-chitin (BCH) particle size on the preparation of nanocrystals/nanowhiskers (CWH) by acid hydrolysis. Regardless this variable, CWH aqueous suspension exhibited outstanding stability and the average degree of acetylation remained nearly constant after the acid treatment. In contrast, the morphology, dimensions, crystallinity, and molecular weight of CHW were significantly affect by the particle size. Although needle-like crystals have predominated, BCH particles sizes significantly affected the dimensions and asymmetry of CWH, as confirmed by the rheological and NMR relaxation (T2) behaviors. According to different SSNMR approaches, the acid hydrolysis meaningless affected the local chain conformation, while the spatial freedom of BCH intersheets, rated upon the mobility of methyl segments, was taken as evidence of higher permeability of acid into small particle sizes. Thus, this study demonstrated the importance of standardizing the surface/bulk proportions of β-chitin aiming to predict and control the CWH morphology and related properties.

Development of a PointNet for Detecting Morphologies of Self-Assembled Block Oligomers in Atomistic Simulations.

Molecular simulations with atomistic or coarse-grained force fields are a powerful approach for understanding and predicting the self-assembly phase behavior of complex molecules. Amphiphiles, block oligomers, and block polymers can form mesophases with different ordered morphologies describing the spatial distribution of the blocks, but entirely amorphous nature for local packing and chain conformation. Screening block oligomer chemistry and architecture through molecular simulations to find promising candidates for functional materials is aided by effective and straightforward morphology identification techniques. Capturing 3-dimensional periodic structures, such as ordered network morphologies, is hampered by the requirement that the number of molecules in the simulated system and the shape of the periodic simulation box need to be commensurate with those of the resulting network phase. Common strategies for structure identification include structure factors and order parameters, but these fail to identify imperfect structures in simulations with incorrect system sizes. Building upon pioneering work by DeFever et al. [Chem. Sci. 2019, 10, 7503-7515] who implemented a PointNet (i.e., a neural network designed for computer vision applications using point clouds) to detect local structure in simulations of single-bead particles and water molecules, we present a PointNet for detection of nonlocal ordered morphologies of complex block oligomers. Our PointNet was trained using atomic coordinates from molecular dynamics simulation trajectories and synthetic point clouds for ordered network morphologies that were absent from previous simulations. In contrast to prior work on simple molecules, we observe that large point clouds with 1000 or more points are needed for the more complex block oligomers. The trained PointNet model achieves an accuracy as high as 0.99 for globally ordered morphologies formed by linear diblock, linear triblock, and 3-arm and 4-arm star-block oligomers, and it also allows for the discovery of emerging ordered patterns from nonequilibrium systems.

Effect of Molecular Architecture on Associating Behavior of Star-Like Amphiphilic Polymers Consisting of Plural Poly(ethylene oxide) and One Alkyl Chain

Associating behavior of star-like amphiphilic polymers consisting of two or three poly(ethylene oxide) (PEO) chains and one stearyl chain (C18) was investigated. Although the aggregation number (Nagg) of linear analogue of amphiphilic polymers monotonically decreased with increasing number-average molecular weight of PEO (Mn,PEO), the Nagg of micelles of star-like amphiphilic polymers with Mn,PEO = 550 g/mol was smaller than that with Mn,PEO = 750 g/mol, whereas that with Mn,PEO ≥ 750 g/mol showed general Mn,PEO dependence. Small-angle X-ray scattering analyses revealed that the occupied area of one PEO chain on the interface between hydrophobic core and corona layer in the micelles of star-like polymers was much narrower than that in the linear amphiphilic polymers. This result indica ted the PEO chains of star-like polymers partially took unfavorable conformation near the core–corona interface in polymer micelles. The effect of local conformation of PEO chains near the interface on the associating behavior became significant as Mn,PEO decreased. Therefore, in polymer micelles of star-like amphiphilic polymers containing PEO with Mn,PEO = 550 g/mol, the enlargement of occupied area of PEO on the core–corona interface should be caused to avoid the formation of unfavorable conformations of partial PEO chains, resulting in a decrease in Naggs.

Limitations of the ABEGO-based backbone design: ambiguity between αα-corner and αα-hairpin.

ABEGO is a coarse-grained representation for poly­peptide backbone dihedral angles. The Ramachandran map is divided into four segments denoted as A, B, E, and G to represent the local conformation of poly­peptide chains in the character strings. Although the ABEGO representation is widely used in backbone building simulation for de novo protein design, it cannot capture minor differences in backbone dihedral angles, which potentially leads to ambiguity between two structurally distinct fragments. Here, I show a nontrivial example of two local motifs that could not be distinguished by their ABEGO representations. I found that two well-known local motifs αα-hairpins and αα-corners are both represented as α-GBB-α and thus indistinguishable in the ABEGO representation, although they show distinct arrangements of the flanking α-helices. I also found that α-GBB-α motifs caused a loss of efficiency in the ABEGO-based fragment-assembly simulations for de novo protein backbone design. Nevertheless, I was able to design amino-acid sequences that were predicted to fold into the target topologies that contained these α-GBB-α motifs, which suggests such topologies that are difficult to build by ABEGO-based simulations are designable once the backbone structures are modeled by some means. The finding that certain local motifs bottleneck the ABEGO-based fragment-assembly simulations for construction of backbone structures suggests that finer representations of backbone torsion angles are required for efficiently generating diverse topologies containing such indistinguishable local motifs.

Polysaccharide conformations measured by solution state X-ray scattering

Polysaccharides are semi-flexible polymers composed of sugar residues with a myriad of important functions including structural support and energy storage. The local conformation of such chains is a crucial factor governing their interactions. Traditionally this conformation has only been directly accessible in the solid-state, using crystallographic techniques such as fibre diffraction. Herein it is demonstrated that improvements in the quality of synchrotron-based X-ray scattering data means that conformation-dependent features, the positions of which are related to the linear repeating distance between single saccharide monomers, can now be measured in solution. This technique is expected to be universally applicable for polysaccharides.

Effect of Local Chain Conformation in Adsorbed Nanolayers on Confined Polymer Molecular Mobility

Interfaces play an important role in modifying the dynamics of polymers confined to the nanoscale. We demonstrate that the distance over which an interface suppresses molecular mobility in poly(styrene) thin films can be systematically increased by tens of nanometers by controlling the chain of conformation, i.e., the height of the loops in irreversibly adsorbed nanolayers. These effects arise from topological interaction between adsorbed and neighboring unadsorbed chains, respectively, which increase their motional coupling to facilitate the propagation of suppressed dynamics originating at the interface, thus highlighting the ability to manipulate interfacial effects by local conformation of chains in adsorbed nanolayers.

Light chain modulates heavy chain conformation to change protection profile of monoclonal antibodies against influenza A viruses

The isolation of human monoclonal antibodies with broadly neutralizing breadth can provide a promising countermeasure for influenza A viruses infection. Most broadly neutralizing antibodies against influenza A viruses bind to the conserved stem region or the receptor-binding cavity of hemagglutinin and the interaction is dominated by the heavy chain. The light chain, however, contributes few or no direct contacts to the antigen. Here we report an H3-clade neutralizing human monoclonal antibody, AF4H1K1, which recognizes the hemagglutinin glycoproteins of all group 2 influenza A viruses. This human monoclonal antibody has been obtained through the screening by pairing different heavy and light chains from an H7N9-infected patient based on the next-generation sequencing technology. Further structural studies revealed that light chains modulate the neutralizing spectrum by affecting the local conformation of heavy chains, instead of direct interaction with the antigen. These findings provide important clues to understand the molecular basis of light chains in antigen recognition and to explore the strategies in particular of the use of light chain modification to develop broadly protective monoclonal antibodies against influenza A viruses and other emerging viruses.

Does local chain conformation affect the chiral recognition ability of an amylose derivative? Comparison between linear and cyclic amylose tris(3,5-dimethylphenylcarbamate)

Coated-type chiral stationary phases (CSPs) for high-performance liquid chromatography (HPLC) were prepared from three cyclic amylose tris(3,5-dimethylphenylcarbamate) (cADMPC) samples, of which weight-average molar mass (Mw) ranges from 19 to 91 kg mol−1, and from three linear ADMPC samples ranging in Mw from 25 to 90 kg mol−1. CSPs made of cADMPC showed appreciably different chiral separation ability comparing with those for ADMPC with a mixed eluent of n-hexane and 2-propanol. Local conformation plays an important role for the chiral separation taking into account that the local helical structure of cADMPC in dilute solution is extended comparing with ADMPC. Immobilized-type CSPs were also prepared from enzymatically synthesized linear and cyclic amylose samples with 3-(triethoxysilyl)propylcarbamate linkers (ADMPCi and cADMPCi) of which Mw’s are in the range from 18 to 130 kg mol−1. When we choose quite high linker contents, CSPs of cADMPCi were fairly close to those of ADMPCi. This suggests that local conformations of ADMPCi and cADMPCi are similar in the stationary phase since they are crosslinked to the other polymer chains with multiple points on the polymer chain.

Generic Model for Lamellar Self-Assembly in Conjugated Polymers: Linking Mesoscopic Morphology and Charge Transport in P3HT.

We develop a generic coarse-grained model of soluble conjugated polymers, capable of describing their self-assembly into a lamellar mesophase. Polymer chains are described by a hindered-rotation model, where interaction centers represent entire repeat units, including side chains. We introduce soft anisotropic nonbonded interactions to mimic the potential of mean force between atomistic repeat units. The functional form of this potential reflects the symmetry of the molecular order in a lamellar mesophase. The model can generate both nematic and lamellar (sanidic smectic) molecular arrangements. We parametrize this model for a soluble conjugated polymer poly(3-hexylthiophene) (P3HT) and demonstrate that the simulated lamellar mesophase matches morphologies of low molecular weight P3HT, experimentally observed at elevated temperatures. A qualitative charge-transport model allows us to link local chain conformations and mesoscale order to charge transport. In particular, it shows how coarsening of lamellar domains and chain extension increase the charge carrier mobility. By modeling large systems and long chains, we can capture transport between lamellar layers, which is due to rare, but thermodynamically allowed, backbone bridges between neighboring layers.

Aggregation States of Poly(4-methylpentene-1) at a Solid Interface

A thin film of poly(4-methylpentene-1) (P4MP1) was prepared on a quartz substrate, which was a model system of an interface in filler-reinforced semicrystalline polymer composites. Grazing-incidence wide-angle X-ray diffraction measurements revealed that P4MP1 in the thin film after isothermal crystallization formed a Form I crystal polymorph composed of a tetragonal unit cell with a 72 helix, in which the chain axis was oriented along the direction parallel to the quartz interface. Combining sum-frequency generation vibrational spectroscopy with molecular dynamics simulation enabled us to gain access to the local conformation of P4MP1 chains at the quartz interface and the changes that occurred with isothermal crystallization. Finally, the way in which the initial chain orientation at the substrate interface impacted the crystalline structure in the thin film was discussed. A poly(4-methylpentene-1) (P4MP1) film was prepared on a quartz substrate, which was a model system of interfaces in a filler-reinforced semicrystalline polymer composite. Grazing-incidence wide-angle X-ray diffraction measurements revealed that P4MP1 in the film after the isothermal crystallization formed a Form I crystal polymorph, in which the chain axis was oriented along the direction parallel to the quartz interface. Combining sum-frequency generation vibrational spectroscopy with molecular dynamics simulation enabled us to study the local conformation of P4MP1 chains at the quartz interface and the changes that occurred with isothermal crystallization.

An Algorithm for Computing Side Chain Conformational Variations of a Protein Tunnel/Channel.

In this paper, a novel method to compute side chain conformational variations for a protein molecule tunnel (or channel) is proposed. From the conformational variations, we compute the flexibly deformed shapes of the initial tunnel, and present a way to compute the maximum size of the ligand that can pass through the deformed tunnel. By using the two types of graphs corresponding to amino acids and their side chain rotamers, the suggested algorithm classifies amino acids and rotamers which possibly have collisions. Based on the divide and conquer technique, local side chain conformations are computed first, and then a global conformation is generated by combining them. With the exception of certain cases, experimental results show that the algorithm finds up to 327,680 valid side chain conformations from 128~1233 conformation candidates within three seconds.