Backbone Conformation Research Articles

Proscan: a structure-based proline design web server.

The ability to control protein conformations and dynamics through structure-based design has been useful in various scenarios, including engineering of viral antigens for vaccines. One effective design strategy is the substitution of residues to proline amino acids, which due to its unique cyclic side chain can favor and rigidify key backbone conformations. To provide the community with a means to readily identify and explore proline designs for target proteins of interest, we developed the Proscan web server. Proscan provides assessment of backbone angles, energetic and deep learning-based favorability scores, and other parameters for proline substitutions at each position of an input structure, along with interactive visualization of backbone angles and candidate substitution sites on structures. It identifies known favorable proline substitutions for viral antigens, and was benchmarked against datasets of proline substitution stability effects from deep mutational scanning and thermodynamic measurements. This tool can enable researchers to identify and prioritize designs for prospective vaccine antigen targets, or other designs to favor stability of key protein conformations. Proscan is available at: https://proscan.ibbr.umd.edu.

Benzodipyrrolidone-based donor-acceptor semiconducting polymers with high hole mobility and noncovalent conformational locks

Constructing highly coplanar polymer backbone plays an important role in boosting the carrier mobility of organic field effect transistors (OFETs) devices. In this study, based on noncovalent conformational locks strategy, we synthesized the electron-acceptor (A) monomer via introducing 3-dodecylthiophene on strong electron-deficient planar benzodipyrrolidone and the electron-donor (D) monomers containing different numbers (0–2) of fluorine atoms at different positon. A series of novel D-A copolymers, namely PBDP-F0, PBDP-F1 and PBDP-F2 with different backbone conformational locks through F⋯S and F⋯H–C noncovalent interactions, were obtained via Stille polycondensation. For the application in an organic field-effect transistor, all the polymers exhibited p-type charge transport characteristics and good performance with the highest hole mobilities as 0.24 cm2 V−1 s−1 for PBDP-F0, 0.87 cm2 V−1 s−1 for PBDP-F1 and 1.93 cm2 V−1 s−1 for PBDP-F2, respectively. AFM and GIXRD investigations indicated that all polymers take predominantly edge-on orientation packing mode because of the rigid and coplanar backbone conformation and the annealing films exhibited small π-π stacking distances of 3.73, 3.71 and 3.69 Å for PBDP-F0, PBDP-F1 and PBDP-F2 respectively. This work demonstrates that modified BDP-based D-A copolymers with conformational locks has a potential application in the high-performance semiconductor materials.

Optical and molecular features of negatively curved surfaces created by POPE lipids: A crucial role of the initial conditions

Membrane fusion is closely related to plasma membrane domains rich in cone-shaped phosphatidylethanolamine (PE) lipids that can reverse membrane curvature under certain conditions. The phase transition of PE-based lipid membranes from the lamellar fluid phase (Lα) to the inverse hexagonal phase (HII) is commonly taken as a general model in reconstructing the membrane fusion pathway, and whose structural features have been mostly described so far using structural and microscopic techniques. The aim of this paper is to decipher the optical and molecular features of Lβ → Lα and especially of Lα → HII transition of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) lipids at pH = 7.0 when they are initially prepared in the form of both multi- and unilamellar liposomes (MLVs and LUVs). The distinction between optical properties of MLS- and LUVs-derived HII phase, provided from turbidity-sensitive temperature-dependent UV–Vis spectra, was attributed to different formation mechanisms of HII phase. Most importantly, from FTIR spectroscopic data of POPE lipids in Lβ (15 °C), Lα (50 °C) and HII (85 °C) phases we identified the changes in molecular features of POPE lipids during phase transitions. Among the latter, by far the most significant is different hydration pattern of POPE lipids in MLVs- and LUVs-derived HII phase which extends from the polar-apolar interface all the way to the terminal amino group of the POPE lipid, along with the changes in the conformation of glycerol backbone as evidenced by the signature of α-methylene groups. Molecular dynamics simulations confirmed higher water penetration in HII phase and provided insight into hydrogen bonding patterns.

Re-examining Correlations Between Synonymous Codon Usage and Protein Bond Angles in Escherichia coli.

Rosenberg AA, Marx A, Bronstein AM (Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon. Nat Commun. 2022:13:2815) recently found a surprising correlation between synonymous codon usage and the dihedral bond angles of the resulting amino acid. However, their analysis did not account for the strongest known correlate of codon usage: gene expression. We re-examined the relationship between bond angles and codon usage by applying the approach of Rosenberg et al. to simulated protein-coding sequences that (i) have random codon usage, (ii) codon usage determined by mutation biases, and (iii) maintain the general relationship between codon usage and gene expression via the assumption of selection-mutation-drift equilibrium. We observed correlations between dihedral bond angle and codon usage when codon usage is entirely random, indicating possible conflation of noise with differences in bond angle distributions between synonymous codons. More relevant to the general analysis of codon usage patterns, we found surprisingly good agreement between the analysis of the real sequences and the analysis of sequences simulated assuming selection-mutation-drift equilibrium, with 91% of significant synonymous codon pairs detected in the former were also detected in the latter. We believe the correlation between codon usage and dihedral bond angles resulted from the variation in codon usage across genes due to the interplay between mutation bias, natural selection for translation efficiency, and gene expression, further underscoring these factors must be controlled for when looking for novel patterns related to codon usage.

Enhanced molecular planarity for high-performance photodetectors: Effect of backbone conformation via alkyl substitution position control in dithienoquinoxaline-based conjugated polymers

Conjugated polymers (CPs) with donor and acceptor units exhibit a flexible conformation due to the rotation of the single bond of the bridge groups which greatly hinders a precise study of their photodetection properties. Moreover, the modulation mechanism related to complex factors of CPs molecular conformation on photodetection performance is not clear, causing CP-based organic photodiodes (OPDs) to generally suffer from high dark current and low specific detectivity. In this work, we synthesized two novel PBQx-i-4F and PBQx-o-4F CPs by combining fluorinated BDT with DTQx units using i- and o-alkylated side chain-based thiophene linkages, respectively. Quantum simulation and photo-physics study revealed that PBQx-i-4F displayed a dominant trans conformation, a more planar molecule structure, and high utilization efficiency of photoinduced excitons. The OPDs based on PBQx-i-4F exhibited higher on–off ratios by over two orders of magnitude and higher detectivity (Dsh*) by nearly one order of magnitude compared with those based on PBQx-o-4F. PBQx-i-4F with the i-alkyl substitution on the thiophene linkage displayed enhanced planarity, resulting in more ordered packing and larger population of face-on orientation in film, where decreased trap density and trap-assisted recombination led to reduced dark current and improved charge transport. In summary, our work provides an insight into the relationship between the fine-tuning of the molecular conformation, planarity, and packing of CPs and their photodetection properties in OPDs.

Reengineering of a flavin-binding fluorescent protein using ProteinMPNN.

Recent advances in machine learning techniques have led to development of a number of protein design and engineering approaches. One of them, ProteinMPNN, predicts an amino acid sequence that would fold and match user-defined backbone structure. Its performance was previously tested for proteins composed of standard amino acids, as well as for peptide- and protein-binding proteins. In this short report, we test whether ProteinMPNN can be used to reengineer a non-proteinaceous ligand-binding protein, flavin-based fluorescent protein CagFbFP. We fixed the native backbone conformation and the identity of 20 amino acids interacting with the chromophore (flavin mononucleotide, FMN) while letting ProteinMPNN predict the rest of the sequence. The software package suggested replacing 36-48 out of the remaining 86 amino acids so that the resulting sequences are 55%-66% identical to the original one. The three designs that we tested experimentally displayed different expression levels, yet all were able to bind FMN and displayed fluorescence, thermal stability, and other properties similar to those of CagFbFP. Our results demonstrate that ProteinMPNN can be used to generate diverging unnatural variants of fluorescent proteins, and, more generally, to reengineer proteins without losing their ligand-binding capabilities.

Pseudodiproline (Pro-Cyp) Oligomers Fold into Helical Polyproline Type secondary structures.

The synthesis and conformational properties of oligo-proline mimetics composed of dimeric and tetrameric Pro-Cyp constructs linked by a hydroxymethylene unit are reported. Oligomers were studied both in the solid state and in solution, unveiling right-handed helical conformation depending on the configuration of the vicinally substituted trans-cyclopentane carboxylic acid unit (Cyp). Unlike polyproline oligomers, the alternating synthetic Pro-Cyp counterparts are not stabilized by n-π* interactions but rely instead on the steric demands of the extended backbone conformation within the hydroxymethylene-linked Pro-Cyp repeating units.

Why Are Left-Handed G-Quadruplexes Scarce?

G-quadruplexes (G4s) are nucleic acid structures crucial for the regulation of gene expression and genome maintenance. While they hold promise as nanodevice components, achieving desired G4 folds requires understanding the interplay between stability and structural properties, like helicity. Although right-handed G4 structures dominate the experimental data, the molecular basis for this preference over left-handed helicity is unclear. To address this, we employ all-atom molecular dynamics simulations and quantum chemical methods. Our results reveal that right-handed G4s exhibit greater thermodynamic and kinetic stability as a result of favorable sugar-phosphate backbone conformations in guanine tracts. Moreover, while hydrogen-bonding patterns influence helicity-specific G4 loop conformations, they minimally affect stability differences. We also elucidate the strong correlation between helicity and the strand progression direction, essential for G4 structures. These findings deepen our understanding of G4s, providing molecular-level insights into their structural and energetic preferences, which could inform the design of novel nanodevices.

Iminoboronate-based chiral dynamic covalent polymer for selective and sensitive fluoride recognition

The construction of chiral polymers using dynamic covalent chemistry is a convenient and straightforward strategy for obtaining functional materials. In this paper, we report the dynamic covalent polymers DCP1, DCP2, and DCP3 with dual dynamic covalent bonds of imine and boronic ester, and their recognition of fluoride ions. The three polymers are prepared from L-DOPA hexyl ester and 2-, 3-, and 4-formylphenylboronic acids, respectively. Iminoboronate, formed within repeated DCP1 units, results in the formation of a spirochiral structure centered at sp3-B and, consequently, the chiral twist or helix conformation of the polymer backbone. DCP1 exhibits distinctive chiroptical features that distinguish it from DCP2 and DCP3. Due to the strong competitive bonding of fluoride with boron, DCP1 has a low LOD (Limit of detection) for fluoride (0.018 mg/L). DCP1 also has good selectivity for fluoride via the responsive destruction of the spirochiral structure and the chiral conformation of the backbone. The construction of these chiral dynamic polymers provides a rapid and effective approach to designing functional polymers.

Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study of the free enzyme and its complex with inhibitor 13b-K.

During the continuing evolution of SARS-CoV-2, the Omicron variant of concern emerged in the second half of 2021 and has been dominant since November that year. Along with its sublineages, it has maintained a prominent role ever since. The Nsp5 main protease (Mpro) of the Omicron virus is characterized by a single dominant mutation, P132H. Here we determined the X-ray crystal structures of the P132H mutant (or O-Mpro) as free enzyme and in complex with the Mpro inhibitor, the alpha-ketoamide 13b-K, and we conducted enzymology, biophysical as well as theoretical studies to characterize the O-Mpro. We found that O-Mpro has a similar overall structure and binding with 13b-K; however, it displays lower enzymatic activity and lower thermal stability compared to the WT-Mpro (with "WT" referring to the original Wuhan-1 strain). Intriguingly, the imidazole ring of His132 and the carboxylate plane of Glu240 are in a stacked configuration in the X-ray structures determined here. The empirical folding free energy calculations suggest that the O-Mpro dimer is destabilized relative to the WT-Mpro due to the less favorable van der Waals interactions and backbone conformation in the individual protomers. The all-atom continuous constant pH molecular dynamics (MD) simulations reveal that His132 and Glu240 display coupled titration. At pH 7, His132 is predominantly neutral and in a stacked configuration with respect to Glu240 which is charged. In order to examine whether the Omicron mutation eases the emergence of further Mpro mutations, we also determined crystal structures of the relatively frequent P132H+T169S double mutant but found little evidence for a correlation between the two sites.

Molecular Dynamics Simulations of Polyelectrolyte Complexes.

Polyelectrolyte complexes (PECs) are currently of great interest due to their applications toward developing new adaptive materials and their relevance in membraneless organelles. These complexes emerge during phase separation when oppositely charged polymers are mixed in aqueous media. Peptide-based PECs are particularly useful toward developing new drug delivery methods due to their inherent biocompatibility. The underlying peptide sequence can be tuned to optimize specific material properties of the complex, such as interfacial tension and viscosity. Given their applicability, it would be advantageous to understand the underlying sequence-dependent phase behavior of oppositely charged peptides. Here, we report microsecond molecular dynamic simulations to characterize the effect of hydrophobicity on the sequence-dependent peptide conformation for model polypeptide sequences that were previously reported by Tabandeh et al. These sequences are designed with alternating chirality of the peptide backbone. We present microsecond simulations of six oppositely charged peptide pairs, characterizing the sequence-dependent effect on peptide size, degree of hydrogen bonding, secondary structure, and conformation. This analysis recapitulates sensible trends in peptide conformation and degree of hydrogen bonding, consistent with experimentally reported results. Ramachandran plots reveal that backbone conformation at the single amino acid level is highly influenced by the neighboring sequence in the chain. These results give insight into how subtle changes in hydrophobic side chain size and chirality influence the strength of hydrogen bonding between the chains and, ultimately, the secondary structure. Furthermore, principal component analysis reveals that the minimum energy structures may be subtly modulated by the underlying sequence.

Twisted Poly(p-terphenyl-co-m-terphenyl)-Based Anion Exchange Membrane for Water Electrolysis.

In order to improve the mechanical and water electrolysis performance of anion exchange membranes (AEMs), we adjusted the ratio between p-terphenyl and m-terphenyl to balance the backbone conformation, which gives it a better suitability for a better combination with cations. The results showed that poly(m-terphenyl-co-p-terphenyl)-based AEMs have excellent mechanical properties. Among them, the m-p-TP-40-BOP-ASU membrane has the highest tensile strength and elongation at break (75.72 MPa and 16.07%). The ionic conductivity reaches 137.14 mS cm-1 at 80 °C owing to the fact that efficient ion-conducting channels are formed by well-balanced molecular structures. The current density of the m-p-TP-40-BOP-ASU membrane reached 1.96 A cm-2 (1 M KOH aq, 2.0 V and 60 °C). After testing for 112 h under a current density of 500 mA cm-2, the voltage increased by 102 mV compared to the initial electrolysis voltage. All results have shown that m-p-TP-x-BOP-ASU has excellent electrolysis performance and electrochemical durability and has a promising application prospect in AEM water electrolyzers.

Impact of ring structure and conjugation on the dielectric properties of polyimides at a high frequency of 10–40 GHz

AbstractPolyimides (PIs) are widely used materials due to their high thermal stability and potentially low dielectric constant (Dk) and dissipation factor (Df). However, Dk and Df values tend to increase at higher frequencies. Therefore, there is a significant need to reduce the Dk and Df values of PIs, which is the main purpose of this study. This research considers multiple factors, including the ring structures and conjugations on the conformation of the PI backbone. The effects of five‐membered and six‐membered PIs and the conjugated length of benzene and naphthalene structures in the repeating units on the thermomechanical and dielectric properties are systematically investigated. As a result, the PI with a six‐membered imide contributes to higher thermal stability, with a glass transition temperature higher than 350 °C, a thermal decomposition point of 529 °C, and a lower Dk of 2.7–2.8. Still, it exhibits a lower molecular weight than that of a five‐membered imide. On the other hand, PIs with esterified structures show an extremely low Df value, 0.002–0.005. This situation can be attributed to the vital correlation between the Df and the volumetric dipole moment. This study also presents the different properties arising from ring structures and conjugations. Meanwhile, the relationships between Dk and volumetric polarizability and between Df and volumetric dipole moment are confirmed. This work provides a guideline for the structure−dielectric relationship of PI at a high frequency of 10–40 GHz.

Pushed to extremes: distinct effects of high temperature versus pressure on the structure of STEP

Protein function hinges on small shifts of three-dimensional structure. Elevating temperature or pressure may provide experimentally accessible insights into such shifts, but the effects of these distinct perturbations on protein structures have not been compared in atomic detail. To quantitatively explore these two axes, we report the first pair of structures at physiological temperature versus. high pressure for the same protein, STEP (PTPN5). We show that these perturbations have distinct and surprising effects on protein volume, patterns of ordered solvent, and local backbone and side-chain conformations. This includes interactions between key catalytic loops only at physiological temperature, and a distinct conformational ensemble for another active-site loop only at high pressure. Strikingly, in torsional space, physiological temperature shifts STEP toward previously reported active-like states, while high pressure shifts it toward a previously uncharted region. Altogether, our work indicates that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.

The impact of solvation on the structure and electric field strength in Li+GlyGly complexes.

To scrutinise the impact of electric fields on the structure and vibrations of biomolecules in the presence of water, we study the sequential solvation of lithium diglycine up to three water molecules with cryogenic infrared action spectroscopy. Conformer-specific IR-IR spectroscopy and H2O/D2O isotopic substitution experiments provide most of the information required to decipher the structure of the observed conformers. Additional confirmation is provided by scaled harmonic vibrational frequency calculations using MP2 and DFT. The first water molecule is shown to bind to the Li+ ion, which weakens the electric field experienced by the peptide and as a consequence, also the strength of an internal NH⋯NH2 hydrogen bond in the diglycine backbone. The strength of this hydrogen bond decreases approximately linearly with the number of water molecules as a result of the decreasing electric field strength and coincides with an increase in the number of conformers observed in our spectra. The addition of two water molecules is already sufficient to change the preferred conformation of the peptide backbone, allowing for Li+ coordination to the lone pair of the terminal amine group.

Assessment of Novel Proteins Triggering Celiac Disease via Docking-Based Approach.

Human leukocyte antigens (HLAs) are pivotal in antigen processing, presenting to CD4+ T cells, and are linked to autoimmune disease susceptibility. In celiac disease, HLA-DQ2.5 and HLA-DQ8.1 bind gluten peptides on APCs, some recognized by CD4+ T cells, prompting inflammation and tissue damage. While extensively studied experimentally, these alleles lack comprehensive in silico analysis. To explore peptide-HLA preferences, we used molecular docking on peptide libraries, deriving quantitative matrices (QMs) for evaluating amino acids at nine-residue peptide binding cores. Our findings tie specific residue preferences to peptide backbone conformations. Validating QMs on known binders and non-binders showed strong predictive power (89-94% accuracy). These QMs excel in screening protein libraries, even whole proteomes, notably reducing time and costs for celiac disease risk assessment in novel proteins. This computational approach aligns with European Food Safety Authority guidance, promising efficient screening for potential celiac disease triggers.

AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination

Artificial intelligence-based protein structure prediction methods such as AlphaFold have revolutionized structural biology. The accuracies of these predictions vary, however, and they do not take into account ligands, covalent modifications or other environmental factors. Here, we evaluate how well AlphaFold predictions can be expected to describe the structure of a protein by comparing predictions directly with experimental crystallographic maps. In many cases, AlphaFold predictions matched experimental maps remarkably closely. In other cases, even very high-confidence predictions differed from experimental maps on a global scale through distortion and domain orientation, and on a local scale in backbone and side-chain conformation. We suggest considering AlphaFold predictions as exceptionally useful hypotheses. We further suggest that it is important to consider the confidence in prediction when interpreting AlphaFold predictions and to carry out experimental structure determination to verify structural details, particularly those that involve interactions not included in the prediction.

Chiral Diketopyrrolopyrrole-Based Conjugated Polymers with Intramolecular Rotation-Isomeric Conformation Asymmetry for Near-Infrared Circularly Polarized Light-Sensing Organic Phototransistors.

Recent advances in chiral nanomaterials interacting with circularly polarized (CP) light open new expectations for optoelectronics in various research fields such as quantum- and biology-related technology. To fully utilize the great potential of chiral optoelectronic devices, the development of chiral optoelectronic devices that function in the near-infrared (NIR) region is required. Herein, we demonstrate a NIR-absorbing, chiroptical, low-band-gap polymer semiconductor for high-performance NIR CP light phototransistors. A newly synthesized diketopyrrolopyrrole-based donor-acceptor-type chiral π-conjugated polymer with an asymmetric alkyl side chain exhibits strong chiroptical activity in a wavelength range of 700-1000 nm. We found that the attachment of an enantiomerically pure stereogenic alkyl substituent to the π-conjugated chromophore backbone led to strong chiroptical activity through symmetry breaking of the π-conjugation of the backbone in a molecular rotational motion while maintaining the coplanar backbone conformation for efficient charge transport. The NIR CP light-sensing phototransistors based on a chiral π-conjugated polymer photoactive single channel layer exhibit a high photoresponsivity of 26 A W-1 under NIR CP light irradiation at 920 nm, leading to excellent NIR CP light distinguishability. This study will provide a rationale and strategy for designing chiral π-conjugated polymers for high-performance NIR chiral optoelectronics.

Ab Initio Prediction of 3-D Conformations for Protein Long Loops with High Accuracy and Applications to Antibody CDRH3 Modeling.

Residue-level potentials of mean force were widely used for protein backbone refinements to avoid simultaneous sampling of side-chain conformations. The interaction energy between the reduced side chains and backbone atoms was not considered explicitly. In this study, we developed novel methods to calculate the residue-atom interaction energy in combination with atomic and residue-level terms. The parameters were optimized step by step to remove the overcounting or overlap problem between different energy terms. The mixing energy functions were then used to evaluate the generated backbone conformations at the initial sampling stage of protein loop modeling (OSCAR-loop), including the interaction energy between the reduced loop residues and full atoms of the protein framework. The accuracies of top-ranked decoys were 1.18 and 2.81 Å for 8-residue and 12-residue loops, respectively. We then selected diverse decoys for side-chain modeling, backbone refinement, and energy minimization. The procedure was repeated multiple times to select one prediction with the lowest energy. Consequently, we obtained an accuracy of 0.74 Å for a prevailing test set of 12-residue loops, compared with >1.4 Å reported by other researchers. The OSCAR-loop was also effective for modeling the H3 loops of antibody complementary determining regions (CDRs) in the crystal environment. The prediction accuracy of OSCAR-loop (1.74 Å) was better than the accuracy of the Rosetta NGK method (3.11 Å) or those achieved by deep learning methods (>2.2 Å) for the CDRH3 loops of 49 targets in the Rosetta antibody benchmark. The performance of OSCAR-loop in a model environment was also discussed.

Poly(fluorenyl-indolinedione) based hydroxide conducting membrane for anion exchange membrane water electrolyzers

Anion exchange membranes (AEMs) serve as the heart of anion exchange membrane water electrolyzers (AEMWE) for green energy conversion electrochemical devices, directly determining the ultimate performance of the electrochemical devices. Conductivity in trade-off with stability (chemical and dimensional stability) is a major target in the development of alkaline membranes. We prepared chemically stable polyisatin-aromatics without ether linkages along the backbone by superacid-catalyzed alkylation. The alkali-stable dimethylpiperidinium cations were covalently linked to the polymer backbone through the aliphatic chain to give comb-type polyelectrolytes. Incorporating the fluorene structural units along the polymer skeleton is expected to improve conductivity and stability. The effect of polymer backbone structure and conformation on AEM properties is systematically elucidated. The results indicate the PipPFTI-25 AEM with 25 mol% dimethylfluorene fragments in the backbone has lower IEC (∼1.36 mmol g−1) but achieves high ionic conductivity (84.6 mS cm−1 at 80 °C). PipPFTI-25 exhibited superior dimensional and alkali stability, mainly reflected in the swelling ratio of less than 10 % while the OH− conductivity remained at 70 % after immersion in 2 M NaOH solution at 80 °C for 1680 h. The AEMWE with PipPFTI-25 operating at 60 °C in 1 M KOH achieves a current of 838 mA cm−2 at 2.5 V. This work demonstrated the feasibility of poly(fluorenyl-indolinedione) AEMs for electrolyzer applications.