All-Atom Protein Sequence Design Based on Geometric Deep Learning.

Designing sequences for specific protein backbones is a key step in creating new functional proteins. Here, we introduce GeoSeqBuilder, a deep learning framework that integrates protein sequence generation with side chain conformation prediction to produce the complete all-atom structures for designed sequences. GeoSeqBuilder uses spatial geometric features from protein backbones and explicitly includes three-body interactions of neighboring residues. GeoSeqBuilder achieves native residue type recovery rate of 51.6%, comparable to ProteinMPNN and  other leading methods, while accurately predicting side chain conformations. We first used GeoSeqBuilder to design sequences for thioredoxin and a hallucinated three-helical bundle protein. All the 15 tested sequences expressed as soluble monomeric proteins with high thermal stability, and the 2 high-resolution crystal structures solved closely match the designed models. The generated protein sequences exhibit low similarity (minimum 23%) to the original sequences, with significantly altered hydrophobic cores. We further redesigned the hydrophobic core of glutathione peroxidase 4, and 3 of the 5 designs showed improved enzyme activity. Although further testing is needed, the high experimental success rate in our testing demonstrates that GeoSeqBuilder is a powerful tool for designing novel sequences for predefined protein structures with atomic details. GeoSeqBuilder is available at https://github.com/PKUliujl/GeoSeqBuilder.

Influence of Side Chain Conformation on the Activity of Glycosidase Inhibitors.

Substrate side chain conformation impacts reactivity during glycosylation and glycoside hydrolysis and is restricted by many glycosidases and glycosyltransferases during catalysis. We show that the side chains of gluco and manno iminosugars can be restricted to predominant conformations by strategic installation of a methyl group. Glycosidase inhibition studies reveal that iminosugars with the gauche,gauche side chain conformations are 6- to 10-fold more potent than isosteric compounds with the gauche,trans conformation; a manno-configured iminosugar with the gauche,gauche conformation is a 27-fold better inhibitor than 1-deoxymannojirimycin. The results are discussed in terms of the energetic benefits of preorganization, particularly when in synergy with favorable hydrophobic interactions. The demonstration that inhibitor side chain preorganization can favorably impact glycosidase inhibition paves the way for improved inhibitor design through conformational preorganization.

Fluorescence Resonance Energy Transfer Measurements in Polymer Science: A Review.

Fluorescence resonance energy transfer (FRET) is a non-invasive characterization method for studying molecular structures and dynamics, providing high spatial resolution at nanometer scale. Over the past decades, FRET-based measurements are developed and widely implemented in synthetic polymer systems for understanding and detecting a variety of nanoscale phenomena, enabling significant advances in polymer science. In this review, the basic principles of fluorescence and FRET are briefly discussed. Several representative research areas are highlighted, where FRET spectroscopy and imaging can be employed to reveal polymer morphology and kinetics. These examples include understanding polymer micelle formation and stability, detecting guest molecule release from polymer host, characterizing supramolecular assembly, imaging composite interfaces, and determining polymer chain conformations and their diffusion kinetics. Finally, a perspective on the opportunities of FRET-based measurements is provided for further allowing their greater contributions in this exciting area.

Interfacial Effect on Dielectric Properties of Self-Assembled Polythiourea-Based Copolymers for Ultrahigh Energy Storage.

Polymer dielectrics are highly desirable in capacitor applications due to their low cost, high stability, and reliability. However, there still remains a lack of feasible methods to prepare polymer dielectrics with high energy density and low dielectric loss, which severely hampers the development of compact and efficient power electronics. Here, an amphiphilic block copolymer, polythiourea-b-polydimethylsiloxane (PTU-b-PDMS), with an extraordinarily high energy density of 29.8 J cm-3 and a low loss is synthesized via polyaddition polymerization. This is highly relevant to the block molecule conformation in the interfacial region of the self-assembled PTU-b-PDMS. The block molecule in the interface adopts an extended conformation when the PTU forms nanodots, whereas the block molecule adopts a coiled conformation when the PTU forms nanostrands. The observation and characterization have proved that the coiled block molecule in the interfacial region can simultaneously induce extra strong charge trapping sites and dipolar polarization. It substantially improves the breakdown strength from 652 to 1166 MV m-1 , while maintaining a high dielectric constant of 5 and a low loss of <0.01. This work offers unprecedented structural insights into the conformation-induced interfacial effect and enables rational design of self-assembled copolymers to boost their dielectric properties and energy density.

Controlling Solution-State Aggregation and Solid-State Microstructures of Conjugated Polymers by Tuning Backbone Conformation.

Molecular ordering of conjugated polymers both in solution-state aggregates and in solid-state microstructures is a determining factor of the charge transport properties in optoelectronic devices. However, the effect of backbone conformation in conjugated polymers on assembly structures is still unclear. Herein, to understand such backbone conformation effect, three novel chlorinated benzodifurandionge-based oligo(p-phenylene vinylene) (BDOPV) polymers are systematically developed. These BDOPV-based polymers exhibit significantly twisted backbone conformation (near 90° interunit torsion angle) between conjugated units, which can prevent polymer chains from forming ordered assembly structures by increasing conformational energy penalty in closely packed chains. A higher rotational barrier of the torsion angle would further prevent polymer chains from assembling, finally resulting in nonaggregated chains in solution and highly disordered solid-state packing structures. This work will deepen the understanding of the relationship between polymer backbone conformation and assembly structures, contributing to the exploration of the structure-property relationship of polymers.

Investigation of Molecular Mechanisms of Polyvinylidene Fluoride under the Effects of Temperature, Electric Poling, and Mechanical Stretching Using Molecular Dynamics Simulations.

This study uses molecular dynamics (MD) simulations to investigate the molecular mechanisms of polyvinylidene fluoride (PVDF) influenced by temperature, electric poling, and mechanical stretching. The ß-phase, with all-trans ⟨T⟩ planar zigzag conformation, is known to have the best potential of energy harvesting, while α-phase, with alternating trans ⟨T⟩ and gauche ⟨G⟩ linkages, is more stable in terms of potential energy. By applying an electric field and uniaxial deformation to an amorphous PVDF system, we study the transformation from α- to ß-phase and corresponding molecular mechanisms by tracking the molecular chain conformation using the trans percentages (PT). After complete relaxation of molecular chains, the chain conformations and PT values indicate a typical distribution pattern of α-phase. Next, we observe that the dipole moment of the system increases significantly with the presence of a strong electric field without immediately affecting the chain conformations. The increment of dipole moment is due to the aligning of side atoms within the chains and the increment becomes more significant with elevated temperature. In contrast, chain conformations change significantly under mechanical stretching. Specifically, before yielding, the total dipole moments are still governed by local orientations of atoms. Later, the chain segments begin to straighten in the large deformation stage, which leads to the increment of the total dipole moment. Our results also show that there exists an optimal temperature window for maximum ⟨G⟩ to ⟨T⟩ transformation rate. Moreover, we look into the synergistic effect of electric poling and mechanical stretching and explain molecular-level mechanisms for this effect. This study contributes to the fundamental understanding of the underlying molecular mechanisms for the piezoelectric PVDF system under different processing conditions.

Molecular design of self-coacervation phenomena in block polyampholytes.

Coacervation is a common phenomenon in natural polymers and has been applied to synthetic materials systems for coatings, adhesives, and encapsulants. Single-component coacervates are formed when block polyampholytes exhibit self-coacervation, phase separating into a dense liquid coacervate phase rich in the polyampholyte coexisting with a dilute supernatant phase, a process implicated in the liquid-liquid phase separation of intrinsically disordered proteins. Using fully fluctuating field-theoretic simulations using complex Langevin sampling and complementary molecular-dynamics simulations, we develop molecular design principles to connect the sequenced charge pattern of a polyampholyte with its self-coacervation behavior in solution. In particular, the lengthscale of charged blocks and number of connections between oppositely charged blocks are shown to have a dramatic effect on the tendency to phase separate and on the accessible chain conformations. The field and particle-based simulation results are compared with analytical predictions from the random phase approximation (RPA) and postulated scaling relationships. The qualitative trends are mostly captured by the RPA, but the approximation fails catastrophically at low concentration.

Ubiquitination in the ERAD Process.

In this review, we focus on the ubiquitination process within the endoplasmic reticulum associated protein degradation (ERAD) pathway. Approximately one third of all synthesized proteins in a cell are channeled into the endoplasmic reticulum (ER) lumen or are incorporated into the ER membrane. Since all newly synthesized proteins enter the ER in an unfolded manner, folding must occur within the ER lumen or co-translationally, rendering misfolding events a serious threat. To prevent the accumulation of misfolded protein in the ER, proteins that fail the quality control undergo retrotranslocation into the cytosol where they proceed with ubiquitination and degradation. The wide variety of misfolded targets requires on the one hand a promiscuity of the ubiquitination process and on the other hand a fast and highly processive mechanism. We present the various ERAD components involved in the ubiquitination process including the different E2 conjugating enzymes, E3 ligases, and E4 factors. The resulting K48-linked and K11-linked ubiquitin chains do not only represent a signal for degradation by the proteasome but are also recognized by the AAA+ ATPase Cdc48 and get in the process of retrotranslocation modified by enzymes bound to Cdc48. Lastly we discuss the conformations adopted in particular by K48-linked ubiquitin chains and their importance for degradation.

Ultrasonic-Assisted Extraction, Structural Characterization, Chain Conformation, and Biological Activities of a Pectic-Polysaccharide from Okra (Abelmoschus esculentus).

The purpose of this study was to better understand the chemical characteristics and chain conformation of okra polysaccharides extracted by ultrasonic-assisted extraction. A pectic-polysaccharide, named OPP-D, was obtained, which was mainly composed of rhamnose, galacturonic acid, and galactose with a molar ratio of 1.01:1.00:2.31. Combined with NMR analysis, -4)-α-d-GalAp-(1,2,4)-α-l-Rhap-(1- were identified as the backbone with galactan side chains substituted partly at O-4 of Rhap. Molecular weight and radius of gyration of OPP-D were determined as 2.19 × 105 Da and 27.0 nm, respectively. OPP-D was determined as an air-core sphere with branching chains in 0.9% NaCl solution by high-performance size-exclusion chromatography coupled with multi-angle laser light scattering and dynamic light scattering for the first time. Moreover, OPP-D exhibited typical shear-thinning behavior. In addition, OPP-D exhibited remarkable in vitro antioxidant activities and prebiotic activities, while the relatively high molecular weight, high degree of esterification, high content of uronic acids, and highly branched globular conformation of OPP-D might contribute to its in vitro anti-diabetic activities and binding capacities. Results can contribute to a better understanding of the structure-bioactivity relationship of OPPs, and OPP-D has great potential applications in the functional food and pharmaceutical industries.

The Sphingosine and Acyl Chains of Ceramide [NS] Show Very Different Structure and Dynamics That Challenge Our Understanding of the Skin Barrier.

The lipid phase of the uppermost human skin layer is thought to comprise highly rigid lipids in an orthorhombic phase state to protect the body against the environment. By synthesizing sphingosine-d28 deuterated N-lignoceroyl-d-erythro-sphingosine (ceramide [NS]), we compare the structure and dynamics of both chains of that lipid in biologically relevant mixtures using X-ray diffraction, 2 H NMR analysis, and infrared spectroscopy. Our results reveal a substantial fraction of sphingosine chains in a fluid and dynamic phase state at physiological temperature. These findings prompt revision of our current understanding of the skin lipid barrier, where an extended ceramide [NS] conformation is preferred and a possible domain structure is proposed. Mobile lipid chains may be crucial for skin elasticity and the translocation of physiologically important molecules.

Identifying the elusive link between amino acid sequence and charge selectivity in pentameric ligand-gated ion channels.

Among neurotransmitter-gated ion channels, the superfamily of pentameric ligand-gated ion channels (pLGICs) is unique in that its members display opposite permeant-ion charge selectivities despite sharing the same structural fold. Although much effort has been devoted to the identification of the mechanism underlying the cation-versus-anion selectivity of these channels, a careful analysis of past work reveals that discrepancies exist, that different explanations for the same phenomenon have often been put forth, and that no consensus view has yet been reached. To elucidate the molecular basis of charge selectivity for the superfamily as a whole, we performed extensive mutagenesis and electrophysiological recordings on six different cation-selective and anion-selective homologs from vertebrate, invertebrate, and bacterial origin. We present compelling evidence for the critical involvement of ionized side chains-whether pore-facing or buried-rather than backbone atoms and propose a mechanism whereby not only their charge sign but also their conformation determines charge selectivity. Insertions, deletions, and residue-to-residue mutations involving nonionizable residues in the intracellular end of the pore seem to affect charge selectivity by changing the rotamer preferences of the ionized side chains in the first turn of the M2 α-helices. We also found that, upon neutralization of the charged residues in the first turn of M2, the control of charge selectivity is handed over to the many other ionized side chains that decorate the pore. This explains the long-standing puzzle as to why the neutralization of the intracellular-mouth glutamates affects charge selectivity to markedly different extents in different cation-selective pLGICs.

Prediction of protein mutation effects based on dehydration and hydrogen bonding - A large-scale study.

Reliable computational prediction of protein side chain conformations and the energetic impact of amino acid mutations are the key aspects for the optimization of biotechnologically relevant enzymatic reactions using structure-based design. By improving the protein stability, higher yields can be achieved. In addition, tuning the substrate selectivity of an enzymatic reaction by directed mutagenesis can lead to higher turnover rates. This work presents a novel approach to predict the conformation of a side chain mutation along with the energetic effect on the protein structure. The HYDE scoring concept applied here describes the molecular interactions primarily by evaluating the effect of dehydration and hydrogen bonding on molecular structures in aqueous solution. Here, we evaluate its capability of side-chain conformation prediction in classic remutation experiments. Furthermore, we present a new data set for evaluating "cross-mutations," a new experiment that resembles real-world application scenarios more closely. This data set consists of protein pairs with up to five point mutations. Thus, structural changes are attributed to point mutations only. In the cross-mutation experiment, the original protein structure is mutated with the aim to predict the structure of the side chain as in the paired mutated structure. The comparison of side chain conformation prediction ("remutation") showed that the performance of HYDEprotein is qualitatively comparable to state-of-the art methods. The ability of HYDEprotein to predict the energetic effect of a mutation is evaluated in the third experiment. Herein, the effect on protein stability is predicted correctly in 70% of the evaluated cases. Proteins 2017; 85:1550-1566. © 2017 Wiley Periodicals, Inc.

Shaping the Light: The Key Factors Affecting the Photophysical Properties of Fluorescent Polymer Nanostructures.

To manipulate the functions of nanomaterials more precisely for diverse applications, the controllability and critical influencing factors of their properties must be thoroughly investigated. In this work, the macroscopic and microscopic effects are studied on the photophysical properties of various pyrene-ended poly(styrene-block-methyl methacrylate) nanostructures. Fluorescent polymer nanospheres, nanorods, and nanotubes are prepared by different template-based methods using anodic aluminum oxide membranes. Chain arrangements and conformations are determined as the key factors affecting the photophysical properties of the fluorescent polymer nanostructures. This work not only gives a deeper understanding of the effects on the photophysical properties of polymer nanomaterials influenced by morphologies, chain arrangements, and chain conformations, but also provides a reference for designing proper fluorescent nanostructures for specific applications.

Assessment of protein side-chain conformation prediction methods in different residue environments.

Computational prediction of side-chain conformation is an important component of protein structure prediction. Accurate side-chain prediction is crucial for practical applications of protein structure models that need atomic-detailed resolution such as protein and ligand design. We evaluated the accuracy of eight side-chain prediction methods in reproducing the side-chain conformations of experimentally solved structures deposited to the Protein Data Bank. Prediction accuracy was evaluated for a total of four different structural environments (buried, surface, interface, and membrane-spanning) in three different protein types (monomeric, multimeric, and membrane). Overall, the highest accuracy was observed for buried residues in monomeric and multimeric proteins. Notably, side-chains at protein interfaces and membrane-spanning regions were better predicted than surface residues even though the methods did not all use multimeric and membrane proteins for training. Thus, we conclude that the current methods are as practically useful for modeling protein docking interfaces and membrane-spanning regions as for modeling monomers.

Preferred side-chain conformation of arginine residues in a triple-helical structure.

The crystal structure of the triple-helical peptide (Pro-Hyp-Gly)3 -Pro-Arg-Gly-(Pro-Hyp-Gly)4 (POG3-PRG-POG4) was determined at 1.45 Å resolution. POG3-PRG-POG4 was designed to permit investigation of the side-chain conformation of the Arg residues in a triple-helical structure. Because of the alternative structure of one of three Arg residues, four side-chain conformations were observed in an asymmetric unit. Among them, three adopt a ttg(-) t conformation and the other adopts a tg(-) g(-) t conformation. A statistical analysis of 80 Arg residues in various triple-helical peptides showed that, unlike those in globular proteins, they preferentially adopt a tt conformation for χ1 and χ2 , as observed in POG3-PRG-POG4. This conformation permits van der Waals contacts between the side-chain atoms of Arg and the main-chain atoms of the adjacent strand in the same molecule. Unlike many other host-guest peptides, in which there is a significant difference between the helical twists in the guest and the host peptides, POG3-PRG-POG4 shows a marked difference between the helical twists in the N-terminal peptide and those in the C-terminal peptide, separated near the Arg residue. This suggested that the unique side-chain conformation of the Arg residue affects not only the conformation of the guest peptide, but also the conformation of the peptide away from the Arg residue.

Exopolysaccharide from Leuconostoc mesenteroides XR1: Yield optimization, partial characterization and properties.

The production conditions of exopolysaccharide (EPS) from Leuconostoc mesenteroides XR1 were optimized by response surface methodology (RSM). Maximum EPS yield was 56.59 ± 0.51 g/L under fermentation conditions with 2.6 g/L ammonium citrate, initial pH 6.5 and temperature 23 °C, which was 6.21-fold greater than the EPS yield before optimization. Characterization of the chain conformation using Congo red test and circular dichroism (CD) showed that EPS exhibited a random coil structure in aqueous solution. The CD results revealed that the EPS concentration altered its hydrogen-bond interactions and chirality, but did not change its chain conformation. The average polydispersity index (PDI) of the EPS solution was only 27.16 %, indicating that it was uniformly distributed in the aqueous solution with high stability. The degradation temperature of EPS was 253.11 °C, indicating high thermal stability. EPS possessed the ability to scavenge activities of free radicals and was protective against oxidative stress-induced plasmid DNA damage. In addition, stable hydrogels could be formed at EPS concentrations above 5 % (w/v). These results collectively showed that EPS can be used commercially as an antioxidant and drug delivery carrier.

Influences of different ultrasonic treatment intensities on the molecular chain conformation and interfacial behavior of sugar beet pectin.

In this study, the effects of different ultrasonic treatment intensities (57, 170, and 283 W/cm2) on the chemical composition, molecular chain characteristics, crystal structure, micromorphology, interfacial adsorption behavior and emulsifying properties of sugar beet pectin (SBP) were investigated. Ultrasonic treatment did not change the types of SBP monosaccharides, but it had impacts on their various monosaccharide contents. Moreover, the feruloylated, acetyl, and methoxy groups of SBP also undergo varying degrees of changes. The increase in ultrasonic treatment intensity led to transition in the molecular chain conformation of SBP from rigid semi-flexible chains to flexible chains, accompanied by modification in its crystal structure. Microstructural analysis of SBP confirmed the significant change in molecular chain conformation. Modified SBP could form an elastic interfacial film with higher deformation resistance on the oil-water interface. The SBP sample modified with 170 W/cm2 exhibited better emulsifying properties owing to its better interfacial adsorption behavior. Moreover, the emulsions prepared with modified SBP exhibited better stability capability under different environmental stresses (pH value, salt ion concentration, heating temperature and freeze-thaw treatment). The results revealed that the ultrasonic technology is useful to improve the emulsifying properties of SBP.

Comparative study on chain conformations, physicochemical and rheological properties of three acidic polysaccharides from Opuntia dillenii Haw. fruits.

In this study, three acidic polysaccharides (OFPP-1, OFPP-2 and OFPP-3) were isolated from the pulps of Opuntia dillenii Haw. fruits, and their chain conformations, physicochemical and rheological properties were investigated. The molecular weight and conformational parameters (Mw, Mn, Mz, Rg and Rh) of OFPPs in 0.1 M NaNO3 solution were detected by HPSEC-MALLS-RI. In addition, based on the parameters ρ and v, it was concluded that these three polysaccharide chains exhibited sphere-like conformation in 0.1 M NaNO3 solution, which was consistent with AFM and TEM observations. Furthermore, the Congo Red experiment showed that OFPP-2 had a triple-helix structure, which may be conducive to its biological activity. This study also found that OFPPs were semi-crystalline structures with high thermal and pH stability. The rheological analyses indicated that the apparent viscosity of OFPPs solutions exhibited concentration-, temperature-, and pH-dependence, and the viscoelasticity of them was affected by molecular characteristics and concentration. The results of this study are helpful to elucidate the structure-activity relationship of OFPPs. Moreover, this study can provide theoretical reference for the application of OFPPs as bioactive ingredients or functional materials in the food, pharmaceutical and cosmetic industries and the development and utilization of the O. dillenii Haw. fruits resource.

Structural characterization and human gut microbiota fermentation in vitro of a polysaccharide from Fucus vesiculosus.

In this study, an acidic polysaccharide (FVP-7 A) was isolated from Fucus vesiculosus by DEAE-Sepharose™ fast flow. The chemical composition, glycosidic bonds and in vitro fecal fermentation characteristics of FVP-7 A were studied. Results shown that FVP-7 A was a homogenous polysaccharide with average molecular weight of 30.94 kDa. Combined with FT-IR, monosaccharide composition, methylation and NMR analysis, the glycosidic bonds of FVP-7 A mainly composed of →4)-ß-D-Manp-(1→, →3)-α-L-Fucp-(1→, α-D-Manp-(1→, →3)-ß-D-Manp-(1 â†’ and →4,6)-α-D-Manp-(1→. The zeta potential and atomic force microscopy images indicated that FVP-7 A could exist stably as a single chain-like structure in dilute solution. After gut fermentation, FVP-7 A was utilized and promoted multiple short-chain fatty acids production, especially acetic acid, butyric acid and valeric acid. For prebiotics, FVP-7 A significantly increased the relative abundance of short-chain fatty acids producing bacteria such as Bacteroides, Lachnospira, Faecalibacterium, Ruminococcus, Oscillospira and Dialister, and inhiited the growth of the harmful bacteria Shigella. These results indicated that FVP-7 A could be used as a potential dietary supplement to improve intestinal health.

Fructose/glycerol/water as a biosourced LTTM solvent to design a variety of sodium alginate-based soft materials with enhanced rheological properties.

Sodium alginate was associated to a ternary solvent composed of fructose, glycerol, and water in a 1:1:5 M ratio (FGW), classified as a natural Low Transition Temperature Mixture (LTTM), to generate various soft materials. The rheological properties of mixtures composed of sodium alginate and FGW were thoroughly analyzed and compared to their aqueous analogues. FGW-based solutions present a pronounced shear-thinning character combined to high viscosity, up to 8000 Pa.s. The overlap concentrations and intrinsic viscosities values evidence a good solvent character of FGW for alginate polymer chains. The increase of alginate concentration in FGW leads to materials with enhanced elasticity (up to 6000 Pa) and high energy of activation (55 kJ/mol). Interestingly, the addition of divalent calcium cations in FGW according to two optimized experimental protocols, allows for the generation of never described ionotropic gels in FGW under various shapes as bulk gels or beads of gels able to encapsulate extracted vegetal actives that are used in the cosmetic industry. Thus, FGW appears as a well-suited solvent of alginate to design a broad range of new biobased soft materials.