Conformational Entropy Research Articles

Aromatic or Hetero-aromatic Directly Attached Tri and Tetrasubstituted Methanes: New Chemical Entities as Anti-Infectives.

Tri and Tetra-substituted Methanes (TRSMs) are a significant structural motif in many approved drugs and prodrugs. There is increasing use of TRSM units in medicinal chemistry, and many derivatives are specifically designed to make drug-target interactions through new chemical space around TRSM moiety. In this perspective, we describe synthetic challenges for accessing a range of functionalized selective TRSMs and their molecular mechanism of action, especially as anti-infectives. Natural anti-infectives like (+)-Bionectin A, B, (+)-Gliocladine C, Balanocarpol having TRSMs selectively and effectively bind to target proteins in comparison to planar motif having more sp2 carbons perhaps due to conformation which reduces the penalty for conformational entropy with the enhancement of three-dimensionality. Properties of repurposed TRSMs like Almitrine, Ifenprodil, Baricitinib and Remdesivir with their recent progress in COVID-19 therapeutics with their mode of action are also delineated. This perspective is expected to deliver a user guide and reference source for scientists, researchers and academicians in pursuing newly designed TRSMs as therapeutics.

Extremal Kerr black hole entropy in Poincaré gauge theory

We analyze the near horizon symmetry of the extremal Kerr black hole within the framework of Poincar\'e gauge theory (PG) for two important limiting cases: Riemannian and teleparallel solution. We show that the algebra of canonical generators is realized by Virasoro algebra, with central charge which depends on the black hole horizon radius . The conformal entropy of the black hole is obtained via Cardy formula.

Deformation Driven Deswelling of Brush Gels

We studied equilibrium swelling in brush gels undergoing large uniaxial deformations in contact with solvent by using a combination of the Flory–Rehner and scaling models of gels and coarse-grained molecular dynamics simulations of swollen brush networks. Our analysis showed that the swelling ratio of the brush gels Qeq(λ), describing the volume change upon swelling, is a nonmonotonic function of the gel uniaxial deformation ratio λ characterizing the gel shape. It first increases with increasing strand elongation from its value for the free-standing gel then begins to decrease. This behavior is a result of the optimization of polymer/solvent interactions and conformational entropy of brush strands in the nonlinear deformation regime. The location of the maximum in the Qeq(λ) function is directly related to the value of the strain-stiffening parameter β. This parameter depends on the degree of polymerization of the brush backbone and the backbone Kuhn length defined by both the grafting density and degree of polymerization of the side chains. Analysis of the nonlinear gel modulus confirmed that the strain-stiffening parameter β is identical in both dry networks and gels. However, the structural modulus of the gels, Gs, is smaller than that of the dry networks, Gdr, by a factor equal to the ratio of the Kuhn length of brush strands in the dry state, bK, and in the gel, bK,s, such that Gs = GdrbK/bK,s.

Macroscopic forces in inhomogeneous polyelectrolyte solutions.

In this paper, we present a self-consistent field theory of macroscopic forces in spatially inhomogeneous flexible chain polyelectrolyte solutions. We derive an analytical expression for a stress tensor which consists of three terms: isotropic hydrostatic stress, electrostatic (Maxwell) stress, and stress rising from conformational entropy of polymer chains-conformational stress. We apply our theory to the description of polyelectrolyte solutions confined in a conductive slit nanopore and observe anomalous behavior of disjoining pressure and electric differential capacitance.

Altered conformational landscape upon sensing guanine nucleotides in a disease mutant of Elongation Factor-like 1 (EFL1) GTPase.

Ribosome biogenesis is a highly regulated process that requires the participation of several accessory proteins that participates in the cytoplasmic last maturation step before entering the pool of translating ribosomes. One of these accessory proteins is the GTPase Elongation Factor-like 1 (EFL1), a homologue of the elongation factor 2 (EF-2). EFL1, together with SBDS (yeast Sdo1), evict the anti-association factor eIF6 (yeast Tif6) from the surface of the 60S subunit, allowing mature ribosome assembly. Defects in the function of any of these two proteins lead to a disease called Shwachman-Diamond Syndrome (SDS). Mutations prevent the release of eIF6 from the 60S subunit, with the consequent imbalance of mature 60S subunits entering the pool of active translating 80S ribosomes and a decrease in global translation. EFL1 is a molecular motor that adopts at least four distinct conformations in solution regulated by SBDS and guanine nucleotides whose malfunction in the SDS has been scarcely studied. The malfunction of the non-synonymous mutations in EFL1 has been scarcely studied, with little effect on its catalytic activity or fold. We used Isothermal Titration Calorimetry to gain further insights into the malfunction of Efl1 mutations. We characterised the binding energetics of S. cerevisiae Efl1 R1086Q equivalent to EFL1 R1095Q reported in patients with SDS. The data presented exhibits a different structural and energetic response in the yeast mutant Efl1 R1086Q compared to that previously reported Efl1 wild type. The heat capacity change (ΔCp) and conformational binding entropy of the complexes formed between the mutant and the wild type proteins showed opposite values suggesting they adopt different conformations. We conclude that mutation R1086Q profoundly disrupts the internal rearrangements necessary to elicit a similar conformational change as that in native EFL1.

Water is a powerful dynamic allosteric modulator in rhodopsin activation.

Rhodopsin is an archetype for G protein-coupled receptors (GPCRs) which are membrane proteins involved in cellular signal transduction. Although GPCR X-ray structures show the presence of structural water molecules, their physiological role in the signaling process remains uncertain. Our previous work has shown that in lipid membranes rhodopsin activation is coupled to bulk water movements into the protein to stabilize the effector binding conformation [1,2]. Here we extend the experimental approach to explore modulation of the conformational energetics of rhodopsin activation in lipid membranes. We hypothesized that the thermodynamic stability of conformational substates of photoactivated rhodopsin is hydration mediated. Accordingly, we changed the osmotic stress on rhodopsin using different hydrophilic polymers including polyethylene glycols (PEGs), dextrans, polyvinylpyrrolidones, and their monomers. Reversible shifting of the metarhodopsin equilibrium due to the osmotic stress was probed using UV-visible spectroscopy. We observed that the rhodopsin activation is associated with a bulk influx of water due to the osmotic dehydration by large, excluded polymers which inhibit GPCR activation. By contrast small penetrable osmolytes and monomers have lower conformational entropy and showed a nonosmotic trend in rhodopsin activation. Small osmolytes penetrate the receptor core and stabilize the more expanded active state of rhodopsin until reaching a quantifiable saturation point. Both PEGs and dextrans with very high molar masses deviated in their trends from other large polymers due to a crowding effect, whereby extremely large osmolytes induce steric forces on rhodopsin and restrict their volume occupancy. Further studies of hydration effects on binding of the G-protein and receptor catalyzed exchange of GTP for GDP are expected to provide significant clues on the complete mechanism of G-protein binding and release

Expression and Characterization of Intein-Cyclized Trimer of Staphylococcus aureus Protein A Domain Z.

Staphylococcus aureus protein A (SpA) is an IgG Fc-binding virulence factor that is widely used in antibody purification and as a scaffold to develop affinity molecules. A cyclized SpA Z domain could offer exopeptidase resistance, reduced chromatographic ligand leaching after single-site endopeptidase cleavage, and enhanced IgG binding properties by preorganization, potentially reducing conformational entropy loss upon binding. In this work, a Z domain trimer (Z3) was cyclized using protein intein splicing. Interactions of cyclic and linear Z3 with human IgG1 were characterized by differential scanning fluorimetry (DSF), surface plasmon resonance (SPR), and isothermal titration calorimetry (ITC). DSF showed a 5 ℃ increase in IgG1 melting temperature when bound by each Z3 variant. SPR showed the dissociation constants of linear and cyclized Z3 with IgG1 to be 2.9 nM and 3.3 nM, respectively. ITC gave association enthalpies for linear and cyclic Z3 with IgG1 of -33.0 kcal/mol and -32.7 kcal/mol, and -T∆S of association 21.2 kcal/mol and 21.6 kcal/mol, respectively. The compact cyclic Z3 protein contains 2 functional binding sites and exhibits carboxypeptidase Y-resistance. The results suggest cyclization as a potential approach toward more stable SpA-based affinity ligands, and this analysis may advance our understanding of protein engineering for ligand and drug development.

Ligands selectively tune the local and global motions of neurotensin receptor 1 (NTS1)

Nuclear magnetic resonance (NMR) studies have revealed that fast methyl sidechain dynamics can report on entropically-driven allostery. Yet, NMR applications have been largely limited to the super-microsecond motional regimes of G protein-coupled receptors (GPCRs). We use13Cε-methionine chemical shift-based global order parameters to test if ligands affect the fast dynamics of a thermostabilized GPCR, neurotensin receptor 1 (NTS1). We establish that the NTS1 solution ensemble includes substates with lifetimes on several, discrete timescales. The longest-lived states reflect those captured in agonist- and inverse agonist-bound crystal structures, separated by large energy barriers. We observe that the rapid fluctuations of individual methionine residues, superimposed on these long-lived states, respond collectively with the degree of fast, global dynamics correlating with ligand pharmacology. This approach lends confidence to interpreting spectra in terms of local structure and methyl dihedral angle geometry. The results suggest a role for sub-microsecond dynamics and conformational entropy in GPCR ligand discrimination.

Method for determining resin cure kinetics with low-frequency Raman spectroscopy.

Characterizing resin extent of cure kinetics is critical to understanding the structure-property-processing relationships of polymers. The disorder band present in the low-frequency region of the Raman spectrum is directly related to conformational entropy and the modulus of amorphous materials, both of which change as the resin polymerizes. Normalizing the disorder band to its shoulder (∼85 cm-1) provides structural conversion kinetics, which we can directly correlate to chemical conversion kinetics for methacrylate and epoxy-amine based resin systems. In addition to fitting both the structural and chemical conversion data to a phenomenological kinetic rate equation, we also demonstrate a relationship between the chemical and structural kinetics which appears to relate to the softness of the material. Lastly, we use the method to investigate a methacrylate/epoxy interpenetrating polymer network resin system. We find that the structural and chemical conversions occur simultaneously during the formation of the primary (methacrylate) network, but there is a lag between the two during the formation of the secondary (epoxy-amine) network.

Entropy-driven formation of binary superlattices assembled from polymer-tethered nanorods and nanospheres.

Integrating binary mixtures of nanoparticles (NPs) into well-defined superstructures gives rise to novel collective properties depending on the shapes and individual properties of both species. In this paper, we studied the entropy-driven formation of binary superlattices assembled from polymer-tethered nanorods and nanospheres. The results indicated that the conformational entropy of the polymer chains and the mixing entropy of the nanorods and nanospheres are two parameters that determine the formation of binary superlattices.

Structural, energetic and dynamic investigation of poly(ethylene oxide) in imidazolium-based ionic liquids with different cationic structures.

In this work, two imidazolium-based ionic liquids (ILs) with different cations including dications (DIL) and monocations (MIL) were blended with poly(ethylene oxide) (PEO). The influence of ILs' structure on the structural and dynamic properties of a PEO/IL system was investigated by molecular dynamics (MD) simulation and density functional theory (DFT) methods. The simulation results show that DIL exhibits weaker interaction with PEO than MIL due to a stronger IL aggregation effect. The intermolecular interaction also makes the PEO chain tend to organize around the imidazolium ring of ILs, which causes the conformational entropy loss. Compared with PEO/MIL, this phenomenon is more significant in PEO/DIL because of the double positive centers of the dication and a longer hydrogen bond lifetime. MD simulation also demonstrates that DIL could act as a "crosslinker" to promote the formation of a physical crosslinking network which has strong dependence on the concentration of IL. The competition between physical crosslinking and plasticizing effects induces non-monotonic variations of relaxation time in PEO/DIL, which is consistent with its unusual change of the glass transition temperature (Tg). Despite stronger hydrogen bonding interactions between PEO and MIL demonstrated by atom-in-molecules (AIM) and reduced density gradient (RDG) analysis, the segmental mobility is slower in PEO/DIL according to the MSD curve. These differences in multiple structural or energetic factors finally lead to different conductive mechanisms and hence obtain different ionic conductivities.

Pressure, motion, and conformational entropy in molecular recognition by proteins

The thermodynamics of molecular recognition by proteins is a central determinant of complex biochemistry. For over a half-century, detailed cryogenic structures have provided deep insight into the energetic contributions to ligand binding by proteins. More recently, a dynamical proxy based on NMR-relaxation methods has revealed an unexpected richness in the contributions of conformational entropy to the thermodynamics of ligand binding. Here, we report the pressure dependence of fast internal motion within the ribonuclease barnase and its complex with the protein barstar. In what we believe is a first example, we find that protein dynamics are conserved along the pressure-binding thermodynamic cycle. The femtomolar affinity of the barnase-barstar complex exists despite a penalty by −TΔSconf of +11.7 kJ/mol at ambient pressure. At high pressure, however, the overall change in side-chain dynamics is zero, and binding occurs with no conformational entropy penalty, suggesting an important role of conformational dynamics in the adaptation of protein function to extreme environments. Distinctive clustering of the pressure sensitivity is observed in response to both pressure and binding, indicating the presence of conformational heterogeneity involving less efficiently packed alternative conformation(s). The structural segregation of dynamics observed in barnase is striking and shows how changes in both the magnitude and the sign of regional contributions of conformational entropy to the thermodynamics of protein function are possible.

The Effect of Temperature on the Critical Micelle Concentration and Micellar Solubilization of Poorly Water Soluble Drugs

Non-ionic surfactants, poly oxyethylene sorbitan adipose acid esters (polysorbate), were used in this work to explore the consequence of temperature on CMC throughout a wide temperature range. The phase separation model is used to analyze the enthalpy and entropy of micelle conformation. The Du Nöuys ring was used to determine the results' face pressure. The CMC standards were derived after the strong break down in surfactant attention plots of face pressure vs. logarithms. The CMC at continuous temperature decreases as the chain length of the surfactants rises, which is completely connected to the reduction in hydrophilicity of the motes. Because of the lower possibility of hydrogen bond conformation on high temperatures, the CMC of each surfactant initially declines and then increases as the system temperature rises. As the temperature rises, the commencement of micellization tends to happen at a faster rate. The focus of this research is on the characterization of solubilization of drugs that aren't sufficiently responsive. Face pressure measurements for nonionic surfactant TritonX-100 were also taken in order to assess the solubilization features. In the presence of colourful organic detergent, the medium's opposition and the likely positions of SMX and TMP were also discussed. TritonX-100, a nonionic surfactant, was also tested. In the presence of colourful organic detergents, the medium's opposition and the likely position of SMX and TMP were also discussed.

Inter-domain Flexibility of Human Ser/Arg-Rich Splicing Factor 1 Allows Variable Spacer Length in Cognate RNA's Bipartite Motifs.

Ser/Arg-rich splicing factor 1 (SRSF1 or ASF/SF2) is the prototypical member of SR proteins. SRSF1 binds to exonic splicing enhancers, which prompts inclusion of corresponding exons in the mature mRNA. The RNA-binding domain of SRSF1 consists of tandem RNA-recognition motifs (RRM1 and RRM2) separated by a 30 amino acid long linker. In this study, we investigate roles of RRM1, RRM2, and the linker in RNA binding. We find that although both RRMs are crucial to RNA binding, RRM2 plays the dominant role. The linker mildly contributes to RNA binding and remains flexible in the RNA-bound state. Flexibility of the linker allows the RRM1-cognate motif to be either upstream or downstream of the RRM2-cognate motif. In addition, we find that the spacer length between the bipartite motifs varies from 0 to 10 nucleotides. Our binding assays reveal that SRSF1 prefers RNA sequences with shorter spacers and the RRM1-cognate motif being placed upstream. Restrained by nuclear magnetic resonance data, we simulate RNA-bound complexes and demonstrate how tandem RRMs bind to RNA of different spacer lengths and swapped bipartite motifs. We find that when the RRM1-cognate motif is placed downstream, either the RRM1/RRM2 linker needs to be more extended or RNA needs to form a U turn, which may reduce conformational entropy. Our study suggests that the RNA-binding specificity of SRSF1 is broader than traditionally recapitulated by consensus sequences of 7 to 8 nucleotides. Instead, centered on the RRM2-cognate motif, an RNA fragment encompassing 10-nucleotide upstream and downstream should be scrutinized.

Effects of Conformational Constraint on Peptide Solubility Limits.

Liquid-liquid phase separation of proteins preferentially involves intrinsically disordered proteins or disordered regions. Understanding the solution chemistry of these phase separations is key to learning how to quantify and manipulate systems that involve such processes. Here, we investigate the effect of cyclization on the liquid-liquid phase separation of short polyglycine peptides. We simulated separate aqueous systems of supersaturated cyclic and linear GGGGG and observed spontaneous liquid-liquid phase separation in each of the solutions. The cyclic GGGGG phase separates less robustly than linear GGGGG and has a higher aqueous solubility, even though linear GGGGG has a more favorable single molecule solvation free energy. The versatile and abundant interpeptide contacts formed by the linear GGGGG stabilize the condensed droplet phase, driving the phase separation in this system. In particular, we find that van der Waals close contact interactions are enriched in the droplet phase as opposed to electrostatic interactions. An analysis of the change in backbone conformational entropy that accompanies the phase transition revealed that cyclic peptides lose significantly less entropy in this process as expected. However, we find that the enhanced interaction enthalpy of linear GGGGG in the droplet phase is enough to compensate for a larger decrease in conformational entropy.

Local conformations and heterogeneities in structures and dynamics of isotactic polypropylene adsorbed onto carbon fiber

Carbon fiber (CF) reinforced polymers (CFRPs) have experienced widespread use in various industries. One of the most important parameters that controls the macroscopic property of CFRPs is the interface between a polymer matrix and CF. There is growing evidence to suggest the formation of a bound polymer layer (BPL), i.e., polymer chains that physically adsorb on a filler surface. However, this interface is always in contact with the thicker part of a polymer matrix, rendering its understanding a difficult task. Therein, we use CF-reinforced isotactic polypropylene (iPP) as a rational CFRP. To characterize the BPL on the CF surface, we extracted it from the CFRP using solvent-rinsing with p-xylene. The physical and thermal properties of the BPL were characterized by differential scanning calorimetry and thermogravimetric analysis, while its microscopic structures and dynamics were probed by small-angle neutron scattering and quasi-elastic neutron scattering (QENS) techniques. Subsequently, we employed atomistic molecular dynamics (MD) simulations to complement the QENS results above the bulk melting temperature and reveal details that were experimentally inaccessible. We observed that the degree of crystallinity of the BPL was quite lower than the bulk, while the melting temperature of the BPL remained the same as the bulks. Within the given length and time scales probed by QENS and MD, we also observed that most of the bound chains were mobile, with the formation of a high-density region (less than 1 nm in thickness) near the CF surface. The segmental dynamics of the bound chains probed by both QENS and MD were also much faster than those of the free chains, possibly due to the presence of a free surface region at the topmost surface of the BPL. Furthermore, the MD results demonstrated that the backbone chains and side groups lie nearly flat on the CF surface, which is the driving force for the flattening process of the iPP BPL to overcome the conformational entropy loss in the total free energy.

Sequence-Based Prediction of Protein Phase Separation: The Role of Beta-Pairing Propensity.

The formation of droplets of bio-molecular condensates through liquid-liquid phase separation (LLPS) of their component proteins is a key factor in the maintenance of cellular homeostasis. Different protein properties were shown to be important in LLPS onset, making it possible to develop predictors, which try to discriminate a positive set of proteins involved in LLPS against a negative set of proteins not involved in LLPS. On the other hand, the redundancy and multivalency of the interactions driving LLPS led to the suggestion that the large conformational entropy associated with non specific side-chain interactions is also a key factor in LLPS. In this work we build a LLPS predictor which combines the ability to form pi-pi interactions, with an unrelated feature, the propensity to stabilize the β-pairing interaction mode. The cross-β structure is formed in the amyloid aggregates, which are involved in degenerative diseases and may be the final thermodynamically stable state of protein condensates. Our results show that the combination of pi-pi and β-pairing propensity yields an improved performance. They also suggest that protein sequences are more likely to be involved in phase separation if the main chain conformational entropy of the β-pairing maintained droplet state is increased. This would stabilize the droplet state against the more ordered amyloid state. Interestingly, the entropic stabilization of the droplet state appears to proceed according to different mechanisms, depending on the fraction of "droplet-driving" proteins present in the positive set.

Insight into polyproline II helical bundle stability in an antifreeze protein denatured state

The use of polyproline II (PPII) helices in protein design is currently hindered by limitations in our understanding of their conformational stability and folding. Recent studies of the snow flea antifreeze protein (sfAFP), a useful model system composed of six PPII helices, suggested that a low denatured state entropy contributes to folding thermodynamics. Here, circular dichroism spectroscopy revealed minor populations of PPII like conformers at low temperature. To get atomic level information on the conformational ensemble and entropy of the reduced, denatured state of sfAFP, we have analyzed its chemical shifts and {1H}-15N relaxation parameters by NMR spectroscopy at four experimental conditions. No significant populations of stable secondary structure were detected. The stiffening of certain N-terminal residues at neutral versus acidic pH and shifted pKa values leads us to suggest that favorable charge-charge interactions could bias the conformational ensemble to favor the formation the C1-C28 disulfide bond during nascent folding, although no evidence for preferred contacts between these positions was detected by paramagnetic relaxation enhancement under denaturing conditions. Despite a high content of flexible glycine residues, the mobility of the sfAFP denatured ensemble is similar for denatured α/β proteins both on fast ps/ns as well as slower μs/ms timescales. These results are in line with a conformational entropy in the denatured ensemble resembling that of typical proteins and suggest that new structures based on PPII helical bundles should be amenable to protein design.

Polymorphism and Perfection in Crystallization of Hard Sphere Polymers

We present results on polymorphism and perfection, as observed in the spontaneous crystallization of freely jointed polymers of hard spheres, obtained in an unprecedentedly long Monte Carlo (MC) simulation on a system of 54 chains of 1000 monomers. Starting from a purely amorphous configuration, after an initial dominance of the hexagonal closed packed (HCP) polymorph and a transitory random hexagonal close packed (rHCP) morphology, the system crystallizes in a final, stable, face centered cubic (FCC) crystal of very high perfection. An analysis of chain conformational characteristics, of the spatial distribution of monomers and of the volume accessible to them shows that the phase transition is caused by an increase in translational entropy that is larger than the loss of conformational entropy of the chains in the crystal, compared to the amorphous state. In spite of the significant local re-arrangements, as reflected in the bending and torsion angle distributions, the average chain size remains unaltered during crystallization. Polymers in the crystal adopt ideal random walk statistics as their great length renders local conformational details, imposed by the geometry of the FCC crystal, irrelevant.

Loss of stability and unfolding cooperativity in hPGK1 upon gradual structural perturbation of its N-terminal domain hydrophobic core

Phosphoglycerate kinase has been a model for the stability, folding cooperativity and catalysis of a two-domain protein. The human isoform 1 (hPGK1) is associated with cancer development and rare genetic diseases that affect several of its features. To investigate how mutations affect hPGK1 folding landscape and interaction networks, we have introduced mutations at a buried site in the N-terminal domain (F25 mutants) that either created cavities (F25L, F25V, F25A), enhanced conformational entropy (F25G) or introduced structural strain (F25W) and evaluated their effects using biophysical experimental and theoretical methods. All F25 mutants folded well, but showed reduced unfolding cooperativity, kinetic stability and altered activation energetics according to the results from thermal and chemical denaturation analyses. These alterations correlated well with the structural perturbation caused by mutations in the N-terminal domain and the destabilization caused in the interdomain interface as revealed by H/D exchange under native conditions. Importantly, experimental and theoretical analyses showed that these effects are significant even when the perturbation is mild and local. Our approach will be useful to establish the molecular basis of hPGK1 genotype–phenotype correlations due to phosphorylation events and single amino acid substitutions associated with disease.