Minor Conformer Research Articles

The de novo assembly and characterization of the complete mitochondrial genome of bottle gourd (Lagenaria siceraria) reveals the presence of homologous conformations produced by repeat-mediated recombination.

Bottle gourd is an annual herbaceous plant that not only has high nutritional value and many medicinal applications but is also used as a rootstock for the grafting of cucurbit crops such as watermelon, cucumber and melon. Organellar genomes provide valuable resources for genetic breeding. A hybrid strategy with Illumina and Oxford Nanopore Technology sequencing data was used to assemble bottle gourd mitochondrial and chloroplast genomes. The length of the bottle gourd mitochondrial genome was 357547 bp, and that of the chloroplast genome was 157121 bp. These genomes had 27 homologous fragments, accounting for 6.50% of the total length of the bottle gourd mitochondrial genome. In the mitochondrial genome, 101 simple sequence repeats (SSRs) and 10 tandem repeats were identified. Moreover, 1 pair of repeats was shown to mediate homologous recombination into 1 major conformation and 1 minor conformation. The existence of these conformations was verified via PCR amplification and Sanger sequencing. Evolutionary analysis revealed that the mitochondrial genome sequence of bottle gourd was highly conserved. Furthermore, collinearity analysis revealed many rearrangements between the homologous fragments of Cucurbita and its relatives. The Ka/Ks values for most genes were between 0.3~0.9, which means that most of the genes in the bottle gourd mitochondrial genome are under purifying selection. We also identified a total of 589 potential RNA editing sites on 38 mitochondrial protein-coding genes (PCGs) on the basis of long noncoding RNA (lncRNA)-seq data. The RNA editing sites of nad1-2, nad4L-2, atp6-718, atp9-223 and rps10-391 were successfully verified via PCR amplification and Sanger sequencing. In conclusion, we assembled and annotated bottle gourd mitochondrial and chloroplast genomes to provide a theoretical basis for similar organelle genomic studies.

Micro Solvation Effect of Methanol on Excited-State Dynamics of Protonated Tryptophan and Dopamine.

The electronic and vibrational cryogenic ion spectroscopy of protonated tryptophan (TrpH+) and dopamine (DAH+) complexed with methanol has been recorded. These two biological chromophores exhibit ultrafast photochemistry due to excited-state proton transfer (ESPT). We have established the relationship between the structure of the complexes and their photodynamics and compared them with recent results obtained in hydrated complexes. For TrpH+, there is no substantial change between methanol and water complexes; ESPT is hindered by a single solvent molecule. In the DAH+(MeOH)1 complex, the most stable conformer adopts a structure that prevents the direct interaction of the ammonium group of the side chain with the catechol ring, thus blocking the ESPT reaction. Such a ring structure is indeed a very minor populated conformer in the single-hydrated complex. The change in conformal stability between water and methanol clusters is due to a weak CH-π attractive interaction of the methyl group of methanol with the catechol.

Competitive Intramolecular Hydrogen Bonding: Offering Molecules a Choice.

The conformational preferences of N-((6-methylpyridin-2-yl)carbamothioyl)benzamide were studied in solution, the gas phase and the solid state via a combination of NMR, density functional theory (DFT) and single crystal X-ray techniques. This acyl thiourea derivative can adopt two classes of low energy conformation, each stabilized by a different 6-membered intramolecular hydrogen bond (IHB) pseudoring. Analysis in different solvents revealed that the conformational preference of this molecule is polarity dependent, with increasingly polar environments yielding a higher proportion of the minor conformer containing an NH⋅⋅⋅N IHB. The calculated barrier to interconversion is consistent with dynamic behaviour at room temperature, despite the propensity of 6-membered IHB pseudorings to be static. This work demonstrates that introducing competitive IHB pathways can render static IHBs more dynamic and that such systems could have potential as chameleons in drug design.

Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography.

Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations, and formation of the thioimidate intermediate selects for catalytically competent substates. The influence of cysteine ionization on the ICH ensemble is validated by determining structures of the enzyme at multiple pH values. Large molecular dynamics simulations in crystallo and time-resolved electron density maps show that Asp17 ionizes during catalysis and causes conformational changes that propagate across the dimer, permitting water to enter the active site for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.

Unmasking the True Identity of Rapamycin's Minor Conformer.

Rapamycin, a well-known macrocyclic natural product with myriad biological activities, has been the subject of intense study since its first isolation and characterization over five decades ago. Rapamycin has been found to adopt a single conformation in the solid state (both when protein bound and uncomplexed) and exists as a mixture of two conformations in solution. Early work established that the major conformer in solution is the trans amide isomer but left the minor conformer mostly uncharacterized. Since that time, it has been widely accepted that the minor conformer of rapamycin is the cis amide, based solely on analogy to FK-506, another potent immunosuppressive compound with some shared key structural elements. To address this long-standing and unresolved question, the solution structure of the minor conformer of rapamycin was investigated using a combination of NMR techniques and computational methods and determined to be a trans amide species with rotation about the ester linkage.

Stereochemical Analysis of Trifluoroacetamide Derivatives Based on Through-Space 1H–19F Spin–Spin Couplings

In this study, the conformational properties of tertiary trifluoroacetamides in dibenzoazepine (1a and 1b) and benzodiazepine (2a and 2b) derivatives, which exist as equilibrated E- and Z-amide conformers in solution, were investigated by 1H and 19F NMR spectroscopy. In all cases, one of the methylene protons neighboring the nitrogen atom of the minor conformer showed a finely split pattern due to coupling with the trifluoromethyl fluorine atoms, as confirmed by 19F-decoupling experiments. One-dimensional (1D) and two-dimensional (2D) 1H-19F heteronuclear Overhauser spectroscopy (HOESY) experiments were performed to confirm whether these couplings are attributable to through-bond spin-spin couplings (TBCs) or through-space spin-spin couplings (TSCs). HOESY cross-peaks between CF3 (19F) and one of the CH2-N protons of the minor conformers indicate that the two nuclei are spatially close to each other, thus establishing the stereochemistry of the major (E-) and minor (Z-) conformers. The E-amide preferences of the trifluoroacetamides are consistent with the results of density functional theory calculations and X-ray crystallographic analyses. Furthermore, the otherwise incomprehensible 1H NMR spectra were accurately assigned using the HOESY-determined TSCs. The 1H NMR assignments of the E- and Z-methyl signals of N,N-dimethyl trifluoroacetamide, the simplest tertiary trifluoroacetamide, were revised for the first time in half a century.

De Novo Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Chaenomeles speciosa (Sweet) Nakai Revealed the Existence of Two Structural Isomers.

As a valuable Chinese traditional medicinal species, Chaenomeles speciosa (Sweet) Nakai (C. speciosa) is a natural resource with significant economic and ornamental value. However, its genetic information is not well understood. In this study, the complete mitochondrial genome of C. speciosa was assembled and characterized to explore the repeat sequences, recombination events, rearrangements, and IGT, to predict RNA editing sites, and to clarify the phylogenetic and evolutionary relationship. The C. speciosa mitochondrial genome was found to have two circular chromosomes as its major conformation, with a total length of 436,464 bp and 45.2% GC content. The mitochondrial genome contained 54 genes, including 33 unique protein-coding genes, 18 tRNAs, and 3 rRNA genes. Seven pairs of repeat sequences involving recombination events were analyzed. Both the repeat pairs, R1 and R2, played significant roles in mediating the major and minor conformations. In total, 18 MTPTs were identified, 6 of which were complete tRNA genes. There were 454 RNA editing sites in the 33 protein-coding sequences predicted by the PREPACT3 program. A phylogenetic analysis based on 22 species of mitochondrial genomes was constructed and indicated highly conserved PCG sequences. Synteny analyses showed extensive genomic rearrangements in the mitochondrial genome of C. speciosa and closely related species. This work is the first to report the C. speciosa mitochondrial genome, which is of great significance for conducting additional genetic studies on this organism.

Stable Enzymatic Nanoparticles from Nucleases, Proteases, Lipase and Antioxidant Proteins with Substrate-Binding and Catalytic Properties.

Limited membrane permeability and biodegradation hamper the intracellular delivery of the free natural or recombinant enzymes necessary for compensatory therapy. Nanoparticles (NP) provide relative protein stability and unspecific endocytosis-mediated cellular uptake. Our objective was the fabrication of NP from 7 biomedicine-relevant enzymes, including DNase I, RNase A, trypsin, chymotrypsin, catalase, horseradish peroxidase (HRP) and lipase, the analysis of their conformation stability and enzymatic activity as well as possible toxicity for eukaryotic cells. The enzymes were dissolved in fluoroalcohol and mixed with 40% ethanol as an anti-solvent with subsequent alcohol evaporation at high temperature and low pressure. The shapes and sizes of NP were determined by scanning electron microscopy (SEM), atomic force microscopy (AFM) and dynamic light scattering (DLS). Enzyme conformations in solutions and in NP were compared using circular dichroism (CD) spectroscopy. The activity of the enzymes was assayed with specific substrates. The cytotoxicity of the enzymatic NP (ENP) was studied by microscopic observations and by using an MTT test. Water-insoluble ENP of different shapes and sizes in a range 50-300 nm consisting of 7 enzymes remained stable for 1 year at +4 °C without any cross-linking. CD spectroscopy of the ENP permitted us to reveal changes in proportions of α-helixes, β-turns and random coils in comparison with fresh enzyme solutions in water. Despite the minor conformation changes of the proteins in the ENP, the enzymes retained their substrate-binding and catalytic properties. Among the studied bioactive ENP, only DNase NP were highly toxic for 3 cell lines with granulation in 1 day posttreatment, whereas other NP were less toxic (if any). Taken together, the enzymes in the stable ENP retained their catalytic activity and might be used for intracellular delivery.

Synthesis and Characterization of Zinc(II), Cadmium(II), and Palladium(II) Complexes with the Thiophene-Derived Schiff Base Ligand.

Zn(II), Pd(II), and Cd(II) complexes, [L TH MCl 2 ] (M = Zn, Pd; X = Br, Cl) and [L TH Cd(μ-X)X] n (X = Cl, Br; n = n, 2), supported by the (E)-N 1,N 1-dimethyl-N 2-(thiophen-2-ylmethylene)ethane-1,2-diamine (L TH ) ligand are synthesized and structurally characterized. Density functional theory (DFT) electronic structure calculations and variable-temperature NMR support the presence of two conformers and a dynamic interconversion process of the minor conformer to the major one in solution. It is found that the existence of two relevant complex conformers and their respective ratios in solution depend on the central metal ions and counter ions, either Cl- or Br-. Among the two relevant conformers, a single conformer is crystallized and X-ray diffraction analysis revealed a distorted tetrahedral geometry for Zn(II) complexes, and a distorted square planar and square pyramidal geometry for Pd(II) and Cd(II) complexes, respectively. It is shown that [L TH MCl 2 ]/LiO i Pr (M = Zn, Pd) and [L TH Cd(μ-Cl)Cl] n /LiO i Pr can effectively catalyze the ring-opening polymerization (ROP) reaction of rac-lactide (rac-LA) with 94% conversion within 30 s with [L TH ZnCl 2 ]/LiO i Pr at 0 °C. Overall, hetero-enriched poly(lactic acid)s (PLAs) were provided by these catalytic systems with [L TH ZnCl 2 ]/LiO i Pr producing PLA with higher heterotactic bias (P r up to 0.74 at 0 °C).

Assembly of the Complete Mitochondrial Genome of Gelsemium elegans Revealed the Existence of Homologous Conformations Generated by a Repeat Mediated Recombination.

Gelsemium elegans (G. elegans) is a Chinese medicinal plant with substantial economic and feeding values. There is a lack of detailed studies on the mitochondrial genome of G. elegans. In this study, the mitochondrial genome of G. elegans was sequenced and assembled, and its substructure was investigated. The mitochondrial genome of G. elegans is represented by two circular chromosomes of 406,009 bp in length with 33 annotated protein-coding genes, 15 tRNA genes, and three rRNA genes. We detected 145 pairs of repeats and found that four pairs of repeats could mediate the homologous recombination into one major conformation and five minor conformations, and the presence of conformations was verified by PCR amplification and Sanger sequencing. A total of 124 SSRs were identified in the G. elegans mitochondrial genome. The homologous segments between the chloroplast and mitochondrial genomes accounted for 5.85% of the mitochondrial genome. We also predicted 477 RNA potential editing sites and found that the nad4 gene was edited 38 times, which was the most frequent occurrence. Taken together, the mitochondrial genome of G. elegans was assembled and annotated. We gained a more comprehensive understanding on the genome of this medicinal plant, which is vital for its effective utilization and genetic improvement, especially for cytoplasmic male sterility breeding and evolution analysis in G. elegans.

Structural dynamics of the N-terminal SH2 domain of PI3K in its free and CD28-bound states.

Protein conformational changes with fluctuations are fundamental aspects of protein-protein interactions (PPIs); understanding these motions is required for the rational design of PPI-regulating compounds. Src homology 2 (SH2) domains are commonly found in adapter proteins involved in signal transduction and specifically bind to consensus motifs of proteins containing phosphorylated tyrosine (pY). Here, we analysed the interaction between the N-terminal SH2 domain (nSH2) of the regulatory subunit in phosphoinositide 3-kinase (PI3K) and the cytoplasmic region of the T-cell co-receptor, CD28, using NMR and molecular dynamics (MD) simulations. First, we assigned the backbone signals of nSH2 on 1 H-15 N heteronuclear single quantum coherence spectra in the absence or presence of the CD28 phosphopeptide, SDpYMNMTPRRPG. Chemical shift perturbation experiments revealed allosteric changes at the BC loop and the C-terminal region of nSH2 upon CD28 binding. NMR relaxation experiments showed a conformational exchange associated with CD28 binding in these regions. The conformational stabilisation of the C-terminal region correlated with the regulation of PI3K catalytic function. Further, using 19 F- and 31 P-labelled CD28 phosphopeptide, we analysed the structural dynamics of CD28 and demonstrated that the aromatic ring of the pY residue fluctuated between multiple conformations upon nSH2 binding. Our MD simulations largely explained the NMR results and the structural dynamics of nSH2 and CD28 in both bound and unbound states. Notably, in addition to its major conformation, we detected a minor conformation of nSH2 in the CD28 bound state that may explain the allosteric conformational change in the BC loop.

Isotope-edited vibrational circular dichroism study reveals a flexible N-terminal structure of islet amyloid peptide (NFGAIL) in amyloid fibril form: A site-specific local structural analysis

The short peptide fragment NFGAIL (IAPf) is a well-known amyloidogenic peptide (22–27), derived from human islet amyloid polypeptide(hIAPP), whose fibrillar structure is often used to better understand the wild-type hIAPP amyloid fibrils, associated with type II diabetes. Despite an extensive study, the fibrillar structure of IAPf at the amino acid residue level is still unclear. Herein, the vibrational circular dichroism(VCD) spectroscopic technique coupled with isotope labelling strategy has been used to study the site-specific local structure of IAPf amyloid fibrils. Two 13C labeled IAPfs were designed and used along with unlabelled IAPf to achieve this. The 13C labelled (on -C=O) glycine(IAPf-G) and phenylalanine (IAPf-F) residues were introduced into the IAPf sequence separately by replacing natural glycine (residue 24) and phenylalanine (residue 23), respectively. VCD spectral analysis on IAPf-G suggests that IAPf fibrils adopt parallel β-sheet conformation with glycine residues are part of β-sheet and in-register. Unlike IAPf-G, VCD analysis on IAPf-F reveals that phenylalanine residues exist in the turn/hairpin conformation rather than β-sheet region. Both VCD results thus suggest that IAPf amyloid fibril consists of a mixture of β-sheet as a major conformation involving GAIL and turn/hairpin as a minor conformation involving NF rather than an idealized β-sheet involving all the amino acids. While previous studies speculated that the full NFGAIL sequence could participate in the β-sheet formation, the present site-specific structural analysis of IAPf amyloid fibrils at residue level using isotope-edited VCD has gained significant attention. Such residue level information has important implications for understanding the role of NFGAIL sequence in the amyloid fibrillation of hIAPP.

Getting in the groove: The selection of MHC-I antigen repertoires by molecular chaperones is governed by a network of protein dynamics

Conformational dynamics have been implicated in regulating key aspects of class I major histocompatibility complex (MHC-I) function, including association with peptide antigens, and recognition of peptide-editing chaperones in an MHC-I allele-specific manner. Molecular dynamics simulations have provided insights into motions up to the microseconds timescale, however biophysical parameters characterizing these processes in solution are largely lacking. Here, we use solution NMR to explore how dynamics affect the interaction between peptide-loaded MHC-I (pMHC-I) and the chaperone TAPBPR, a structural homolog of tapasin which serves as the main catalytic enhancer of antigen loading in cells. We characterize motions up to the milliseconds timescale for a representative set of common mouse and human pMHC-I molecules exhibiting varying affinities for human TAPBPR in vitro. Our results establish that, in aqueous solution, pMHC-I molecules sample a minor conformation involving a network of dynamically coupled sites. The extent of dynamics at “hotspot” surfaces, including the heavy chain α2-1 helix, the pleated β-sheet underpinning the MHC-I groove, and α3 domain, correlate with the specificity of TAPBPR recognition by different alleles. Conversely, restriction of MHC-I groove dynamics through an engineered disulfide bond at the α2-1 helix abrogates interactions with TAPBPR, both in vitro and on a cellular membrane. Our results suggest that TAPBPR exploits localized structural adaptations, both near and distant to the peptide-binding groove, to selectively recognize distinct MHC-I alleles towards editing the repertoire of displayed antigens.

Large-Scale Ligand Perturbations of the Protein Conformational Landscape Reveal State-Specific Interaction Hotspots.

Protein flexibility is important for ligand binding but often ignored in drug design. Considering proteins as ensembles rather than static snapshots creates opportunities to target dynamic proteins that lack FDA-approved drugs, such as the human chaperone, heat shock protein 90 (Hsp90). Hsp90α accommodates ligands with a dynamic lid domain, yet no comprehensive analysis relating lid conformations to ligand properties is available. To date, ∼300 ligand-bound Hsp90α crystal structures are deposited in the Protein Data Bank, which enables us to consider ligand binding as a perturbation of the protein conformational landscape. By estimating binding site volumes, we classified structures into distinct major and minor lid conformations. Supported by retrospective docking, each conformation creates unique hotspots that bind chemically distinguishable ligands. Clustering revealed insightful exceptions and the impact of crystal packing. Overall, Hsp90α's plasticity provides a cautionary tale of overinterpreting individual crystal structures and motivates an ensemble-based view of drug design.

A molecular bridge-like binding mode of buspirone to BSA: Multispectroscopic and molecular docking investigation

• Binding interaction of buspirone with BSA has been studied. • Flexibility of buspirone played a critical role in binding process to BSA with change in the structure. • Buspirone simultaneously bound on sub domain IIIA and IIA of BSA. • Fluorescence of BSA quenched by buspirone. • Molecular docking results were explained, conventional hydrogen bond, carbon-hydrogen bonds, van-der-Waals forces and alkyl interactions were found in BSA-Buspirone complex. The anxiolytic psychotropic drug buspirone from the azapirone class of tranquilizer treats seizures, panic disorder, and anxiety disorder. The buspirone's binding interaction to bovine serum albumin (BSA) was investigated using UV-visible, fluorescence spectroscoy with molecular docking methods. Findings are indicative that buspirone is bound simultaneously on two subdomains IIA and IIIA of albumin through conventional hydrogen bond, carbon-hydrogen bonds, van-der-Waals forces and alkyl interactions. The binding sites ( n ) and binding constant ( K b ) of the buspirone-BSA complex were about 2 and 1.64217×10 5 M −1 at 298 K. The buspirone binding to BSA was spontaneous and enthalpy-driven. The buspirone's binding interaction with BSA brings about a minor conformation change in BSA and apparent conformation change in buspirone, suggesting that the flexibility of buspirone also played a role in the cumulative stability of the buspirone-BSA complex.

Inherent Minor Conformer of Bordetella Effector BteA Directs Chaperone-Mediated Unfolding.

The pathogen Bordetella pertussis uses a type-3 secretion system (T3SS) to inject its cytotoxic effector BteA into the host cell via a designated needle structure. Prior to injection BteA is bound to its cognate chaperone BtcA presumed to assist in effector unfolding en route to needle passage. We utilized NMR and EPR spectroscopy to uncover the molecular mechanism of BtcA-mediated unfolding of BteA. BtcA induces a global structural change in the effector, which adopts a more extended and partially unfolded conformation. EPR distance measurements further show that the structured helical-bundle form of free BteA exists in conformational equilibrium with a lowly populated minor species. The nature of this equilibrium was probed using NMR relaxation dispersion experiments. At 283 K structural effects are most pronounced for a contiguous surface spanning the A- and B-helices of BteA, extending at 303 K to a second surface including the D- and E-helices. Residues perturbed in the minor conformation coincide with those exhibiting a BtcA-induced increase in flexibility, identifying this conformation as the BtcA-bound form of the effector. Our findings hint at a conformational-selectivity mechanism for the chaperone interaction with the effector, a paradigm that may be common to effector-chaperones secretion complexes in this family of pathogens.

Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting

Thermodynamic preferences to form non-native conformations are crucial for understanding how nucleic acids fold and function. However, they are difficult to measure experimentally because this requires accurately determining the population of minor low-abundance (<10%) conformations in a sea of other conformations. Here, we show that melting experiments enable facile measurements of thermodynamic preferences to adopt nonnative conformations in DNA and RNA. The key to this "delta-melt" approach is to use chemical modifications to render specific minor non-native conformations the major state. The validity and robustness of delta-melt is established for four different non-native conformations under various physiological conditions and sequence contexts through independent measurements of thermodynamic preferences using NMR. Delta-melt is faster relative to NMR, simple, and cost-effective and enables thermodynamic preferences to be measured for exceptionally low-populated conformations. Using delta-melt, we obtained rare insights into conformational cooperativity, obtaining evidence for significant cooperativity (1.0 to 2.5 kcal/mol) when simultaneously forming two adjacent Hoogsteen base pairs. We also measured the thermodynamic preferences to form G-C+ and A-T Hoogsteen and A-T base open states for nearly all 16 trinucleotide sequence contexts and found distinct sequence-specific variations on the order of 2 to 3 kcal/mol. This rich landscape of sequence-specific non-native minor conformations in the DNA double helix may help shape the sequence specificity of DNA biochemistry. Thus, melting experiments can now be used to access thermodynamic information regarding regions of the free energy landscape of biomolecules beyond the native folded and unfolded conformations.

AlphaFold 2 and NMR Spectroscopy: Partners to Understand Protein Structure, Dynamics and Function.

The artificial intelligence program AlphaFold 2 is revolutionizing the field of protein structure determination as it accurately predicts the 3D structure of two thirds of the human proteome. Its predictions can be used directly as structural models or indirectly as aids for experimental structure determination using X-ray crystallography, CryoEM or NMR spectroscopy. Nevertheless, AlphaFold 2 can neither afford insight into how proteins fold, nor can it determine protein stability or dynamics. Rare folds or minor alternative conformations are also not predicted by AlphaFold 2 and the program does not forecast the impact of post translational modifications, mutations or ligand binding. The remaining third of human proteome which is poorly predicted largely corresponds to intrinsically disordered regions of proteins. Key to regulation and signaling networks, these disordered regions often form biomolecular condensates or amyloids. Fortunately, the limitations of AlphaFold 2 are largely complemented by NMR spectroscopy. This experimental approach provides information on protein folding and dynamics as well as biomolecular condensates and amyloids and their modulation by experimental conditions, small molecules, post translational modifications, mutations, flanking sequence, interactions with other proteins, RNA and virus. Together, NMR spectroscopy and AlphaFold 2 can collaborate to advance our comprehension of proteins.

Tunable Solid-State Thermochromism: Alkyl Chain Length-Dependent Conformational Isomerization of Bianthrones.

The introduction of linear alkoxy chains into bianthrone promoted the aggregation of the minor twisted conformer and made it compete with the major folded conformer in the solid-state. Rapid evaporation approach to the methoxy- and n-butoxy-substituted derivatives provided powder mixtures of folded and twisted conformers as metastable solids. Upon heating the powders, different lengths of alkyl chains converged to different conformers via solid-state isomerization reaction with an apparent color change. Monitoring by FT-IR spectroscopy and powder XRD ensured that these isomerization reactions involve only conformational isomerization without pyrolysis. In addition, single crystal X-ray structure analysis revealed that twisted conformers with longer alkyl chains are stabilized in the solid-state by the synergistic effect of their inter-chain hydrophobic interactions and π-π stacking interactions.

Quantification of Entropic Excluded Volume Effects Driving Crowding-Induced Collapse and Folding of a Disordered Protein.

We investigate the conformational properties of the intrinsically disordered DNA-binding domain of CytR in the presence of the polymeric crowder polyethylene glycol (PEG). Integrating circular dichroism, nuclear magnetic resonance, and single-molecule Förster resonance energy transfer measurements, we demonstrate that disordered CytR populates a well-folded minor conformation in its native ensemble, while the unfolded ensemble collapses and folds with an increase in crowder density independent of the crowder size. Employing a statistical-mechanical model, the effective reduction in the accessible conformational space of a residue in the unfolded state is estimated to be 10% at 300 mg/mL PEG8000, relative to dilute conditions. The experimentally consistent PEG-temperature phase diagram thus constructed reveals that entropic effects can stabilize disordered CytR by 10 kJ mol-1, driving the equilibrium toward folded conformations under physiological conditions. Our work highlights the malleable conformational landscape of CytR, the presence of a folded conformation in the disordered ensemble, and proposes a scaling relation for quantifying excluded volume effects on protein stability.