Conformational Studies Research Articles

The 2021 FASEB Virtual Science Research Conference on Protein Aggregation: Function, Dysfunction, and Disease, June 23-25, 2021.

The 2021 FASEB Virtual Science Research Conference on Protein Aggregation: Function, Dysfunction, and Disease, June 23-25, 2021.

The conformity between dermoscopy imaging and Wood’s lamp diagnostic on periorbital hyperpigmentation

Introduction: Periorbital hyperpigmentation (POH) is a common skin problem characterized by homogeneous/dark brown hyperchromic/pigmented macules around the lower eyelid and upper eyelid up to the malar area temporal area and the sides of the nose. POH is a multifactorial condition caused by both endogenous factors and exogenous factors, without one aspect dominating. Dermoscopy and Wood's lamp can assist the diagnosis of POH types when the inspection is regarded as weak. The assessment of the suitability of the dermoscopic image and Woods’ lamp diagnosis indicates an alternative supporting test in POH diagnosis. This study aimed to examine the conformity between dermoscopic images and Wood's lamp examination in POH diagnosis.Methods: This observational conformity study was conducted using a cross-sectional design. There were 38 subjects diagnosed with POH who went to the Cosmetics Division of Dermatology and Venereology, Universitas Sumatra Utara Hospital participated as subjects. Assessments regarded the types of POH analyzed based on dermoscopic images and Wood's lamp examination. Data analysed with SPSS version 20 using Kappa test.Results: On dermoscopy examination, the mixed type was the type most obtained, as many as 18 subjects (47,4%), whilst on Wood's lamp examination, the most dominant type obtained was pigment type, as much as 21 subjects (55,3%). Moderate conformity value on POH examination was obtained with dermoscopy and Wood’s lamp.Conclusion: Dermoscopic images and Wood's lamp examination shared a sufficient conformity value in POH diagnosis.

A simple method for predicting alkane‐water partition coefficients of surfactants

AbstractAlkane/water (logPalk) partitioning systems are gaining relevance in applied surfactant science but there is still a challenge to calculate logPalk values for surfactants. In this contribution, a simple method of calculating logPalk at sub‐micellar concentrations for a wide range of nonionic surfactants is presented, using a linear combination of octanol/water partition and hydrogen‐bonding contribution parameters of surfactants. These two parameters can be easily calculated using many commercial or open‐access software packages. The model requires a critical folding chain length factor to account for entropic effects arising from conformational behavior of the ethylene‐oxide chain for alcohol ethoxylate surfactants. This observation is substantiated by conducting a conformational lipophilicity study by molecular dynamics simulations of two alkylphenol ethoxylates as model surfactants. Polydispersity is not seen as a major factor in calculating the logPalk of surfactants. The model is shown to outperform previously published methods and can be applied directly in surfactant research and regulatory submissions when experimental data are not available.

Design, Synthesis and Conformational Studies of Cyclic Tetrapeptides having βγ Fused Turns as HDAC Inhibitors

AbstractHistone deacetylases (HDACs) belong to a class of major targets for the development of anticancer drugs for which cyclic peptide‐based molecules are attracting wide attention. Here we show the synthesis, conformational and in silico analysis of tetrahydrofuran amino acid (TAA) based 15‐membered cyclic tetrapeptides (CTPs) containing hydroxamic acid side chain as potential HDAC inhibitors. NMR based solution studies in protected and deprotected forms reveal that the macrocycles are stabilized by 10‐membered β‐turn as well as a 7‐membered γ‐turn. This type of fused structures within the same macrocycle is not frequently sighted. Our initial in silico docking results indicated that the hydroxamic acid protected CTPs show promising binding with the class‐1 HDACs. We also noticed that the C‐chain with hydroxamic functional group attached on the ornithine sidechain did not affect the core structure of the peptide ring. Moreover, some of these cyclic tetrapeptides with hydroxamic acid side chain exhibited an induction of acetylation of histones on preliminary cell‐based experiments. Our initial results provide an insight into the development of HDAC inhibitors based on the CTPs with novel βγ fused turns which have not been explored yet.

Effect of Differential Geminal Substitution of γ Amino Acid Residues at the (i + 2) Position of αγ Turn Segments on the Conformation of Template β-Hairpin Peptides.

The effect of insertion of three geminally dimethyl substituted γ amino acid residues [γ2,2 (4-amino-2,2-dimethylbutanoic acid), γ3,3 (4-amino-3,3-dimethylbutanoic acid), and γ4,4 (4-amino-4,4-dimethylbutanoic acid)] at the (i + 2) position of a two-residue αγ C12 turn segment in a model octapeptide sequence Leu-Phe-Val-Aib-Xxx-Leu-Phe-Val (where Xxx = γ amino acid residues) has been investigated in this study. Solution conformational studies (NMR, CD, and IR) and ab initio calculations indicated that γ3,3 and γ4,4 residues were well accommodated in the β-hairpin nucleating αγ C12 turns, which gave rise to well-registered hairpins, in contrast to γ2,2, which was unable to form a tight C12 β-hairpin nucleating turn and promote a well-registered β-hairpin. Geminal disubstitution at the Cα carbon in γ2,2 led to unfavorable steric contacts, disabling its accommodation in the αγ C12 hairpin nucleating turn unlike the γ3,3 and γ4,4 residues. Geminal substitutions at different carbons along the backbone constrained backbone torsion angles for the three γ amino acid residues differently, generating diverse conformational preferences in them. Folded hairpins were energetically more stable (∼8 to 9 kcal/mol) than the unfolded peptides. Conformational preference of the peptides was independent of the N-terminal protecting group. Such fundamental understanding will instrumentalize the future directed design of foldamers.

Optimizing the Expression of Human Dopamine Receptors in Escherichia coli.

The human dopamine receptors D2S and D3 belong to the group of G protein-coupled receptors (GPCRs) and are important drug targets. Structural analyses and development of new receptor subtype specific drugs have been impeded by low expression yields or receptor instability. Fusing the T4 lysozyme into the intracellular loop 3 improves crystallization but complicates conformational studies. To circumvent these problems, we expressed the human D2S and D3 receptors in Escherichia coli using different N- and C-terminal fusion proteins and thermostabilizing mutations. We optimized expression times and used radioligand binding assays with whole cells and membrane homogenates to evaluate KD-values and the number of receptors in the cell membrane. We show that the presence but not the type of a C-terminal fusion protein is important. Bacteria expressing receptors capable of ligand binding can be selected using FACS analysis and a fluorescently labeled ligand. Improved receptor variants can thus be generated using error-prone PCR. Subsequent analysis of clones showed the distribution of mutations over the whole gene. Repeated cycles of PCR and FACS can be applied for selecting highly expressing receptor variants with high affinity ligand binding, which in the future can be used for analytical studies.

Computational study of non-conductive selectivity filter conformations and C-type inactivation in a voltage-dependent potassium channel.

C-type inactivation is a time-dependent process of great physiological significance that is observed in a large class of K+ channels. Experimental and computational studies of the pH-activated KcsA channel show that the functional C-type inactivated state, for this channel, is associated with a structural constriction of the selectivity filter at the level of the central glycine residue in the signature sequence, TTV(G)YGD. The structural constriction is allosterically promoted by the wide opening of the intracellular activation gate. However, whether this is a universal mechanism for C-type inactivation has not been established with certainty because similar constricted structures have not been observed for other K+ channels. Seeking to ascertain the general plausibility of the constricted filter conformation, molecular dynamics simulations of a homology model of the pore domain of the voltage-gated potassium channel Shaker were performed. Simulations performed with an open intracellular gate spontaneously resulted in a stable constricted-like filter conformation, providing a plausible nonconductive state responsible for C-type inactivation in the Shaker channel. While there are broad similarities with the constricted structure of KcsA, the hypothetical constricted-like conformation of Shaker also displays some subtle differences. Interestingly, those are recapitulated by the Shaker-like E71V KcsA mutant, suggesting that the residue at this position along the pore helix plays a pivotal role in determining the C-type inactivation behavior. Free energy landscape calculations show that the conductive-to-constricted transition in Shaker is allosterically controlled by the degree of opening of the intracellular activation gate, as observed with the KcsA channel. The behavior of the classic inactivating W434F Shaker mutant is also characterized from a 10-μs MD simulation, revealing that the selectivity filter spontaneously adopts a nonconductive conformation that is constricted at the level of the second glycine in the signature sequence, TTVGY(G)D.

Anharmonic Vibrational Spectrum and Experimental Matrix Isolation Study of Thioformic Acid Conformers—Potential Candidates for Molecular Cloud and Solar System Observations?

Abstract Thioformic acid (TFA) is the sulfur analog of formic acid, the simplest organic acid. It has three analogs, HCOSH, HCSOH, and HCSSH, each of them having two rotational isomeric (rotameric) forms: trans and cis where the trans form is energetically more stable. In this article, we study computational energetics and anharmonic vibrational spectrum of TFA, including overtone and combination vibrations. We also studied experimental photoisomerization and photodecomposition channels of HCOSH molecules with different wavelengths. We suggest that TFA is a potential sulfur-containing candidate molecule for interstellar and planetary observations and discuss these in light of different radiation environments in space. More generally, we discuss that infrared radiation-driven photoisomerization reactions may be a common phenomenon in such environments and can affect the chemical reaction pathways of organic and other interstellar molecules.

Impact of DNA sequences on DNA ‘opening’ by the Rad4/XPC nucleotide excision repair complex

Rad4/XPC recognizes diverse DNA lesions to initiate nucleotide excision repair (NER). However, NER propensities among lesions vary widely and repair-resistant lesions are persistent and thus highly mutagenic. Rad4 recognizes repair-proficient lesions by unwinding (‘opening’) the damaged DNA site. Such ‘opening’ is also observed on a normal DNA sequence containing consecutive C/G’s (CCC/GGG) when tethered to Rad4 to prevent protein diffusion. However, it was unknown if such tethering-facilitated DNA ‘opening’ could occur on any DNA or if certain structures/sequences would resist being ‘opened’. Here, we report that DNA containing alternating C/G’s (CGC/GCG) failed to be opened even when tethered; instead, Rad4 bound in a 180°-reversed manner, capping the DNA end. Fluorescence lifetime studies of DNA conformations in solution showed that CCC/GGG exhibits local pre-melting that is absent in CGC/GCG. In MD simulations, CGC/GCG failed to engage Rad4 to promote ‘opening’ contrary to CCC/GGG. Altogether, our study illustrates how local sequences can impact DNA recognition by Rad4/XPC and how certain DNA sites resist being ‘opened’ even with Rad4 held at that site indefinitely. The contrast between CCC/GGG and CGC/GCG sequences in Rad4-DNA recognition may help decipher a lesion’s mutagenicity in various genomic sequence contexts to explain lesion-determined mutational hot and cold spots.

Conformational stability of cyclopropanecarboxaldehyde is ruled by vibrational effects

Cyclopropanecarboxaldehyde (CPCA) has two main conformers, syn and anti, that are renowned for being very close in energy. The stability order of these two main species is constantly reversed by changing the level of theory or the experimental technique employed in its determination. The anti conformer is predicted to be the most favoured in condensed states of matter, but uncertainty still remains on the relative stability in the gas phase. To gain further insights into this issue, the investigation of the rotational spectrum of both syn- and anti-CPCA has been extended in the 246–294 GHz frequency region and complemented by a detailed computational study of both conformers. A fit incorporating the recorded rotational transitions as well as those reported in the literature led to the accurate determination of the rotational parameters, also including high-order centrifugal distortion constants. Accurately computed vibrational frequencies were used to re-analyse the infrared spectrum of both conformers, thereby allowing a re-assignment of two vibrational bands, namely of anti-CPCA and of the syn conformer. While our state-of-the-art computations favour the anti conformer in the stability order, estimates from analysis of rotational spectra are rather controversial and are strongly affected by several factors, such as the zero-point vibrational correction.

Perturbative and nonperturbative studies of CFTs with MN global symmetry

Fixed points in three dimensions described by conformal field theories with \ensuremath{M N}_{m,n} = O(m)^n\rtimes S_nMNm,n=O(m)n⋊Sn global symmetry have extensive applications in critical phenomena. Associated experimental data for m=n=2m=n=2 suggest the existence of two non-trivial fixed points, while the \varepsilonε expansion predicts only one, resulting in a puzzling state of affairs. A recent numerical conformal bootstrap study has found two kinks for small values of the parameters mm and nn, with critical exponents in good agreement with experimental determinations in the m=n=2m=n=2 case. In this paper we investigate the fate of the corresponding fixed points as we vary the parameters mm and nn. We find that one family of kinks approaches a perturbative limit as mm increases, and using large spin perturbation theory we construct a large mm expansion that fits well with the numerical data. This new expansion, akin to the large NN expansion of critical O(N)O(N) models, is compatible with the fixed point found in the \varepsilonε expansion. For the other family of kinks, we find that it persists only for n=2n=2, where for large mm it approaches a non-perturbative limit with \Delta_\phi\approx 0.75Δϕ≈0.75. We investigate the spectrum in the case \ensuremath{M N}_{100,2}MN100,2 and find consistency with expectations from the lightcone bootstrap.

Conformational study, FT-IR, FT-Raman, solvent effect on UV–Vis, charge transfer and protein–ligand interactions of Methyl-2-pyrazinecarboxylate

The conformational firmness, spectroscopic depiction, molecular (inter- and intra-); and protein–ligand interactions on the organic material Methyl-2-pyrazinecarboxylate (M2PC) are performed with speculative quantum chemical computations. The experimental FT-IR, FT-Raman bands are compared with the ascended theoretical wavenumbers of M2PC and assigned expending the potential energy distribution analysis. The conformational stability of syn and anti-conformers and the molecular geometry of M2PC was optimized by DFT/B3LYP/6–311++G (d, p) as a basis set. The UV–Vis spectra of the M2PC in different solvents have been simulated and projected with TD-DFT/B3LYP/6–311++G (d, p) level of theory. The orbital contributions of molecule were deliberated by DOS and PDOS. The determined HOMO-LUMO energies reveal that charge transfer interactions are occurring between the molecules. Molecular composition, reactivity of the molecule were obtained by topology analyses. The nucleophilic and electrophilic spots were acknowledged by expending the MEP, Mulliken charges, and Fukui's function. NBO analysis subsidizes the reliability of molecule impending from hyper conjugative interactions. Into the effort, the biological activities of M2PC were investigated by molecular docking analysis. The binding affinity shows that M2PC could have a great impact on binding the protein to exhibit the cerebral anti-ischemia inhibition.

Computer-Assisted Conformational Analysis of Small Molecules Using VEGA ZZ, a Freely Available Software Program, as an Introduction to Molecular Modeling

We report a molecular modeling study for undergraduate students aimed at carrying out an analysis of small molecules using a systematic conformational search with VEGA ZZ, a freely available software program. Conformational analyses were performed using a systematic search based on variations of torsion angles. First, the conformations of n-butane were characterized from its energetic diagram, showing the anti/gauche conformations as well as the unfavorable eclipsed conformations. A similar conformation analysis of buta-1,3-diene illustrated the mesomeric effect, leading to the preferential s-cis/s-trans conformations. Then, using the same approach, the conformational study of ethane-1,2-diol gave access to conformations with an intramolecular hydrogen bond. Another example of conformational analysis was the investigation of a cyclic acetal, in chair conformation, showing a preferential conformation with the equatorial substituent, rather than the axial substituent that results from unfavorable 1,3-diaxial interactions. Finally, a study of the amino acid derivative N-acetyl-N′-methyl-l-alanylamide revealed the planar amide functional group. For this example, the analysis, again using the systematic conformational search, was based on the variation of φ/ψ torsion angles, exemplifying these important angles in protein conformations.

Synthesis, Characterization, Antioxidant Activity and Conformational Study of 4-Hydroxychalcone

The objective of this work was to develop a synthesis, characterization, and conformational study of 4-hydroxychalcone. The chalcone was obtained using Claisen-Schmidt reaction. The product was characterized by IR and NMR spectroscopy. The latter technique was extremely important to verify the presence of the vinyl double bond formed in the reaction and to determine its trans configuration. The antioxidant activity of 4-hydroxychalcone showed a satisfactory result when compared to antioxidants already reported in the literature, with 63.4% inhibition of the DPPH radical. Also, theoretical calculations were performed to determine conformational preference. The s-cis (b) (52.0%) and the s-cis (a) (35.0%) conformers showed less energy when compared to s-trans conformers, due to the higher stabilizing effect of electron delocalization involving the p orbitals resulting from the higher planarity of s-cis conformers. However, the s-cis (a) conformer showed greater stabilization energy (510.37 kcal mol-1) in relation to the s-cis (b) conformer (505.32 kcal mol-1), this fact might be explained by the hydroxyl group interaction with the aromatic ring B, as observed by the NBO calculations. DOI: http://dx.doi.org/10.17807/orbital.v13i2.1485

Electronic Structure and Bistable Conformational Study of the Tetraphenylporphyrin Erbium(III) Acetylacetonate Complex on the CaF2/Si(100) Surface at Low Temperatures

The synthesis of tetraphenylporphyrin erbium(III) acetylacetonate (acac) complexes is realized and their properties studied at the nanoscale when adsorbed on a semi-insulating CaF 2 /Si(100) surface. Our findings reveal that the ErTPP-(acac) molecules can adsorb in two main on-site conformations. Following precisely located dI/dV measurements at various specific positions [phenyls, pyrroles, and Er-(acac)], the relative locations of the Er cation and the apical ligand (acac) can be deciphered for each observed conformation. Hence, one of the adsorbate conformations presents the acac ligand parallel to the porphyrin plane with the Er atom outside the macrocycle plane. The second conformation is related to what is known in the gas phase, where the acac ligand is oriented vertically on top of the Er atom. This work is combined with a theoretical investigation that uses density functional theory methods to bring into light details of the two observed conformations. Additional proofs of our discoveries are related to the vibrational excitations of ErTPP-(acac). A comparison with a theoretical estimation of the vibrational modes reveals how the electronic resonance near the valence-band edge of the insulting layer is suitable to distinguish between the two adsorbed conformations.

Solvent Exposure and Ionic Condensation Drive Fuzzy Dimerization of Disordered Heterochromatin Protein Sequence.

Proteins with low complexity, disordered sequences are receiving increasing attention due to their central roles in the biogenesis and regulation of membraneless organelles. In eukaryotic organisms, a substantial fraction of disordered proteins reside in the nucleus, thereby facilitating the formation of nuclear bodies, nucleolus, and chromatin compartmentalization. The heterochromatin family of proteins (HP1) is an important player in driving the formation of gene silenced mesoscopic heterochromatin B compartments and pericentric regions. Recent experiments have shown that the HP1a sequence of Drosophila melanogaster can undergo liquid-liquid phase separation under both in vitro and in vivo conditions, induced by changes of the monovalent salt concentration. While the phase separation of HP1a is thought to be the mechanism underlying chromatin compartmentalization, the molecular level mechanistic picture of salt-driven phase separation of HP1a has remained poorly understood. The disordered hinge region of HP1a is seen as the driver of salt-induced condensation because of its charge enriched sequence and post-translational modifications. Here, we set out to decipher the mechanisms of salt-induced condensation of HP1a through a systematic study of salt-dependent conformations of single chains and fuzzy dimers of disordered HP1a hinge sequences. Using multiple independent all-atom simulations with and without enhanced sampling, we carry out detailed characterization of conformational ensembles of disordered HP1a chains under different ionic conditions using various polymeric and structural measures. We show that the mobile ion release, enhancement of local transient secondary structural elements, and side-chain exposure to solvent are robust trends that accompany fuzzy dimer formation. Furthermore, we find that salt-induced changes in the ensemble of conformations of HP1a disordered hinge sequence fine-tune the inter-chain vs. self-chain interactions in ways that favor fuzzy dimer formation under low salt conditions in the agreement with condensation trends seen in experiments.

Interpretations on the Interaction between Protein Tyrosine Phosphatase and E7 Oncoproteins of High and Low-Risk HPV: A Computational Perception.

The most prevalent and common sexually transmitted infection is caused by human papillomavirus (HPV) among sexually active women. Numerous genotypes of HPV are available, among which the major oncoproteins E6 and E7 lead to the progression of cervical cancer. The E7 oncoprotein interacts with cytoplasmic tumor suppressor protein PTPN14, which is the key regulator of cellular growth control pathways effecting the reduction of steady-state level. Disrupting the interaction between the tumor suppressor and the oncoprotein is vital to cease the development of cancer. Hence, the mechanism of interaction between E7 and tumor suppressor is explored through protein–protein and protein–ligand binding along with the conformational stability studies. The obtained results state that the LXCXE domain of HPV E7 of high and low risks binds with the tumor suppressor protein. Also, the small molecules bind in the interface of E7–PTPN14 that disrupts the interaction between the tumor suppressor and oncoprotein. These results were further supported by the dynamics simulation stating the stability over the bounded complex and the energy maintained during postdocking as well as postdynamics calculations. These observations possess an avenue in the drug discovery that leads to further validation and also proposes a potent drug candidate to treat cervical cancer caused by HPV.

Poincare–Einstein approach to Penrose’s conformal cyclic cosmology * *Dedicated to C Robin Graham for the occasion of his 65th birthday.

We consider two consecutive eons in Penrose’s conformal cyclic cosmology and study how the matter content of the past eon determines the matter content of the present eon by means of the reciprocity hypothesis of Roger Penrose. We assume that the only matter content in the final stages of the past eon is a spherical wave described by Einstein’s equations with a pure radiation energy momentum tensor and with a cosmological constant. Using the Poincare-Einstein type of expansion to determine the metric in the past eon, applying the reciprocity hypothesis to get the metric in the present eon, and using the Einstein equations in the present eon to interpret its matter content, we show that the single spherical wave from the previous eon in the new eon splits into three portions of radiation: the two spherical waves, one which is a damped continuation from the previous eon, the other is focusing in the new eon as it encountered a mirror at the Big Bang surface, and in addition a lump of scattered radiation described by the statistical physics.

Guest-Mediated Reversal of the Tumbling Process in Phosphorus-Dendritic Compounds Containing β-Cyclodextrin Units: An NMR Study.

The conformational study of dendritic platforms containing multiple β-cyclodextrin (βCD) units in the periphery is relevant to determine the availability of βCD cavities for the formation of inclusion complexes in aqueous biological systems. In this work, we performed a detailed conformational analysis in D2O, via 1D and 2D NMR spectroscopy of a novel class of phosphorus dendritic compounds of the type P3N3-[O-C6H4-O-(CH2)n-βCD]6 (where n = 3 or 4). We unambiguously demonstrated that a functionalized glucopyranose unit of at least one βCD unit undergoes a 360° tumbling process, resulting in a deep inclusion of the spacer that binds the cyclodextrin to the phosphorus core inside the cavity, consequently limiting the availability of the inner cavities. In addition, we confirmed through NMR titrations that this tumbling phenomenon can be reversed for all βCD host units using a high-affinity guest, namely 1-adamantanecarboxylic acid (AdCOOH). Our findings have demonstrated that it is possible to create a wide variety of multi-functional dendritic platforms.

Conformational dynamics of 13 amino acids long NSP11 of SARS-CoV-2 under membrane mimetics and different solvent conditions

The intrinsically disordered proteins/regions (IDPs/IDPRs) are known to be responsible for multiple cellular processes and are associated with many chronic diseases. In viruses, the existence of a disordered proteome is also proven and is related to its conformational dynamics inside the host. The SARS-CoV-2 has a large proteome, in which, structure and functions of all proteins are not known yet, along with non-structural protein 11 (nsp11). In this study, we have performed extensive experimentation on nsp11. Our results based on the CD spectroscopy gives characteristic disordered spectrum for IDPs. Further, we investigated the conformational behavior of nsp11 in the presence of membrane mimetic environment, α-helix inducer, and natural osmolyte. In the presence of negatively charged and neutral liposomes, nsp11 remains disordered. However, with SDS micelle, it adopted an α-helical conformation, suggesting the helical propensity of nsp11. Finally, we again confirmed the IDP behavior of nsp11 using MD simulations. In future, this conformational dynamic study could help to clarify its functional importance in SARS-CoV-2 infection.