Minor Conformer Research Articles

Synthesis of Flake-shaped [3]Cyclo-4,6-dibenzofuranylene

The cyclic trimer of dibenzofuran linked at the 4,6-positions, named [3]cyclo-4,6-dibenzofuranylene, was synthesized by Ni(0)-mediated reductive coupling of 4,6-dibromodibenzofuran. DFT calculation indicated that the flake-shaped C2 symmetric structure is the most stable conformer and the propeller-shaped D3 symmetric structure is the minor conformer with a higher energy (+19.1 kcal mol−1). The calculated inversion energy of the C2 conformer through a Cs symmetric transition state was +4.1 kcal mol−1, showing rapid fluctuation, which is consistent with the observation of only one set of 1H NMR signals of dibenzofuran of [3]cyclo-4,6-dibenzofuranylene.

Unusual zinc-binding mode of HDAC6-selective hydroxamate inhibitors

Histone deacetylases (HDACs) regulate myriad cellular processes by catalyzing the hydrolysis of acetyl-l-lysine residues in histone and nonhistone proteins. The Zn2+-dependent class IIb enzyme HDAC6 regulates microtubule function by deacetylating α-tubulin, which suppresses microtubule dynamics and leads to cell cycle arrest and apoptosis. Accordingly, HDAC6 is a target for the development of selective inhibitors that might be useful in new therapeutic approaches for the treatment of cancer, neurodegenerative diseases, and other disorders. Here, we present high-resolution structures of catalytic domain 2 from Danio rerio HDAC6 (henceforth simply "HDAC6") complexed with compounds that selectively inhibit HDAC6 while maintaining nanomolar inhibitory potency: N-hydroxy-4-[(N(2-hydroxyethyl)-2-phenylacetamido)methyl)-benzamide)] (HPB), ACY-1215 (Ricolinostat), and ACY-1083. These structures reveal that an unusual monodentate Zn2+ coordination mode is exploited by sterically bulky HDAC6-selective phenylhydroxamate inhibitors. We additionally report the ultrahigh-resolution structure of the HDAC6-trichostatin A complex, which reveals two Zn2+-binding conformers for the inhibitor: a major conformer (70%) with canonical bidentate hydroxamate-Zn2+ coordination geometry and a minor conformer (30%) with monodentate hydroxamate-Zn2+ coordination geometry, reflecting a free energy difference of only 0.5 kcal/mol. The minor conformer is not visible in lower resolution structure determinations. Structural comparisons of HDAC6-inhibitor complexes with class I HDACs suggest active site features that contribute to the isozyme selectivity observed in biochemical assays.

15N CEST data and traditional model-free analysis capture fast internal dynamics of DJ-1

Previous studies have shown that relaxation parameters and fast protein dynamics can be quickly elucidated from 15N-CEST experiments [1]. Longitudinal R1 and transverse R2 values were reliably derived from fitting of CEST profiles. Herein we show that 15N-CEST experiments and traditional modelfree analysis provide the internal dynamics of three states of human protein DJ-1 at physiological temperature. The chemical exchange profiles show the absence of a minor state conformation and, in conjunction with 1H-15N NOEs, show increased mobility. R1 and R2 values remained relatively unchanged at the three naturally occurring oxidation states of DJ-1, but exhibit striking NOE differences. The NOE data was, therefore, essential in determining the internal motions of the DJ-1 proteins. To the authors' knowledge, we present the first study that combines 15N CEST data with traditional model-free analyses in the study of a biological system and affirm that more ‘lean’ model-free approaches should be used cautiously.

Direct observation of conformational population shifts in crystalline human hemoglobin

Although X-ray crystallography is the most commonly used technique for studying the molecular structure of proteins, it is not generally able to monitor the dynamic changes or global domain motions that often underlie allostery. These motions often prevent crystal growth or reduce crystal order. We have recently discovered a crystal form of human hemoglobin that contains three protein molecules allowed to express a full range of quaternary structures, whereas maintaining strong X-ray diffraction. Here we use this crystal form to investigate the effects of two allosteric effectors, phosphate and bezafibrate, by tracking the structures and functions of the three hemoglobin molecules following the addition of each effector. The X-ray analysis shows that the addition of either phosphate or bezafibrate not only induces conformational changes in a direction from a relaxed-state to a tense-state, but also within relaxed-state populations. The microspectrophotometric O2 equilibrium measurements on the crystals demonstrate that the binding of each effector energetically stabilizes the lowest affinity conformer more strongly than the intermediate affinity one, thereby reducing the O2 affinity of tense-state populations, and that the addition of bezafibrate causes an ∼5-fold decrease in the O2 affinity of relaxed-state populations. These results show that the allosteric pathway of hemoglobin involves shifts of populations rather than a unidirectional conversion of one quaternary structure to another, and that minor conformers of hemoglobin may have a disproportionate effect on the overall O2 affinity.

A Crystalline π-Stack Containing Five Stereoisomers: Insights into Conformational Isomorphism, Chirality Inversion, and Disorder.

An unprecedented crystal-packing arrangement of a tetramethoxy-bay-substituted perylene bisimide (PBI) consists of three crystallographically independent molecules, that is, an achiral (AC) PBI of saddle-shaped geometry along with two pairs of propeller-like twisted (P)- and (M)-enantiomeric PBI frameworks. All these five conformations are observed within a single π-stack revealing an intriguing packing sequence with an inversion of chirality from P to M via AC. Nudged elastic band calculations for the isolated molecule show that AC is a local minimum of the P to M interconversion path. In addition, two minor conformations were observed in the crystal, one of which resembles a transition-state molecule. Theoretical studies of dimeric and trimeric stacks reveal that the coexistence of all these structures in the crystal lattice is aided by the strong dispersion interactions between PBI cores and perfectly interdigitated dodecyl chains which stabilize energetically higher conformations.

A Crystalline π‐Stack Containing Five Stereoisomers: Insights into Conformational Isomorphism, Chirality Inversion, and Disorder

AbstractAn unprecedented crystal‐packing arrangement of a tetramethoxy‐bay‐substituted perylene bisimide (PBI) consists of three crystallographically independent molecules, that is, an achiral (AC) PBI of saddle‐shaped geometry along with two pairs of propeller‐like twisted (P)‐ and (M)‐enantiomeric PBI frameworks. All these five conformations are observed within a single π‐stack revealing an intriguing packing sequence with an inversion of chirality from P to M via AC. Nudged elastic band calculations for the isolated molecule show that AC is a local minimum of the P to M interconversion path. In addition, two minor conformations were observed in the crystal, one of which resembles a transition‐state molecule. Theoretical studies of dimeric and trimeric stacks reveal that the coexistence of all these structures in the crystal lattice is aided by the strong dispersion interactions between PBI cores and perfectly interdigitated dodecyl chains which stabilize energetically higher conformations.

Conformational Changes in 5-Methoxyindole: Effects of Thermal, Vibrational, and Electronic Excitations

The molecule of 5-methoxyindole (5MOI) may adopt two conformational states, syn and anti, with respect to the relative orientation of the NH and OCH3 groups. The structure of monomeric 5MOI was characterized spectroscopically, in mid- and near-infrared domains. The conformational composition of 5MOI could be controlled in three different ways. Thermally, two conformers of 5MOI could be trapped in xenon matrixes at 16 K. Upon annealing the xenon matrix to temperatures about 30-40 K, the higher-energy syn form converted to the ground-state anti conformer. Vibrational excitations in the near-infrared domain, at the frequency of the first NH stretching overtone, 6853 cm-1, afforded the inverse conformational transformation, and a part of the anti conformer was upconverted to the syn form. Electronic excitations in the UV domain, at 315-310 nm, resulted in a total consumption of the syn form again, in favor of anti. Upon further irradiations at 308 nm, a partial repopulation of the syn form, at the expense of anti, was observed. We propose a mechanistic explanation of the observed transformations, which is based on computations of the vibrational spectra of the two conformers and also on computations of the ground state S0 and the first excited state S1 potential energy surfaces along the coordinate for conformational isomerization. The highlights of the present work are the first experimental observation of the minor syn conformer of 5MOI, evidence of the long-range vibrational energy transfer resulting in conformational isomerization upon excitation of the NH stretching overtone, and the possibility of partial conformational control of 5MOI by using electronic excitations.

Separating Dipolar and Chemical Exchange Magnetization Transfer Processes in 1H‐CEST

An amide 1 H-Chemical Exchange Saturation Transfer (CEST) experiment is presented for studies of conformational exchange in proteins. The approach, exploiting spin-state-selective magnetization transfer, completely suppresses undesired NOE-based dips in CEST profiles so that chemical exchange processes can be studied. The methodology is demonstrated with applications involving proteins that interconvert on the millisecond timescale between major and invisible minor states, and accurate amide 1 H chemical shifts of the minor conformer are obtained in each case. The spin-state-selective magnetization transfer approach offers unique possibilities for quantitative studies of protein exchange through 1 H-CEST.

Separating Dipolar and Chemical Exchange Magnetization Transfer Processes in 1H‐CEST

AbstractAn amide 1H‐Chemical Exchange Saturation Transfer (CEST) experiment is presented for studies of conformational exchange in proteins. The approach, exploiting spin‐state‐selective magnetization transfer, completely suppresses undesired NOE‐based dips in CEST profiles so that chemical exchange processes can be studied. The methodology is demonstrated with applications involving proteins that interconvert on the millisecond timescale between major and invisible minor states, and accurate amide 1H chemical shifts of the minor conformer are obtained in each case. The spin‐state‐selective magnetization transfer approach offers unique possibilities for quantitative studies of protein exchange through 1H‐CEST.

Effect of low-temperature argon matrices on the IR spectra and structure of flexible N-acetylglycine molecules

A study of how the matrix environment impacts the structure and IR spectra of N-acetylglycine conformers. The conformational composition of this compound is determined according to an analysis of the FTIR spectra of N-acetylglycine isolated in low temperature argon matrices. Bands of three N-acetylglycine conformers are identified based on the spectra: one major and two minor. The structure of all observed conformers is stabilized by different intramolecular hydrogen bonds. The Gibbs free energies of the conformers were calculated (CCSD(T)/CBS method), and these energy values were used to calculate conformer population at a temperature of 360 K, of which 85.3% belonged to the main conformer, and 9.6% and 5.1% to the minor conformers. We also determined the size and shape of the cavities that form when the N-acetylglycine conformers are embedded in the argon crystal during matrix deposition. It is established that the most energetically favorable cavity for the planar main conformer is the cavity that forms when 7 argon atoms are replaced. At the same time, bulky minor conformers were embedded into cavities that correspond to 8 removed argon atoms. We calculated the complexation energy between argon clusters and conformers, and the deformation energy of the argon crystal and the N-acetylglycine conformers. The matrix-induced shifts to the conformer oscillation frequency are calculated.

Monoclinic-to-orthorhombic phase transition of the hexamethylenetetramine-2-methylbenzoic acid (1/2) cocrystal with temperature-dependent dynamic molecular disorder.

As a function of temperature, the hexamethylenetetramine-2-methylbenzoic acid (1/2) cocrystal, C6H12N4·2C8H8O2, undergoes a reversible structural phase transition. The orthorhombic high-temperature phase in the space group Pccn has been studied in the temperature range between 165 and 300 K. At 164 K, a t2 phase transition to the monoclinic subgroup P21/c space group occurs; the resulting twinned low-temperature phase was investigated in the temperature range between 164 and 100 K. The domains in the pseudomerohedral twin are related by a twofold rotation corresponding to the matrix (100/0-10/00-1. Systematic absence violations represent a sensitive criterium for the decision about the correct space-group assignment at each temperature. The fractional volume contributions of the minor twin domain in the low-temperature phase increases in the order 0.259 (2) → 0.318 (2) → 0.336 (2) → 0.341 (3) as the temperature increases in the order 150 → 160 → 163 → 164 K. The transformation occurs between the nonpolar point group mmm and the nonpolar point group 2/m, and corresponds to a ferroelastic transition or to a t2 structural phase transition. The asymmetric unit of the low-temperature phase consists of two hexamethylenetetramine molecules and four molecules of 2-methylbenzoic acid; it is smaller by a factor of 2 in the high-temperature phase and contains two half molecules of hexamethylenetetramine, which sit across twofold axes, and two molecules of the organic acid. In both phases, the hexamethylenetetramine residue and two benzoic acid molecules form a three-molecule aggregate; the low-temperature phase contains two of these aggregates in general positions, whereas they are situated on a crystallographic twofold axis in the high-temperature phase. In both phases, one of these three-molecule aggregates is disordered. For this disordered unit, the ratio between the major and minor conformer increases upon cooling from 0.567 (7):0.433 (7) at 170 K via 0.674 (6):0.326 (6) and 0.808 (5):0.192 (5) at 160 K to 0.803 (6):0.197 (6) and 0.900 (4):0.100 (4) at 150 K, indicating temperature-dependent dynamic molecular disorder. Even upon further cooling to 100 K, the disorder is retained in principle, albeit with very low site occupancies for the minor conformer.

Complete NMR assignment and conformational analysis of 17-α-ethinylestradiol by using RDCs obtained in grafted graphene oxide.

The 1 H and 13 C NMR spectra of 17-α-ethinylestradiol (EE2), a well-known contraceptive, including diastereotopic methylene groups, were fully assigned with the help of residual dipolar couplings (RDC) measured in the recently developed grafted graphene oxide orienting medium. RDC analysis, which included all 1 DCH couplings and the long-range 2 DCH1 H-C≡13 C coupling, also pointed to the presence of a minor conformation arising from pseudo-rotation of the steroid B ring. Saturation-transfer difference (STD) measurements revealed that the most likely interaction between EE2 and orienting medium occurred on the C and D ring. Copyright © 2016 John Wiley & Sons, Ltd.

DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions.

Binding-induced conformational changes of a protein at regions distant from the binding site may play crucial roles in protein function and regulation. The p53 tumour suppressor is an example of such an allosterically regulated protein. Little is known, however, about how DNA binding can affect distal sites for transcription factors. Furthermore, the molecular details of how a local perturbation is transmitted through a protein structure are generally elusive and occur on timescales hard to explore by simulations. Thus, we employed state-of-the-art enhanced sampling atomistic simulations to unveil DNA-induced effects on p53 structure and dynamics that modulate the recruitment of cofactors and the impact of phosphorylation at Ser215. We show that DNA interaction promotes a conformational change in a region 3 nm away from the DNA binding site. Specifically, binding to DNA increases the population of an occluded minor state at this distal site by more than 4-fold, whereas phosphorylation traps the protein in its major state. In the minor conformation, the interface of p53 that binds biological partners related to p53 transcription-independent functions is not accessible. Significantly, our study reveals a mechanism of DNA-mediated protection of p53 from interactions with partners involved in the p53 transcription-independent signalling. This also suggests that conformational dynamics is tightly related to p53 signalling.

Mapping transiently formed and sparsely populated conformations on a complex energy landscape.

Determining the structures, kinetics, thermodynamics and mechanisms that underlie conformational exchange processes in proteins remains extremely difficult. Only in favourable cases is it possible to provide atomic-level descriptions of sparsely populated and transiently formed alternative conformations. Here we benchmark the ability of enhanced-sampling molecular dynamics simulations to determine the free energy landscape of the L99A cavity mutant of T4 lysozyme. We find that the simulations capture key properties previously measured by NMR relaxation dispersion methods including the structure of a minor conformation, the kinetics and thermodynamics of conformational exchange, and the effect of mutations. We discover a new tunnel that involves the transient exposure towards the solvent of an internal cavity, and show it to be relevant for ligand escape. Together, our results provide a comprehensive view of the structural landscape of a protein, and point forward to studies of conformational exchange in systems that are less characterized experimentally.

A novel lipid transfer protein from the pea Pisum sativum: isolation, recombinant expression, solution structure, antifungal activity, lipid binding, and allergenic properties.

BackgroundPlant lipid transfer proteins (LTPs) assemble a family of small (7–9 kDa) ubiquitous cationic proteins with an ability to bind and transport lipids as well as participate in various physiological processes including defense against phytopathogens. They also form one of the most clinically relevant classes of plant allergens. Nothing is known to date about correlation between lipid-binding and IgE-binding properties of LTPs. The garden pea Pisum sativum is widely consumed crop and important allergenic specie of the legume family. This work is aimed at isolation of a novel LTP from pea seeds and characterization of its structural, functional, and allergenic properties.ResultsThree novel lipid transfer proteins, designated as Ps-LTP1-3, were found in the garden pea Pisum sativum, their cDNA sequences were determined, and mRNA expression levels of all the three proteins were measured at different pea organs. Ps-LTP1 was isolated for the first time from the pea seeds, and its complete amino acid sequence was determined. The protein exhibits antifungal activity and is a membrane-active compound that causes a leakage from artificial liposomes. The protein binds various lipids including bioactive jasmonic acid. Spatial structure of the recombinant uniformly 13C,15N-labelled Ps-LTP1 was solved by heteronuclear NMR spectroscopy. In solution the unliganded protein represents the mixture of two conformers (relative populations ~ 85:15) which are interconnected by exchange process with characteristic time ~ 100 ms. Hydrophobic residues of major conformer form a relatively large internal tunnel-like lipid-binding cavity (van der Waals volume comes up to ~1000 Å3). The minor conformer probably corresponds to the protein with the partially collapsed internal cavity.ConclusionsFor the first time conformational heterogeneity in solution was shown for an unliganded plant lipid transfer protein. Heat denaturation profile and simulated gastrointestinal digestion assay showed that Ps-LTP1 displayed a high thermal and digestive proteolytic resistance proper for food allergens. The reported structural and immunological findings seem to describe Ps-LTP1 as potential cross-reactive allergen in LTP-sensitized patients, mostly Pru p 3+ ones. Similarly to allergenic LTPs the potential IgE-binding epitope of Ps-LTP1 is located near the proposed entrance into internal cavity and could be involved in lipid-binding.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0792-6) contains supplementary material, which is available to authorized users.

Single-Point Remote Control of Flapping Motion in Clothespin-Shaped Bimetallic Palladium Complexes Based on the N(sp(2))-N(sp(3)) Interconversion in Amide Functionalities.

The synthesis, structure, and flapping motion of clothespin-shaped binuclear trans-bis(salicylaldiminato)palladium(II) complexes (anti-1) with 4-azaheptamethylene linkers bearing amide (a-g), urethane (h), or urea (i) functionalities are described in this report. Various 2D (1)H NMR experiments and XRD analyses indicate that the amide- and urethane-linked anti-1 a,b,d-h complexes exist as equilibrated mixtures of major and minor conformers I and II in CDCl3, whereas the complexes anti-1 c and i were observed as a single species. The mapping of NOESY cross-peaks between conformers I and II revealed that the equilibration of the major and minor conformers of anti-1 a,b,d-h proceeds by two pathways, namely a nonrotatory flapping motion of the coordinated blades and a nonflapping rotation of C-N bonds, whereas the equilibration of anti-1 c proceeds by simultaneous flapping and rotation motions. Kinetic studies carried out by means of (1)H-(1)H EXSY experiments revealed that 1) the ΔG(≠) 298K values for the flapping motion are controlled remotely by the steric and electronic effects of the RCON functionalities and 2) the activation parameters for the nonrotatory flapping process are identical to those for the nonflapping peptide rotation in the complexes anti-1 a,b,d-h, which indicates that the present multistep conformational transformation induced by the flapping motion is controlled by the rate-determining pyramidalization/depyramidalization (i.e., sp(2)/sp(3) interconversion) of the nitrogen atoms of the functionalities. The static and controllable molecular mobility of anti-1 bearing peptide linkers has been discussed by comparison with the dynamic behavior of its analogues anti-2-4 with flexible polymethylene linkers.

Implication of Natural Polymorphism in Hinge Region of HIV-1 Protease on Protein Conformations, Local Structures and Backbone Dynamics

HIV-1 protease (PR) serves as an important drug target because its inhibition generates immature non-infectious virions. However, drug-pressure selected mutations, along with natural polymorphisms, can lead to drug resistance to HIV-1 protease inhibitors (PIs), which change the drug binding configuration and equilibrium protease conformational sampling. As was suggested in our previous study, (1) a new protease conformation, curled-open, was identified in constructs carrying natural polymorphisms including E35D, and consequently, these constructs displayed higher protein backbone dynamics compared with wild-type subtype B construct characterized by nuclear magnetic resonance (NMR) spectroscopy. In the present work, we discuss the impact of the single E35D natural polymorphism on generating a minor protease conformation (curled-open), and consequently, influencing the protein structure and dynamics. The combined results from Double electron-electron resonance (DEER), NMR spectroscopy and X-ray crystallography structures provide a possible structural mechanism for altered conformational dynamics.

Conformation-specific spectroscopy of capped, gas-phase Aib oligomers: tests of the Aib residue as a 310-helix former.

The conformational preferences of a series of capped peptides containing the helicogenic amino acid aminoisobutyric acid (Aib) (Z-Aib-OH, Z-(Aib)2-OMe, and Z-(Aib)4-OMe) are studied in the gas phase under expansion-cooled conditions. Aib oligomers are known to form 310-helical secondary structures in solution and in the solid phase. However, in the gas phase, accumulation of a macrodipole as the helix grows could inhibit helix stabilization. Implementing single-conformation IR spectroscopy in the NH stretch region, Z-Aib-OH and Z-(Aib)2-OMe are both observed to have minor conformations that exhibit dihedral angles consistent with the 310-helical portion of the Ramachandran map (ϕ, ψ = -57°, -30°), even though they lack sufficient backbone length to form 10-membered rings which are a hallmark of the developed 310-helix. For Z-(Aib)4-OMe three conformers are observed in the gas phase. Single-conformation infrared spectroscopy in both the NH stretch (Amide A) and C[double bond, length as m-dash]O stretch (Amide I) regions identifies the main conformer as an incipient 310-helix, having two free NH groups and two C10 H-bonded NH groups, labeled an F-F-10-10 structure, with a calculated dipole moment of 13.7 D. A second minor conformer has an infrared spectrum characteristic of an F-F-10-7 structure in which the third and fourth Aib residues have ϕ, ψ = 75°, -74° and -52°, 143°, Ramachandran angles which fall outside of the typical range for 310-helices, and a dipole moment that shrinks to 5.4 D. These results show Aib to be a 310-helix former in the gas phase at the earliest stages of oligomer growth.

Small molecule regulated dynamic structural changes of human G-quadruplexes.

The changes in structure and dynamics of oncogenic (c-MYC) and telomeric (h-TELO) G-rich DNA sequences due to the binding of a novel carbazole derivative (BTC) are elucidated using single-molecule Förster resonance energy transfer (sm-FRET), fluorescence correlation spectroscopy (FCS) and NMR spectroscopy. In contrast to the previous reports on the binding of ligands to pre-folded G-quadruplexes, this work illustrates how ligand binding changes the conformational equilibria of both unstructured G-rich DNA sequences and K+-folded G-quadruplexes. The results demonstrate that K+ free c-MYC and h-TELO exist as unfolded and partially folded conformations. The binding of BTC shifts the equilibria of both investigated DNA sequences towards the folded G-quadruplex structure, increases the diffusion coefficients and induces faster end-to-end contact formation. BTC recognizes a minor conformation of the c-MYC quadruplex and the two-tetrad basket conformations of the h-TELO quadruplex.

Conformational Selection in a Protein-Protein Interaction Revealed by Dynamic Pathway Analysis.

Molecular recognition plays a central role in biology, and protein dynamics has been acknowledged to be important in this process. However, it is highly debated whether conformational changes happen before ligand binding to produce a binding-competent state (conformational selection) or are caused in response to ligand binding (induced fit). Proposals for both mechanisms in protein/protein recognition have been primarily based on structural arguments. However, the distinction between them is a question of the probabilities of going via these two opposing pathways. Here, we present a direct demonstration of exclusive conformational selection in protein/protein recognition by measuring the flux for rhodopsin kinase binding to its regulator recoverin, an important molecular recognition in the vision system. Using nuclear magnetic resonance (NMR) spectroscopy, stopped-flow kinetics, and isothermal titration calorimetry, we show that recoverin populates a minor conformation in solution that exposes a hydrophobic binding pocket responsible for binding rhodopsin kinase. Protein dynamics in free recoverin limits the overall rate of binding.