Preferred Solution Conformation Research Articles

Two Structures of a λ Cro Variant Highlight Dimer Flexibility but Disfavor Major Dimer Distortions upon Specific Binding of Cognate DNA

Previously reported crystal structures of free and DNA-bound dimers of λ Cro differ strongly (about 4 Å backbone rmsd), suggesting both flexibility of the dimer interface and induced-fit protein structure changes caused by sequence-specific DNA binding. Here, we present two crystal structures, in space groups P3 221 and C2 at 1.35 and 1.40 Å resolution, respectively, of a variant of λ Cro with three mutations in its recognition helix (Q27P/A29S/K32Q, or PSQ for short). One dimer structure ( P3 221; PSQ form 1) resembles the DNA-bound wild-type Cro dimer (1.0 Å backbone rmsd), while the other ( C2; PSQ form 2) resembles neither unbound (3.6 Å) nor bound (2.4 Å) wild-type Cro. Both PSQ form 2 and unbound wild-type dimer crystals have a similar interdimer β-sheet interaction between the β1 strands at the edges of the dimer. In the former, an infinite, open β-structure along one crystal axis results, while in the latter, a closed tetrameric barrel is formed. Neither the DNA-bound wild-type structure nor PSQ form 1 contains these interdimer interactions. We propose that β-sheet superstructures resulting from crystal contact interactions distort Cro dimers from their preferred solution conformation, which actually resembles the DNA-bound structure. These results highlight the remarkable flexibility of λ Cro but also suggest that sequence-specific DNA binding may not induce large changes in the protein structure.

Conformational Analysis of TOAC‐Labelled Alamethicin F50/5 Analogues

In the preceding paper in this issue, we reported the total syntheses in solution of a set of four TOAC-containing analogues of the [L-Glu(OMe)(7,18,19)] F50/5 component of alamethicin, the prototype of peptaibol antibiotics forming channels in the biological membranes. In this article, we have expanded this work to the examination of their preferred conformation in solution by use of a combination of CD, FT-IR absorption, and NMR spectroscopies. The results are strongly in favor of the view that replacement of the Aib residues at positions 1, 8, and 16 with TOAC (both are members of the helicogenic sub-class of C(alpha)-tetrasubstituted alpha-amino acids) does not significantly affect the overwhelmingly populated alpha-helical 3D structure of alamethicin. The X-ray diffraction crystal structure of the N(alpha)-protected, C-terminal, hexapeptide amide segment Z-L-Pro-L-Val-(Aib)(2)-[L-Glu(OMe)](2)-Fol lends further support to our conformational conclusions.

Synthesis and structure of environmentally relevant perfluorinated sulfonamides

Alkylated perfluorooctanesulfonamides are compounds of environmental concern. To make these compounds available for environmental and toxicological studies, a series of N-alkylated perfluorooctanesulfonamides and structurally related compounds were synthesized by reaction of the corresponding perfluoroalkanesulfonyl fluoride with a suitable primary or secondary amine. Perfluoroalkanesulfonamidoethanols were obtained from the N-alkyl perfluoroalkanesulfonamides either by direct alkylation with bromoethanol or alkylation with acetic acid 2-bromo-ethyl ester followed by hydrolysis of the acetate. N-Alkyl perfluorooctanesulfonamidoacetates were synthesized in an analogous way by alkylation of N-alkyl perfluoroalkanesulfonamides with a bromo acetic acid ester, followed by basic ester hydrolysis. Alternatively, N-alkyl perfluoroalkanesulfonamides can be alkylated with an appropriate alcohol using the Mitsunobu reaction. Perfluorooctanesulfonamide was synthesized from the perfluorooctanesulfonyl fluoride via the azide by reduction with Zn/HCl. All perfluorooctanesulfonamides contained linear as well as branched C 8F 17 isomers, typically in a 10:1 to 30:1 ratio. The crystal structures of N-ethyl and N, N-diethyl perfluorooctanesulfonamide show that the S–N bond has considerable double bond character. This double bond character results in a significant rotational barrier around the S–N bond (Δ G ≠ = 62–71 kJ mol −1) and a preferred solid state and solution conformation in which the N-alkyl groups are oriented opposite to the perfluorooctyl group to minimize steric crowding around the S–N bond.

Probing nascent structures in peptides using natural abundance 13C NMR relaxation and reduced spectral density mapping

The main chain motional properties for a series of peptides that appear to have preferred conformations in solution have been systematically studied using solution-state nuclear magnetic resonance spectroscopy. The series of peptides were derived from the N-termini of pro-inflammatory chemokine proteins and HoxB1, a transcriptional regulator. As an unstructured control, a ten residue peptide was designed, synthesized, and found to be minimally structured from solution NMR data. The dynamic properties of the main chain for the peptides were assessed through longitudinal and transverse main chain (13)Calpha relaxation rates and the heteronuclear nuclear Overhauser effect. Motional parameters were interpreted using reduced spectral density mapping and compared with those derived from an extended Lipari-Szabo model in which the rotational correlation time was calculated for each main chain site of the peptide. Comparison of spectral density and Lipari-Szabo analyses for the peptides to those of the unstructured control peptide reveals significant differences in the dynamic behavior of the peptides. The amplitude of picosecond to nanosecond timescale motions for the main chain is observed to decrease for all of the chemokine peptides and HoxB1 over the regions that show partial structure at low temperatures. Comparatively, changes in picosecond to nanosecond timescale motions for the unstructured control peptide show no correlation with sequence position. These results indicate that there are distinguishable low temperature motional differences between an intrinsically unstructured peptide and peptides that have an inherent propensity to structure.

Molecular dynamics study of the conformational dynamics and energetics of some large‐ring cyclodextrins (CDn, n = 24, 25, 26, 27, 28, 29)

Molecular dynamics simulations in water solution were performed on six large-ring cyclodextrins (LR-CDs) with a degree of polymerization 24, 25, 26, 27, 28, and 29. The AMBER parm99 force field and explicit water molecules (TIP3P) were used in the simulations. The present research was aimed at further extending our knowledge on the structural dynamics and the energetics of this new class of compounds that may eventually provide chiral cavities suitable for formation of inclusion complexes with small molecules, and, accordingly, to serve as host structures for chiral recognition. The study focused on several representatives flanking CD26-the largest LR-CD for which X-ray data is available. Both the monitoring of the structural variations during the simulations as well as the analyses of energy balances are indicative for high flexibility of the macrorings. Slight differences of the overall preferred shapes were detected with diminishing the size of the macromolecules from CD29 to CD24. An elongated cavity (CD28) or a double parallel strand in different specific representations are the dominating motifs in the LR-CDs studied: with loops at the two ends (CD25, CD28, CD29), with a loop at one end (CD25), twisted (CD26, CD27) or twisted with an open portion in the middle (CD24), helical (CD24, CD25), or linking two loops from one of their sides (CD27). Two loops connected by an arc (CD28, CD29) and a cavity with the shape of an extended rectangular (CD24, CD28) appear preferentially during the conformational interconversions of the two larger CDs, whereas helical motifs are present in the smaller macrorings: an extended helix with ends linked by an arc (CD24), helical turn and helical portion (CD26, CD27). A triple propeller conformation or three symmetrical loops of almost equal size were also detected for CD26 and CD29, respectively. The present results further support the hypothesis for the existence of more than one cavity in large-ring cyclodextrins and suggest preferred conformations in water solution for the LR-CDs with degree of polymerization from 24 to 29.

Large‐ring cyclodextrins. Further support for the preferred conformations of CD26 in water solution: Molecular dynamics studies on CD26‐derived conformations of CDn (n = 24, 25, 27, 28, 29, 30)

AbstractMolecular dynamics (MD) simulations in water solution were performed on six large ring cyclodextrins (LR‐CDs) with a degree of polymerization (DP) 24, 25, 27, 28, 29, and 30, using as starting structures geometries derived from CD26, which was studied previously by MD. The present research was aimed at further extending our knowledge on the structural dynamics and the energetics of this new class of compounds, focusing on several representatives flanking CD26, the largest LR‐CD for which X‐ray data are available. The most recent parameterization for carbohydrates, Glycam‐04, and explicit water molecules (TIP3P) were used in the 10.0‐ns simulations. Preceding 10.0‐ns simulations of CD26, with the AMBER parm99 force field, revealed that the overall shape of the macromolecule did not change significantly during the last 5.0‐ns simulations. We now further test for the probability of prevalence of this conformation by using a different force field and by examining the effect of the size of the macro‐ring on the preferred conformations of LR‐CDs with DP within a range of 24–30. Indeed, we found CD26‐like geometries present for CD25, CD27, and CD28, which could be interpreted as an indication for an enhanced stability of the CD26 conformation in water solution. Again, we witnessed high flexibility of the macro‐cycles, and different local structural motifs were detected: twisted helical double parallel strand (CD25, CD30), single helix of three turns (CD29), a spiral (CD25, CD27, CD30), open‐shaped loops and helical turns (CD28; “CD26‐like geometry”), a rectangular cavity (CD24), a triple‐lobe fragment (CD29) or a portion shaped like a jaw (CD24, CD27), and an overall shape of the macromolecule that resembled a butterfly (CD27) or “X” (CD28). Thus, we conclude that the same conformation of CD26 could be also the preferred conformation in water solution of other LR‐CDs with DP in the close vicinity of 26. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007

Synthesis, conformation and biological activity of centrally modified pseudopeptidic analogues of For-Met-Leu-Phe-OMe

For-Met-betaAlapsi[CSNH]-Phe-OMe (3), For-Met-betaAlapsi[CH2NH]-Phe-OMe (5), For-Met-NH-pC6H4-SO(2-Phe-OMe 8a), For-Met-NH-mCH4-SO2-Phe-OMe (8b) and the corresponding N-Boc precursors (2, 4, 7a, b) have been synthesized and their activity towards human neutrophils has been evaluated in comparison with that shown by the reference tripeptide For-Met-Leu-Phe-OMe (fMLF-OMe). Chemotaxis, lysozyme release and superoxide anion production have been measured. (1)H NMR titration experiments and IR spectra have been discussed in order to ascertain the preferred solution conformation adopted by the tripeptide 3 with particular reference to the presence of a folded conformation centred at the centrally positioned thionated beta-residue.

Conformational analysis of methyl 5- O-methyl septanosides: effect of glycosylation on conformer populations

Methyl 5- O-methyl-α- d- glycero- d-idoseptanoside ( 3) and methyl 5- O-methyl-β- d- glycero- d-guloseptanoside ( 4) were investigated as (1→5)-linked di-/oligoseptanoside mimetics. Here we report the synthesis of 3 and 4 and describe their preferred solution conformations through a combination of ab initio/DFT calculations and 1H 3 J H,H NMR coupling constant analysis. The conformations of 3 and 4 observed in this study are discussed in comparison to those of the parent (C5 hydroxy) compounds 1 and 2. The results indicate that methyl 5- O-methyl-α-septanoside 3 is relatively rigid and adopts the same 3,4TC 5,6 conformation as 1. Methyl 5- O-methyl-β-septanoside 4 is somewhat less rigid than its parent septanoside ( 2). In addition to the 6,OTC 4,5 conformation adopted by 2, β-septanoside 4 also populates the adjacent 3,4TC 5,6 conformation. Glycosylation at C5 on β-septanoside 4 therefore increases its overall flexibility and allows access to alternative ring conformations.

Siglec-7 Undergoes a Major Conformational Change When Complexed with the α(2,8)-Disialylganglioside GT1b

The siglecs are a group of mammalian sialic acid binding receptors expressed predominantly in the immune system. The CD33-related siglecs show complex recognition patterns for sialylated glycans. Siglec-7 shows a preference for alpha(2,8)-disialylated ligands and provides a structural template for studying the key interactions that drive this selectivity. We have co-crystallized Siglec-7 with a synthetic oligosaccharide corresponding to the alpha(2,8)-disialylated ganglioside GT1b. The crystal structure of the complex offers a first glimpse into how this important family of lectins binds the structurally diverse gangliosides. The structure reveals that the C-C' loop, a region implicated in previous studies as driving siglec specificity, undergoes a dramatic conformational shift, allowing it to interact with the underlying neutral glycan core of the ganglioside. The structural data in combination with mutagenesis studies show that binding of the ganglioside is driven by extensive hydrophobic contacts together with key polar interactions and that the binding site structure is complementary to preferred solution conformations of GT1b.

Prelude&Fugue, predicting local protein structure, early folding regions and structural weaknesses

Prelude&Fugue are bioinformatics tools aiming at predicting the local 3D structure of a protein from its amino acid sequence in terms of seven backbone torsion angle domains, using database-derived potentials. Prelude(&Fugue) computes all lowest free energy conformations of a protein or protein region, ranked by increasing energy, and possibly satisfying some interresidue distance constraints specified by the user. (Prelude&)Fugue detects sequence regions whose predicted structure is significantly preferred relative to other conformations in the absence of tertiary interactions. These programs can be used for predicting secondary structure, tertiary structure of short peptides, flickering early folding sequences and peptides that adopt a preferred conformation in solution. They can also be used for detecting structural weaknesses, i.e. sequence regions that are not optimal with respect to the tertiary fold. http://babylone.ulb.ac.be/Prelude_and_Fugue.

Hybrid α/β-peptides: For-Met-Leu-Phe-OMe analogues containing geminally disubstituted β2,2- and β3,3-amino acids at the central position

The two fMLF-OMe analogues For-Met-beta(3)hAc(6)c-Phe-OMe (6) and For-Met-beta(2)hAc(6)c-Phe-OMe (12) and their corresponding N-Boc derivatives 5 and 11 have been synthesized and their biological activity towards human neutrophils evaluated. The N-formyl peptides 6 and 12 exhibit good activity as chemoattractans and 12 is highly active in superoxide anion production. The preferred solution conformation of the two N-formyl derivatives has been discussed.

Capisterones A and B, which Enhance Fluconazole Activity in Saccharomyces cerevisiae, from the Marine Green Alga Penicillus capitatus

A whole-cell-based assay using Saccharomyces cerevisiae strains that overexpress Candida albicans CDR1 and MDR1 efflux pumps has been employed to screen natural product extracts for reversal of fluconazole resistance. The tropical green alga Penicillus capitatus was selected for bioassay-guided isolation, leading to the identification of capisterones A and B (1 and 2), which were recently isolated from this alga and shown to possess antifungal activity against the marine pathogen Lindra thallasiae. Current work has assigned their absolute configurations using electronic circular dichroism and determined their preferred conformations in solution based on detailed NOE analysis. Compounds 1 and 2 significantly enhanced fluconazole activity in S. cerevisiae, but did not show inherent antifungal activity when tested against several opportunistic pathogens or cytotoxicity to several human cancer and noncancerous cell lines (up to 35 microM). These compounds may have a potential for combination therapy of fungal infections caused by clinically relevant azole-resistant strains.

Aggregation of Antifreeze Glycoprotein Fraction 8 and Its Effect on Antifreeze Activity

Antifreeze glycoproteins (AFGPs) have many potential applications ranging from the cryopreservation and hypothermic storage of tissues and organs to the preservation of various frozen food products. Since supplying native AFGP for these applications is a labor-intensive and costly process, the rational design and synthesis of functional AFGP analogues is a very attractive alternative. While structure-function studies have implicated specific structural motifs as essential for antifreeze activity in AFGP, the relationship between solution conformation and antifreeze activity is poorly understood. Toward this end, we have analyzed AFGP8 in aqueous solutions using dynamic light scattering (DLS) and circular dichroism (CD). Our results indicate that AFGP8 forms discrete aggregates in solution. These aggregates are predominantly composed of dimers that form at solution concentrations greater than 20 mM. CD spectroscopy indicates that the preferred solution conformation of AFGP8 is consistent with that of random coil. However, significant beta-sheet and alpha-helix character is observed in more concentrated solutions, indicating that these glycopeptides are highly flexible in solution. Aggregation appears to have a minimal effect on the overall solution conformation. Thermal hysteresis (TH) activity of the aggregated solutions is much higher than that of less concentrated solutions that do not form aggregates. While cooperative functioning between lower and higher molecular weight AFGPs has been reported, this is the first instance where cooperative functioning in lower molecular weight AFGPs has been observed.

Septanose Carbohydrates: Synthesis and Conformational Studies of Methyl α-d-glycero-d-Idoseptanoside and Methyl β-d-glycero-d-Guloseptanoside

We report the synthesis of methyl alpha-D-glycero-D-idoseptanoside (1) and methyl beta-D-glycero-D-guloseptanoside (2) and the characterization of their preferred solution conformations by computational chemistry and (1)H NMR (3)J(H,H) coupling constant analysis. Central to the synthetic approach was the epoxidation of glucose-derived oxepine 3 using DMDO. Nucleophilic attack on the resulting 1,2-anhydroseptanose using NaOCH(3) in CH(3)OH followed by deprotection provided the 1,2-trans diastereomers 1 and 2. The computational approach for determining the preferred low energy septanose conformations began with a pseudo Monte Carlo search for each isomer using minimization with the AMBER force field. Single-point energy calculations (HF/6-31G *and B3LYP/6-31+G**) as well as full geometry optimizations in a model for aqueous solvent were then conducted using the conformers within 5 kcal/mol of the AMBER global minimum. Calculated (3)J(H,H) values, based on a Boltzmann distribution of the computed low energy conformers, were compared to experimental (3)J(H,H) values from (1)H NMR coupling constant analyses. The correlation between calculated and observed values suggest that septanose carbohydrates are not so flexible and should generally prefer one twist-chair (TC) conformation.

Dissection Study on the Severe Acute Respiratory Syndrome 3C-like Protease Reveals the Critical Role of the Extra Domain in Dimerization of the Enzyme: DEFINING THE EXTRA DOMAIN AS A NEW TARGET FOR DESIGN OF HIGHLY SPECIFIC PROTEASE INHIBITORS

The severe acute respiratory syndrome (SARS) 3C-like protease consists of two distinct folds, namely the N-terminal chymotrypsin fold containing the domains I and II hosting the complete catalytic machinery and the C-terminal extra helical domain III unique for the coronavirus 3CL proteases. Previously the functional role of this extra domain has been completely unknown, and it was believed that the coronavirus 3CL proteases share the same enzymatic mechanism with picornavirus 3C proteases, which contain the chymotrypsin fold but have no extra domain. To understand the functional role of the extra domain and to characterize the enzyme-substrate interactions by use of the dynamic light scattering, circular dichroism, and NMR spectroscopy, we 1) dissected the full-length SARS 3CL protease into two distinct folds and subsequently investigated their structural and dimerization properties and 2) studied the structural and binding interactions of three substrate peptides with the entire enzyme and its two dissected folds. The results lead to several findings; 1) although two dissected parts folded into the native-like structures, the chymotrypsin fold only had weak activity as compared with the entire enzyme, and 2) although the chymotrypsin fold remained a monomer within a wide range of protein concentrations, the extra domain existed as a stable dimer even at a very low concentration. This observation strongly indicates that the extra domain contributes to the dimerization of the SARS 3CL protease, thus, switching the enzyme from the inactive form (monomer) to the active form (dimer). This discovery not only separates the coronavirus 3CL protease from the picornavirus 3C protease in terms of the enzymatic mechanism but also defines the dimerization interface on the extra helical domain as a new target for design of the specific protease inhibitors. Furthermore, the determination of the preferred solution conformation of the substrate peptide S1 together with the NMR differential line-broadening and transferred nuclear Overhauser enhancement study allows us to pinpoint the bound structure of the S1 peptide.

Group 13 Complexes of 5‐Methyl‐1,3,5‐dithiazinane

AbstractThe synthesis of mono‐N adducts of 5‐methyl‐1,3,5‐dithiazinane (1) with Al(CH3)3, Al(CH3)2Cl, AlCl3, AlBr3 (5−8), a bis‐N adduct with InCl3 (9), and the corresponding dithiazinanium salts with the anions AlBr4−, AlCl4−, GaCl4− and BCl4− (10−14) are reported. Compounds 5−7 adopt a preferred conformation in solution at room temperature and 8 at −10 °C. ΔG≠ values for the ring inversion were calculated for 5−8. Compounds 6−14 were studied by single‐crystal X‐ray diffraction. The solution and solid‐state analyses showed that the rings are present in all cases in a chair conformation. In compounds 5−8 the tetrahedral aluminum atom is found in an equatorial position. In the indium compound 9 the metal atom has a tbp geometry. For dithiazinanium rings 10−14 dipolar intra‐ and intermolecular interactions between halogen atoms and C−H and N−H are reported. Two different conformations for the N−CH3 were found in compound 14. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)

Chondrochloren A and B, New β‐Amino Styrenes fromChondromyces crocatus(Myxobacteria)

AbstractIn a screening for biologically active metabolites of the genusChondromyces, two novel metabolites, chondrochloren A (1) and B (2), were isolated from several strains ofC. crocatus. Compounds1and2are unique chloro‐hydroxy‐styryl amides of a highly modified C14carboxylic acid, which comprises an unsaturated ketone, two hydroxy, two methoxy and three methyl groups. After assignment of the absolute configuration of both carbinol stereocenters by Mosher’s method, NMR spectroscopic data combined with MM2 calculations allowed the prediction of the preferred conformation in solution. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)

Tert-Butyl-Substituted Tripyrranes: Insights into the Steric and Conformational Factors that Influence Porphyrinoid Ring Formation in the “3 + 1” Methodology

The MacDonald "3 + 1" route for porphyrinoid synthesis involves the acid-catalyzed condensation of tripyrranes with monocyclic dialdehydes, followed by an oxidation step. In the present study, yields were found to be greatly diminished when tert-butyl substituents were introduced on to the tripyrrane unit. Analysis of the proton NMR spectra for the tripyrranes indicates that the preferred conformation in solution has been radically altered by the presence of these tert-butyl moieties. This appears to be the first time that the NMR properties of an intermediate in porphyrin or porphyrin analogue synthesis have been correlated to its effectiveness in macrocycle formation.

Molecular modeling of four stereoisomers of the major B[a]PDE adduct (at N(2)-dG) in five cases where the structure is known from NMR studies: molecular modeling is consistent with NMR results.

The potent mutagen/carcinogen benzo[a]pyrene (B[a]P) is metabolically activated to (+)-anti-B[a]PDE, which is known to induce a variety of mutations (e.g., GC --> TA, GC --> AT, etc.). One hypothesis for this complexity is that different mutations are induced by different conformations of its major adduct [+ta]-B[a]P-N(2)-dG when bypassed during DNA replication (perhaps by different DNA polymerases). Our previous molecular modeling studies have suggested that conformational complexity might be extensive in that B[a]P-N(2)-dG adducts appeared capable of adopting at least sixteen potential conformational classes in ds-DNA [e.g., Kozack and Loechler (1999) Carcinogenesis 21, 1953], although only eight seemed likely to be relevant to base substitution mutagenesis. Such molecular modeling studies are only likely to be valuable for the interpretation of mutagenesis results if global minimum energy conformations for adducts are found and if the differences in the energies of these different conformations can be computed reasonably accurately. One approach to assessing the reliability of our molecular modeling techniques is considered herein. Using a five-step molecular modeling protocol, which importantly included a molecular dynamics version of simulated annealing, eight conformations are studied in each of five cases. (The five cases are listed below, and were chosen because in each case the preferred solution conformation is known from a NMR study.) Of the eight conformations studied, the one computed to be lowest in energy is the same conformation as the one observed by NMR in four of the five cases: 5'-CGC sequence with [+ta]-, [-ta]-, and [+ca]-B[a]P-N(2)-dG, and 5'-TGC sequence with [+ta]-B[a]P-N(2)-dG. In the fifth case (5'-CGC sequence with [-ca]-B[a]P-N(2)-dG), the known NMR conformation is computed to be second lowest in energy, but it is within approximately 1.7 kcal of the computed lowest energy conformation. These results suggest that molecular modeling is surprisingly accurate in computing lowest energy conformations and that it should be useful in assessing the relative energies of different conformations. This is especially important given that currently molecular modeling is the only means available to study the energetics of minor conformations of DNA adducts.

HISTIDYL TAGS AND STRUCTURAL STABILIZATION OF LINEAR PEPTIDES

Histidyl tags of variable length at the carboxy and amino termini of the ASYQDL sequence have been added. The hexapeptide has been chosen for its predicted low propensity to assume a preferred conformation in solution. The NMR data indicate the presence in solution of different folded conformations for two histidyl derivatives of the hexapeptide upon additions of the Ni(II) ion. Thus, presence of four or five histidines located at the extremities of an unfolded peptide seems not to be suitable for a structural ordering inducible by the metal ion to trigger specific biological functions.