Investigation of restriction endonuclease EcoRII complex with DNA in solution by FTIR spectroscopy

The X-ray structure of type IIE EcoRII restriction endonuclease has been solved but the structure of the R.EcoRII-DNA complex is still unknown. We report here on the structure of the pre-reactive R.EcoRII-DNA-Ca²⁺ complex in solution examined by FTIR spectroscopy. The secondary structure of R.EcoRII as well as the structure of the target DNA in the R.EcoRII-DNA-Ca²⁺ complex was characterized. It was shown that the R.EcoRII-DNA-Ca²⁺ complex formation is accompanied by changes in the spectrum of both DNA bases and DNA sugar-phosphate backbone that suggest contacts of the enzyme with different groups of atoms in DNA. The change of the R.EcoRII secondary structure in the R.EcoRII-DNA-Ca²⁺ complex is also observed.     

Interpreting protein structural dynamics from NMR chemical shifts

In this investigation, semiempirical NMR chemical shift prediction methods are used to evaluate the dynamically averaged values of backbone chemical shifts obtained from unbiased molecular dynamics (MD) simulations of proteins. MD-averaged chemical shift predictions generally improve agreement with experimental values when compared to predictions made from static X-ray structures. Improved chemical shift predictions result from population-weighted sampling of multiple conformational states and from sampling smaller fluctuations within conformational basins. Improved chemical shift predictions also result from discrete changes to conformations observed in X-ray structures, which may result from crystal contacts, and are not always reflective of conformational dynamics in solution. Chemical shifts are sensitive reporters of fluctuations in backbone and side chain torsional angles, and averaged (1)H chemical shifts are particularly sensitive reporters of fluctuations in aromatic ring positions and geometries of hydrogen bonds. In addition, poor predictions of MD-averaged chemical shifts can identify spurious conformations and motions observed in MD simulations that may result from force field deficiencies or insufficient sampling and can also suggest subsets of conformational space that are more consistent with experimental data. These results suggest that the analysis of dynamically averaged NMR chemical shifts from MD simulations can serve as a powerful approach for characterizing protein motions in atomistic detail.     

Modelling CreA protein–DNA recognition determinants. A molecular dynamics study of fully charged CreA–DNA model in water

CreA, the negative regulator mediating carbon catabolism repression in Aspergillus nidulans, is a protein that contains a DNA-binding domain comprising two zinc finger motifs. A 3D model for the CreA–G4 (5′-GCGGGGGCGT-3′) complex is constructed on the basis of the structure of the Zif268–DNA crystal complex [Science 252 (1991) 809] and using similarity analysis and computer assisted modelling techniques. The CreA–G4 model was then subjected to a set of molecular dynamics (MD) studies. Based on our previous nano second long Zif268–DNA MD simulation, a 170 ps long trajectory was deemed sufficient to test possible DNA–protein interactions. A screening of the static model and of the trajectory was performed for protein amino acids, nucleotide bases, phosphates backbone and water molecules mediating protein–DNA contacts. Energy, root mean square deviation (RMSD), principal inertial moment and distances were analysed. For this time span, the stability shown in fluctuation patterns reveals the presence of a complex behaving in a manner similar to Zif268–DNA.

An unambiguous characterisation of the amino acids involved in DNA-binding was obtained. These results could contribute towards the establishment of a code of protein–DNA recognition for this class of DNA-binding motifs.     

High-sensitivity observation of dipolar exchange and NOEs between exchangeable protons in proteins by 3D solid-state NMR spectroscopy

A highly sensitive new 1H-detected 3D solid-state NMR method is described for characterizing 1H-1H spin exchange in nanocrystalline samples of 15N- and 2H-enriched protein. Long-range contacts are observed in human ubiquitin. The method is also used to show that numerous NOEs between backbone amides and crystal water protons can be observed.     

Solution structure of a peptide nucleic acid duplex from NMR data: features and limitations

This paper describes the results of a 1D and 2D NMR spectroscopy study of a palindromic 8-base pair PNA duplex GGCATGCC in H2O and H2O-D2O solutions. The (1)H NMR peaks have been assigned for most of the protons of the six central base pairs, as well as for several amide protons of the backbone. The resulting 36 interbase and base-backbone distance restraints were used together with Watson-Crick restraints to generate the PNA duplex structure in the course of 10 independent simulated annealing runs followed by restrained molecular dynamics (MD) simulations in explicit water. The resulting PNA structures correspond to a P-type helix with helical parameters close to those observed in the crystal structures of PNA. Based on the current limited number of restraints obtained from NMR spectra, alternative structures obtained by MD from starting PNA models based on DNA cannot be ruled out and are also discussed.     

The relative helix and hydrogen bond stability in the B domain of protein A as revealed by integrated tempering sampling molecular dynamics simulation

Molecular dynamics simulations using the integrated tempering sampling method were performed for the folding of wild-type B domain of protein A (BdpA). Starting from random and stretched structures, these simulations allow us to fold this protein into the native-like structure frequently, achieving very small backbone (1.7 A?) and all heavy-atom root-mean-square deviation (2.6 A?). Therefore, the method used here increases the efficiency of configuration sampling and thermodynamics characterization by molecular dynamics simulation. Although inconsistency exists between the calculation and experiments for the absolute stabilities, as a limitation of the force field parameters, the calculated order of helix stability (H3 > H2 > H1) is consistent with that determined by experiments for individual separate helices. The lowest free energy folding pathway of BdpA was found to start with a barrierless and non-cooperative structural collapse from the entirely extended (E) state, which leads to a physiologically unfolded (P) state consisting of multiple stable structures with few native inter-helical hydrophobic interactions formed. In the P state, only H3 is fully structured. The final formation of H1 (and to a lesser extent, H2) in the folded (F) state requires the packing of the inter-helical hydrophobic contacts. In addition, it was found that stabilities of backbone hydrogen bonds are significantly affected by their positions relative to the inter-helical hydrophobic core. As temperature increases, the stability of the hydrogen bonds exposed to the solvent tends to increase while that of the hydrogen bonds buried within the hydrophobic core decreases. Finally, we discuss implications of this study on the general folding mechanism of proteins.     

Combining crystallographic and quantum chemical data to understand DNA-protein π-interactions in nature

Noncovalent interactions are accepted to be prevalent across biochemical systems, including governing interactions between nucleic acids and proteins. The present review summarizes work done to characterize the abundance, structure and strength of DNA–protein π interactions by combining rigorous searches of experimental X-ray crystal structures of DNA–protein complexes and quantum chemical calculations. Focus is placed on interactions that occur between the π-containing amino acids (W, H, F, Y, R, E, and D) and the canonical DNA nucleobases (A, T, G, and C) or 2′-deoxyribose moiety. These studies highlight the considerable frequency of both DNA–protein π–π and sugar–π interactions in nature, which can involve any π-containing amino acid arranged in many unique binding orientations with respect to any DNA component. When combined with the significant strength predicted for the identified DNA–protein π contacts using density functional theory, these works underscore the potential impact of these interactions on critical biological functions. This conclusion is supported by a review of examples from the recent literature that have acknowledged the role of DNA–protein π interactions in binding, specificity, and catalysis.

     

Molecular dynamics simulation of trp-repressor/operator complex: analysis of hydrogen bond patterns of protein–DNA interaction

Molecular dynamics simulation of Escherichia coli trp-repressor/operator complex was performed to elucidate protein–DNA interactions in solution for 800 ps on special-purpose computer MD-GRAPE. The Ewald summation method was employed to treat the electrostatic interaction without cutoff. DNA kept stable conformation in comparison with the result of the conventional cutoff method. Thus, the trajectories obtained were used to analyze the protein–DNA interaction and to understand the role of dynamics of water molecules forming sequence specific recognition interface. The dynamical cross-correlation map showed a significant positive correlation between the helix-turn-helix DNA-binding motifs and the major grooves of operator DNA. The extensive contact surface was stable during the simulation. Most of the contacts consisted of direct interactions between phosphates of DNA and the protein, but several water-mediated polar contacts were also observed. These water-mediated interactions, which were also seen in the crystal structure (Z. Otwinowski, et al., Nature, 335 (1998) 321) emerged spontaneously from the randomized initial configuration of the solvent. This result suggests the importance of the water-mediated interaction in specific recognition of DNA by the trp-repressor, consistent with X-ray structural information.     

Hydrogen bonding in high-resolution protein structures: a new method to assess NMR protein geometry

An analysis of backbone hydrogen bonds has been performed on nine high-resolution protein X-ray crystal structures. Backbone hydrogen-bond geometry is compared in the context of X-ray crystal structure resolution. A strong correlation between the hydrogen-bond distance, R(HO), and the hydrogen-bond angle, theta(NHO), is observed when the X-ray crystal structure resolution is <1.00 A. Ab initio calculations were performed to substantiate these results. The angle and distance limits found in our correlation for the backbone hydrogen-bond geometry can be used to evaluate the quality of protein structures and for further NMR structure refinement.     

Close contacts between carbonyl oxygen atoms and aromatic centers in protein structures: pi...pi or lone-pair...pi interactions?

Lone-pair...pi and, more recently, pi...pi interactions have been studied in small molecule crystal structures, and they are the focus of attention in some biomolecules. In this study, we have systematically analyzed 500 high-resolution protein structures (resolution < or =1.8 A) and identified 286 examples in which carbonyl oxygen atoms approach the aromatic centers within a distance of 3.5 A. Contacts involving backbone carbonyl oxygens are frequently observed in helices and, to some extent, in strands. Geometrical characterization indicates that these contacts have geometry in between that of an ideal pi...pi and a lone-pair...pi interaction. Quantum mechanical calculations using 6-311++G** basis sets reveal that these contacts give rise to energetically favorable interactions and, along with MD simulations, indicate that such interactions could stabilize secondary structures.     

Intermolecular interactions in group 14 hydrides: Beyond CH···HC contacts

In line with previous work in which we established the factors that enhance attractive C?H···H?C dihydrogen interactions in alkanes, an extended theoretical analysis of noncovalent intermolecular interactions in group 14 hydrides is presented here. Remarkably, these weak interactions may play a major role in determining the crystal structures adopted by several families of molecules. A combined structural and computational analysis at the MP2 level allowed us to identify and characterize different interactions of the type E?H···H?E and E···H?E (E = Si, Ge, Sn, and Pb), and to find also the most suitable scenario for the establishment of each particular type. The nature of the interactions has been analyzed in terms of natural charges of the atoms involved and a topological analysis of the electron density of several dimers confirms the existence of H···H and H···E attractive contacts. We have observed that the interaction strength increases when descending down the periodic group and that silicon has a marked tendency to establish Si···H?Si interactions. A size‐dependent backbone effect that reinforces H···H dihydrogen interactions in polyhedral systems has also been found.     

Intermolecular interactions in group 14 hydrides: Beyond C?H···H?C contacts

In line with previous work in which we established the factors that enhance attractive C? H···H? C dihydrogen interactions in alkanes, an extended theoretical analysis of noncovalent intermolecular interactions in group 14 hydrides is presented here. Remarkably, these weak interactions may play a major role in determining the crystal structures adopted by several families of molecules. A combined structural and computational analysis at the MP2 level allowed us to identify and characterize different interactions of the type E? H···H? E and E···H? E (E = Si, Ge, Sn, and Pb), and to find also the most suitable scenario for the establishment of each particular type. The nature of the interactions has been analyzed in terms of natural charges of the atoms involved and a topological analysis of the electron density of several dimers confirms the existence of H···H and H···E attractive contacts. We have observed that the interaction strength increases when descending down the periodic group and that silicon has a marked tendency to establish Si···H? Si interactions. A size‐dependent backbone effect that reinforces H···H dihydrogen interactions in polyhedral systems has also been found.     

Silver-phosphine complexes of the highly methylated carborane monoanion [closo-1-H-CB11Me11]-

The synthesis of the silver(I) salt of the highly methylated carborane anion [closo-1-H-CB(11)Me(11)](-) is described, Ag[closo-1-H-CB(11)Me(11)] 1, which in the solid state shows close intermolecular Ag...H(3)C contacts. Addition of various monodentate phosphines to 1 results in the formation of the complexes (R(3)P)Ag[closo-1-H-CB(11)Me(11)] [R = Ph, 2; cyclohexyl (C(6)H(11)), 3; (3,5-Me(2)-C(6)H(3)), 4]. All these complexes show close intermolecular Ag.H(3)C contacts in the solid state that are considerably shorter than the sum of the van der Waals radius of methyl (2.00 A) and the ionic radius of silver(I) (1.29 A). For 2 and 3 there are other close intermolecular Ag...H(3)C contacts in the solid state, arising from proximate carborane anions in the crystal lattice. Addition of methyl groups to the periphery of the phosphine ligand (complex 4) switches off the majority of these interactions, leaving essentially a single cage interacting with the cationic silver-phosphine fragment through three CH(3) groups. In solution (CD(2)Cl(2)) Ag...H(3)C contacts remain, as evidenced by both the downfield chemical shift change and the significant line-broadening observed for the cage methyl signals. These studies also show that the metal fragment is fluxional over the surface of the cage. The Ag...H(3)C interactions in solution may be switched off by addition of a stronger Lewis base than [closo-1-H-CB(11)Me(11)](-). Thus, addition of [NBu(4)][closo-1-H-CB(11)H(5)Br(6)] to 2 affords (Ph(3)P)Ag[closo-1-H-CB(11)H(5)Br(6)], while adding Et(2)O or PPh(3) affords the well-separated ion-pairs [(Ph(3)P)(L)Ag][closo-1-H-CB(11)Me(11)] (L = OEt(2) 5, PPh(3) 6,) both of which have been crystallographically characterized. DFT calculations on 2 (at the B3LYP/DZVP level) show small energy differences between the possible coordination isomers of this compound, with the favored geometry being one in which the [(Ph(3)P)Ag](+) fragment interacts with three of the [BCH(3)] vertices on the lower surface of the cage, similar to the experimentally observed structure of 4.     

X‐Ray Crystal Structure of a Second‐Generation Peptide Dendrimer in Complex with Pseudomonas aeruginosa Lectin LecB

Dendrimers are regularly branched molecular trees which are notoriously difficult to crystallize. Herein we report the crystal structure of a C‐fucosylated second generation peptide dendrimer as complex with lectin LecB in which the only dendrimer‐lectin contact is the LecB bound glycoside (PDB 6S5S). In contrast to a previously reported crystal structure of a first‐generation peptide dendrimer as LecB complex in which the dendrimer formed trimers connected by intermolecular β‐sheets (PDB 5D2A), the present structure features a globular monomeric state held together by intramolecular backbone hydrogen bonds and assembled into a non‐covalent dimer stabilized by hydrophobic contacts between leucine side‐chains and proline‐phenylalanine CH‐π stacking interactions. Molecular dynamics and circular dichroism studies suggest that this crystal structure resembles the structure of the peptide dendrimer in solution. Structures of a partially resolved dendrimer (PDB 6S5R) and of C‐fucosylated disulfide bridged peptide dimers connecting different LecB tetramers are also reported (PDB 6S7G, PDB 6S5P).     

The role of plastic beta-hairpin and weak hydrophobic core in the stability and unfolding of a full sequence design protein

In this study, the thermal stability of a designed alpha/beta protein FSD (full sequence design) was studied by explicit solvent simulations at three moderate temperatures, 273 K, 300 K, and 330 K. The average properties of the ten trajectories at each temperature were analyzed. The thermal unfolding, as judged by backbone root-mean-square deviation and percentage of native contacts, was displayed with increased sampling outside of the native basin as the temperature was raised. The positional fluctuation of the hairpin residues was significantly higher than that of the helix residues at all three temperatures. The hairpin segment displayed certain plasticity even at 273 K. Apart from the terminal residues, the highest fluctuation was shown in the turn residues 7-9. Secondary structure analysis manifested the structural heterogeneity of the hairpin segment. It was also revealed by the simulation that the hydrophobic core was vulnerable to thermal denaturation. Consistent with the experiment, the I7Y mutation in the double mutant FSD-EY (FSD with mutations Q1E and I7Y) dramatically increased the protein stability in the simulation, suggesting that the plasticity of the hairpin can be partially compensated by a stronger hydrophobic core. As for the unfolding pathway, the breathing of the hydrophobic core and the separation of the two secondary structure elements (alpha helix and beta hairpin) was the initiation step of the unfolding. The loss of global contacts from the separation further destabilized the hairpin structure and also led to the unwinding of the helix.     

Structure of the fully modified left-handed cyclohexene nucleic acid sequence GTGTACAC

CeNA oligonucleotides consist of a phosphorylated backbone where the deoxyribose sugars are replaced by cyclohexene moieties. The X-ray structure determination and analysis of a fully modified octamer sequence GTGTACAC, which is the first crystal structure of a carbocyclic-based nucleic acid, is presented. This particular sequence was built with left-handed building blocks and crystallizes as a left-handed double helix. The helix can be characterized as belonging to the (mirrored) A-type family. Crystallographic data were processed up to 1.53 A, and the octamer sequence crystallizes in the space group R32. The sugar puckering is found to adopt the 3H2 half-chair conformation which mimics the C3'-endo conformation of the ribose sugar. The double helices stack on top of each other to form continuous helices, and static disorder is observed due to this end-to-end stacking.