Sequence specificity of bacteriophage 434 repressor-operator complexation

SYMMETRY, FORM, AND SHAPE: Guiding Principles for Robustness in Macromolecular Machines

Computational studies of large macromolecular assemblages have come a long way during the past 10 years. With the explosion of computer power and parallel computing, timescales of molecular dynamics simulations have been extended far beyond the hundreds of picoseconds timescale. However, limitations remain for studies of large-scale conformational changes occurring on timescales beyond nanoseconds, especially for large macromolecules. In this review, we describe recent methods based on normal mode analysis that have enabled us to study dynamics on the microsecond timescale for large macromolecules using different levels of coarse graining, from atomically detailed models to those employing only low-resolution structural information. Emerging from such studies is a control principle for robustness in Nature's machines. We discuss this idea in the context of large-scale functional reorganization of the ribosome, virus particles, and the muscle protein myosin.

ARTIST: An activated method in internal coordinate space for sampling protein energy landscapes

We present the first applications of an activated method in internal coordinate space for sampling all-atom protein conformations, the activation-relaxation technique for internal coordinate space trajectories (ARTIST). This method differs from all previous internal coordinate-based studies aimed at folding or refining protein structures in that conformational changes result from identifying and crossing well-defined saddle points connecting energy minima. Our simulations of four model proteins containing between 4 and 47 amino acids indicate that this method is efficient for exploring conformational space in both sparsely and densely packed environments, and offers new perspectives for applications ranging from computer-aided drug design to supramolecular assembly.

The role of the minor groove substituents in indirect readout of DNA sequence by 434 repressor

The sequence of non-contacted bases at the center of the 434 repressor binding site affects the strength of the repressor-DNA complex by influencing the structure and flexibility of DNA (Koudelka, G. B., and Carlson, P. (1992) Nature 355, 89-91). We synthesized 434 repressor binding sites that differ in their central sequence base composition to test the importance of minor groove substituents and/or the number of base pair hydrogen bonds between these base pairs on DNA structure and strength of the repressor-DNA complex. We show here that the number of base pair H-bonds between the central bases apparently has no role in determining the relative affinity of a DNA site for repressor. Instead we find that the affinity of DNA for repressor depends on the absence or presence the N2-NH(2) group on the purine bases at the binding site center. The N2-NH(2) group on bases at the center of the 434 binding site appears to destabilize 434 repressor-DNA complexes by decreasing the intimacy of the specific repressor-DNA contacts, while increasing the reliance on protein contacts to the DNA phosphate backbone. Thus, the presence of an N2-NH(2) group on the purines at the center of a binding site globally alters the precise conformation of the protein-DNA interface.

Operator recognition by the phage 434 cI repressor: MD simulations of free and bound 50-bp DNA reveal important differences between the OR1 and OR2 sites

Using molecular dynamics simulations in explicit solvent, we investigated the behavior of a 50-bp DNA sequence containing the 434 bacteriophage operators OR1 and OR2 separated by an 8-bp spacer. Two simulations of 1 ns each were carried out, with DNA alone and with DNA complexed to dimers of the R1-69 DNA binding domain of the phage 434 cI repressor protein at the OR1 and OR2 sites. Strong correlations among average structural parameters are observed between our simulations and available experimental data for the bound OR1/OR2 subsites. In the free state, some differences appear between the three relevant fragments (OR1, the spacer, and OR2). Unbound OR1 exhibits a large, shallow major groove into which the base atoms protrude and is also bent toward the major groove. This structure is maintained because structural fluctuations are weak. Unbound OR2 resembles canonical B-DNA although the structural parameters show greater fluctuations, essentially due to a malleable step (the innermost CpA/TpG), absent in OR1. Complexation with the proteins slightly alters the base positions but strongly modifies the sugar and backbone motions. The most crucial repressor effects are changes in the flexibility of the OR1/OR2 sites. Structural fluctuations are enhanced for OR1, conferring a favorable energetic contribution to the OR1 binding, whereas they are reduced for OR2. Therefore, both structural and dynamic properties of DNA suggest OR1 is the most attractive site for the repressor, which may explain the different binding association constants observed for the OR1 and OR2 sites. Finally, we also investigated the impact of the protein on the DNA backbone dynamics and find that direct or indirect interactions facilitate the DNA structural variations required for achieving complementarity with the protein.

The papillomavirus E2 proteins: structure, function, and biology

Nearly twenty years after the first high-resolution crystal structures of specific protein-DNA complexes were determined, the stereo-chemical basis for protein-DNA recognition remains an active area of investigation. One outstanding question is, how are proteins able to detect noncontacted sequences in their binding sites? The papillomavirus E2 proteins represent a particularly suitable group of proteins in which to examine the mechanisms of "indirect readout." Coordinated structural and thermodynamic studies of the E2-DNA interaction conducted over the past five years are summarized in this review. The data support a model in which the electrostatic properties of the individual E2 proteins correlate with their affinities for intrinsically flexible or rigidly prebent DNA targets.

Sequence-dependent motions of DNA: a normal mode analysis at the base-pair level

Computer simulation of the dynamic structure of DNA can be carried out at various levels of resolution. Detailed high resolution information about the motions of DNA is typically collected for the atoms in a few turns of double helix. At low resolution, by contrast, the sequence-dependence features of DNA are usually neglected and molecules with thousands of base pairs are treated as ideal elastic rods. The present normal mode analysis of DNA in terms of six base-pair "step" parameters per chain residue addresses the dynamic structure of the double helix at intermediate resolution, i.e., the mesoscopic level of a few hundred base pairs. Sequence-dependent effects are incorporated into the calculations by taking advantage of "knowledge-based" harmonic energy functions deduced from the mean values and dispersion of the base-pair "step" parameters in high-resolution DNA crystal structures. Spatial arrangements sampled along the dominant low frequency modes have end-to-end distances comparable to those of exact polymer models which incorporate all possible chain configurations. The normal mode analysis accounts for the overall bending, i.e., persistence length, of the double helix and shows how known discrepancies in the measured twisting constants of long DNA molecules could originate in the deformability of neighboring base-pair steps. The calculations also reveal how the natural coupling of local conformational variables affects the global motions of DNA. Successful correspondence of the computed stretching modulus with experimental data requires that the DNA base pairs be inclined with respect to the direction of stretching, with chain extension effected by low energy transverse motions that preserve the strong van der Waals' attractions of neighboring base-pair planes. The calculations further show how one can "engineer" the macroscopic properties of DNA in terms of dimer deformability so that polymers which are intrinsically straight in the equilibrium state exhibit the mesoscopic bending anisotropy essential to DNA curvature and loop formation.

Comparison of molecular dynamics and harmonic mode calculations on RNA

Conformational fluctuations of a double-stranded RNA oligonucleotide have been calculated from a two nanosecond molecular dynamics simulation including explicit waters and ions and from a harmonic mode analysis. The harmonic mode analysis was performed in the absence of solvent using various effective dielectric screening functions. RNA flexibility was analyzed and compared at the level of atomic position fluctuations, helical base-pair descriptor fluctuations and global helix bending, stretching, and twisting flexibilities. Although quantitative differences were found, the qualitative pattern of atomic position and helical descriptor fluctuations along the sequence was similar for both methods. For the helical descriptor flexibility, the largest differences were observed for base-pair roll and rise that showed two times larger fluctuations in the molecular dynamics simulation. A significant overlap between the sub-space spanned by soft principal components calculated from the molecular dynamics simulation and harmonic modes was found. Both approaches predict a negative covariation for most helical base-pair step descriptors of neighboring base pair steps (with the exception of rise), which tend to stiffen the RNA at the global level. The RNA persistence length extracted from the molecular dynamics simulation (350-600 A) is smaller than the experimental value ( approximately 720 A) and estimates based on the harmonic mode approach (1100-1700 A).

The structural basis of DNA target discrimination by papillomavirus E2 proteins

The papillomavirus E2 proteins regulate the transcription of all papillomavirus genes and are necessary for viral DNA replication. Disruption of the E2 gene is commonly associated with malignancy in cervical carcinoma, indicating that E2 has a role in regulating tumor progression. Although the E2 proteins from all characterized papillomaviruses bind specifically to the same 12-base pair DNA sequence, the cancer-associated human papillomavirus E2 proteins display a unique ability to detect DNA flexibility and intrinsic curvature. To understand the structural basis for this phenomenon, we have determined the crystal structures of the human papillomavirus-18 E2 DNA-binding domain and its complexes with high and low affinity binding sites. The E2 protein is a dimeric beta-barrel and the E2-DNA interaction is accompanied by a large deformation of the DNA as it conforms to the E2 surface. DNA conformation and E2-DNA contacts are similar in both high and low affinity complexes. The differences in affinity correlate with the flexibility of the DNA sequence. Preferences of E2 proteins from different papillomavirus strains for flexible or prevent DNA targets correlate with the distribution of positive charge on their DNA interaction surfaces, suggesting a role for electrostatic forces in the recognition of DNA deformability.

Conformational deformability of RNA: a harmonic mode analysis

The harmonic mode analysis method was used to characterize the conformational deformability of regular Watson-Crick paired, mismatch- and bulge-containing RNA. Good agreement between atomic Debye-Waller factors derived from x-ray crystallography of a regular RNA oligonucleotide and calculated atomic fluctuations was obtained. Calculated helical coordinate fluctuations showed a small sequence dependence of up to approximately 30-50%. A negative correlation between motions at a given base pair step and neighboring steps was found for most helical coordinates. Only very few calculated modes contribute significantly to global motions such as bending, twisting, and stretching of the RNA molecules. With respect to a local helical description of the RNA helix our calculations suggest that RNA bending is mostly due to a periodic change in the base pair step descriptors slide and roll. The presence of single guanine:uridine or guanine:adenine mismatches had little influence on the calculated RNA flexibility. In contrast, for tandem guanine:adenine base pairs the harmonic mode approach predicts a significantly reduced conformational flexibility in the case of a sheared arrangement and slightly enhanced flexibility for a face-to-face (imino proton) pairing relative to regular RNA. The presence of a single extra adenine bulge nucleotide stacked between flanking sequences resulted in an increased local atomic mobility around the bulge site (approximately 40%) and a slightly enhanced global bending flexibility. For an adenine bulge nucleotide in a looped-out conformation a strongly enhanced bulge nucleotide mobility but no increased bending flexibility compared to regular RNA was found.

The role of DNA-protein salt bridges in molecular recognition: a model study

A theoretical study is presented of the influence of salt bridges between cationic side chains and DNA phosphates on DNA conformation and flexibility. The DNA sequence studied is that of the catabolite activator protein binding oligomer from the crystallized complex. The effect of salt bridges is modeled by neutralization of net phosphate charges for the groups involved in such interactions in the crystallized complex. Energy-optimized conformations are obtained by molecular mechanics using the JUMNA program. Base sequence dependence is studied by moving the phosphate neutralization pattern along the sequence and also by point mutations. Normal mode analysis is used to evaluate DNA flexibility. The results obtained show that the free oligomer is already precurved in the direction favored by the protein, and the effect of phosphate neutralization is principally to increase this curvature. This effect is, however, strongly sequence dependent. In addition, it is shown that oligomer flexibility cannot be explained by a simple superposition of the properties of successive dinucleotide steps, strong long-range coupling effects are observed. In all the cases examined, phosphate neutralization, however, leads to a reduction in oligomer flexibility.

Collective variable modelling of nucleic acids

Collective variable models continue to contribute to our knowledge of nucleic acids. The past year has seen considerable progress both in modelling sequence-dependent effects on nucleic acid conformation and in understanding how proteins or external stresses influence nucleic acid structure. Algorithmic developments have also allowed collective models to be applied to studies of thermal fluctuations and dynamics. For larger systems, models with varying degrees of resolution are being refined and applied to nucleic acids containing hundreds or thousands of nucleotides.

DNA curvature and phosphate neutralization: an important aspect of specific protein binding

A theoretical study is presented of the influence of salt bridges between protein cationic side chains and DNA phosphates on DNA conformation and flexibility. Two DNA sequences are studied containing respectively the HNF3 and CAP binding sites. The effect of salt bridges is modelled by the neutralisation of net phosphate charges for the groups involved in such interactions in the complex. Energy optimised conformations are obtained by molecular mechanics calculations using the JUMNA program. Base sequence dependence is studied by moving the phosphate neutralisation pattern along the sequence, while normal mode analysis is used to evaluate DNA flexibility. The results show that phosphate neutralisation has a strong influence on DNA conformation. For the HNF3 binding sequence, the free oligomer is bent in direction very different from that observed in the protein complex. Phosphate neutralisation changes this direction by 45 degrees to within only 4 degrees of the direction in the complex, without changing the bending angle. For the CAP binding sequence, the free oligomer is already intrinsically curved in the direction favoured by the protein, but phosphate neutralisation increases the bending angle. For both oligomers studied these effects are strongly sequence dependent. It is also shown that oligomer flexibility cannot be explained by a simple superposition of the properties of successive dinucleotide steps. Important long range coupling effects are observed. However, for both sequence studied, phosphate neutralisation however leads to a reduction in oligomer flexibility.