The deformability of double helical DNA is critical for its packaging in the cell, recognition by other molecules, and transient opening during biochemically important processes. Here, a complete set of sequence-dependent empirical energy functions suitable for describing such behavior is extracted from the f luctuations and correlations of structural parameters in DNA-protein crystal complexes. These elastic functions provide useful stereochemical measures of the local base step movements operative in sequencespecific recognition and protein-induced deformations. In particular, the pyrimidine-purine dimers stand out as the most variable steps in the DNA-protein complexes, apparently acting as f lexible ''hinges'' fitting the duplex to the protein surface. In addition to the angular parameters widely used to describe DNA deformations (i.e., the bend and twist angles), the translational parameters describing the displacements of base pairs along and across the helical axis are analyzed. The observed correlations of base pair bending and shearing motions are important for nonplanar folding of DNA in nucleosomes and other nucleoprotein complexes. The knowledge-based energies also offer realistic threedimensional models for the study of long DNA polymers at the global level, incorporating structural features beyond the scope of conventional elastic rod treatments and adding a new dimension to literal analyses of genomic sequences. In addition to the genetic message, DNA base sequence carries a multitude of other signals related to the manipulation of the long, thread-like molecule. Primary sequences of nucleic acid bases determine three-dimensional structures whose physical properties reflect the constituent residues. The existing library of solved DNA crystal structures (1), for example, reveals subtle sequence-dependent irregularities in the orientation and displacement of adjacent residues (2). Duplex stability under a given set of environmental conditions also depends to good approximation on the identity of the 10 nearest neighbor base pairs (3). The linear sequence of genetic information thus expands into a base sequence-dependent spatial and energetic code that governs the global organization of the double helix and its susceptibility to interactions with other molecules. Interest in understanding the physical properties of genomic DNA has prompted the development of new approaches to analyze and depict the sequence-dependent bending and twisting of neighboring base pairs. Studies of gel migration (4), chain cyclization kinetics (4, 5), and nucleosome phasing (6) have yielded a variety of sequence-dependent models to account for the observed data. Furthermore, collected oligonucleotide crystal structures show similar conformational trends (2), although there are discrepancies between the x-ray and solution assessments of the direction of bending at a few dimer steps (7, 8) . The solid state data additionally reveal sequence-dependent differences in the displacement of base pairs [see, e.g., Slide (2)], a feature not usually considered in simple models fitted to solution data (4-6). The thermal fluctuations deduced from solution studies of long DNA (9) constitute yet another important feature of the double helix. These macroscopic properties, which are not easily interpreted at the base pair level, typically are described by changes in the elastic constants of idealized sequenceindependent models that match the observed data. The sequence-specific recognition of DNA by proteins and other ligands, however, calls for a more sophisticated description of chain flexibility than can be deduced from uniform elastic models. In particular, DNA responds to protein binding through sequence-dependent kinking and intercalation (10-12). This deformability is essential at both the global and local levels, serving as a potential long-range signal for molecular recognition as well as accommodating the local distortions of the double helix induced by tight binding, i.e., the so-called conformational recognition or indirect readout of DNA residues (13, 14) . Analysis of such systems requires models that incorporate detailed stereochemical features of DNA sequences. One of the best sources of this information is the database of protein-DNA crystal complexes (1), which has grown to the point where there are now enough data to extract duplex properties (means and fluctuations) at the level of nearest neighbors, i.e., the 10 unique base pair steps. Although trimers and tetramers may be preferable in principle, there are not yet sufficient crystallographic data to address DNA deformability at this level. A further limitation of the current data is that anisotropic structure factors are infrequently reported, e.g., only one B-DNA structure (15) and no protein-DNA complexes. Therefore, the ''real-time'' flexibility of DNA in any given complex cannot be determined directly from the co-crystal data. Still, one can use the ensemble-averaged parameters characterizing the DNA variability in these complexes to learn about the intrinsic motions of the double helix. This approach can be justified as follows. Different proteins impose different sorts of forces on DNA, so the distortions of DNA brought about by many kinds of proteins effectively cancel one another (major vs. minor groove bending, etc.). Therefore, we presume that, after averaging over a large ensemble of complexes, the natural conformational response of DNA will surface. (These general principles will not necessarily predict the interactions of DNA with amino acids in specific complexes.) Here, we report the behavior of dimer steps collected from 92 protein-DNA crystal complexes and offer a set of empirical energy functions that describe the observed sequencedependent deformability of the composite structures. To describe the DNA variability in this way, we apply a formal ''culling'' procedure to the x-ray data set to obtain Gaussian distributions of conformational parameters. Table 1 summarizes this information in terms of the spread of the six The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked ''advertisement'' in accordance with 18 U.S.C. §1734 solely to indicate this fact.
They used knowledge-based harmonic energy functions deduced from the crystal structures of protein-DNA complexes REF , which can be easily replaced with those derived in the present study; moreover, they can be substituted with tetramer versions of the functions to more precisely describe the sequence-dependent motions of DNA.
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
Proceedings of the National Academy of Sciences of the United States of America
Proceedings of the National Academy of Sciences of the United States of America
Chemistry Medicine