Masashi Suzuki

A framework for the DNA–protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules

BACKGROUNDnUnderstanding the general mechanisms of sequence specific DNA recognition by proteins is a major challenge in structural biology. The existence of a DNA recognition code for proteins, by which certain amino acid residues on a protein surface confer specificity for certain DNA bases, has been the subject of much discussion. However, no simple code has yet been established.nnnRESULTSnThe principles of DNA recognition can be described at two levels. The chemical rules describe the partnerships between amino acid side chains and DNA bases making favourable interactions in the major groove of DNA. Here I analyze the occurrence of nucleotide-amino acid contacts in previously determined crystal structures of DNA-protein complexes and find that simple rules pertain. I also describe stereochemical rules for the probe helix type of DNA-binding motif found in certain transcription factors including leucine zipper and homeodomain proteins. These are a consequence of the binding geometry, and specify the amino acid and base positions used for the contacts, and the sizes of residues in the contact interface.nnnCONCLUSIONSnThe chemical rules can be generalized for any DNA-binding motif, while the stereochemical rules are specific to a particular DNA-binding motif. The recognition code for a particular binding motif can be described by combining the two sets of rules.

Role of base-backbone and base-base interactions in alternating DNA conformations

Sequence‐specific conformational differences between dinucleotide steps are characterised using published crystal coordinates with special attention to steric hindrance of the methyl group of a T base to the neighbouring base, and, more importantly, to the sugar‐phosphate backbone. The TT step is inflexible and B‐like, as it has two methyl groups which interlock with each other and with the sugar‐phosphate backbones. AT slides, or overtwists, so that the methyl groups move away from the backbones, both lead the step towards the A‐conformation. TA is most flexible as it does not have such restriction. These characteristics are observed with other pyrimidine‐pyrimidine, pyrimidine‐purine, purine‐pyrimidine steps, respectively, but to less extent, depending on the number of non‐A: T basepairs in the steps.

Classification of multi-helical DNA-binding domains and application to predict the DBD structures of σ factor, LysR, OmpR/PhoB, CENP-B, Rap1, and XylS/Ada/AraC

We have systematically compared structures of multihelical DNA‐binding domains (DBDs) which have been determined by crystallography or NMR spectroscopy. All the known multi‐helical DBDs are very similar. The core of these structures consists of two α‐helices in the helix‐turn‐helix combination, associated with one or two other helices. The structures can be classified according to either additional structural compositions or the configuration of the helices. Many DBDs, whose structures are currently unknown, have sequences which resemble those of known structures, permitting outlines of the new structures to be predicted.

Structure of the SPXX motif

To understand the structure of the DNA -binding SPXX motif, an analysis of Ser4—Pro2—X3—X 4 and Thr1-Pro2- X3- X4 structures observed in proteins is presented. About half (43-46 %) of the (S or T) PXX sequences fold into a (3-turn of type (I) or one of a few closely related turn structures. The turn structure has either or both of two compatible hydrogen bonds, one between CO of (Ser or Thr) and NH of X 4 (a standard P-turn type), and the other between OH of (Ser or Thr) and NH of X 3 (which we name the a type). Within the P-turn of the TPXX sequence, another type of hydrogen bond (which we name the I type) occurs between OH of Thr and NH of X 4 with the frequency of 72 %. These observations support a previous proposal that the (S or T) PXX sequences of DNA -binding proteins fold into a compact P-turn stabilized by a side-chain-main-chain interaction, which may be suitable to fit into the groove of DNA.

DNA conformation and its changes upon binding transcription factors

Abstract Pyrimidine-purine steps are flexible and can roll around the major groove. This feature is used to follow the protein surface and thereby create a particular superstructure of DNA. The interaction of the two molecules can be understood in terms of a close fitting of the two surfaces, in particular, how the DNA surface adapts to the protein surface. For analysing the fitting the widths of two DNA grooves are useful parameters. Much progress has been made since Schrodinger predicted “a gene to be an aperiodic solid (or a crystal)” ( 29 ) and we hope that our review may contribute in a small way.