Changes in conformational dynamics of basic side chains upon protein–DNA association

Abstract

Basic side chains play major roles in recognition of nucleic acids by proteins. However, dynamic properties of these positively charged side chains are not well understood. In this work, we studied changes in conformational dynamics of basic side chains upon protein–DNA association for the zinc-finger protein Egr-1. By nuclear magnetic resonance (NMR) spectroscopy, we characterized the dynamics of all side-chain cationic groups in the free protein and in the complex with target DNA. Our NMR order parameters indicate that the arginine guanidino groups interacting with DNA bases are strongly immobilized, forming rigid interfaces. Despite the strong short-range electrostatic interactions, the majority of the basic side chains interacting with the DNA phosphates exhibited high mobility, forming dynamic interfaces. In particular, the lysine side-chain amino groups exhibited only small changes in the order parameters upon DNA-binding. We found a similar trend in the molecular dynamics (MD) simulations for the free Egr-1 and the Egr-1–DNA complex. Using the MD trajectories, we also analyzed side-chain conformational entropy. The interfacial arginine side chains exhibited substantial entropic loss upon binding to DNA, whereas the interfacial lysine side chains showed relatively small changes in conformational entropy. These data illustrate different dynamic characteristics of the interfacial arginine and lysine side chains.

Internal Motions of Basic Side Chains of the Antennapedia Homeodomain in the Free and DNA-Bound States

“…14 This trend was confirmed in the current study on the Antp homeodomain. The side chains R3, R28, R43, K46, K55, and K57 in the DNA-bound state exhibited order parameters S 2 between 0.19 and 0.55, indicating substantial mobility, although they form intermolecular ion pairs with DNA.…”

“…Using these data, we determined the generalized order parameters ( S 2 ) 21 for the Arg N ε -H ε bonds of the Antp homeodomain in the free and DNA-bound states, as described. 14 The S 2 parameter satisfies the inequalities of 0 ≤ S 2 ≤ 1, and represents a measure of the degree of spatial restriction of internal motion. 21 Changes in order parameters upon molecular association are related to changes in conformational entropy.…”

“…5–13 Using these methods, we recently studied changes in the mobility of the basic side chains of the Egr-1 zinc-finger protein upon association with its target DNA. 14 Interestingly, the basic side chains that form ion pairs with the DNA phosphates were found to retain high mobility despite the simultaneous presence of hydrogen bonds and strong short-range electrostatic interactions. This trend was particularly remarkable for the Lys side chains.…”

Protein–DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors

“…This is in line with recent NMR and simulations studies of the dynamics of lysine salt bridges in protein/DNA complexes (5,41,42). A very recent extension of this work shows that, in contrast, arginines bound to guanine in a bidentate manner within a Zn-finger complex are much less dynamic (43). The proteins we have studied here have no such cases, but we do see the almost permanent presence of interactions from a single arginine (R7) to two adjacent bases, and a similar double interaction involving an asparagine (N10) within the SRY complex.…”

Structural Basis of MeCP2 Distribution on Non-CpG Methylated and Hydroxymethylated DNA

“…1A) [12]. The genetic, biochemical and biophysical properties of mCG and hmCG binding by MBD proteins have been extensively studied [10,15–19]. MeCP2, however, is the first MBD protein with demonstrated selectivity for asymmetrically methylated mCH and hmCH [5–8].…”