NMR studies of dynamic biomolecular conformational ensembles

Abstract

Multidimensional heteronuclear NMR approaches can provide nearly complete sequential signal assignments of isotopically enriched biomolecules. The availability of assignments together with measurements of spin relaxation rates, residual spin interactions, J-couplings and chemical shifts provides information at atomic resolution about internal dynamics on timescales ranging from ps to ms, both in solution and in the solid state. However, due to the complexity of biomolecules, it is not possible to extract a unique atomic-resolution description of biomolecular motions even from extensive NMR data when many conformations are sampled on multiple timescales. For this reason, powerful computational approaches are increasingly applied to large NMR data sets to elucidate conformational ensembles sampled by biomolecules. In the past decade, considerable attention has been directed at an important class of biomolecules that function by binding to a wide variety of target molecules. Questions of current interest are: “Does the free biomolecule sample a conformational ensemble that encompasses the conformations found when it binds to various targets; and if so, on what time scale is the ensemble sampled?” This article reviews recent efforts to answer these questions, with a focus on comparing ensembles obtained for the same biomolecules by different investigators. A detailed comparison of results obtained is provided for three biomolecules: ubiquitin, calmodulin and the HIV-1 trans-activation response RNA.

Information content of long-range NMR data for the characterization of conformational heterogeneity

“…In many experimental studies RDCs have been shown to be precious restraints for analyzing molecular conformational freedom (Montalvao et al., 2014; Ravera et al, 2014; Camilloni and Vendruscolo, 2015; Torchia, 2015). Here we compared paramagnetic and diamagnetic RDCs and found substantial differences in their information content in the case of multidomain proteins.…”

“…Characterization of such rearrangements and the relevant conformational states can provide important clues about the mechanisms underlying biological function. This however is a challenging task because the system is underdetermined, implying a large degeneracy in the reconstructed solutions, and requires extensive experimental work often involving multiple techniques (Bonvin and Brunger, 1996; Choy and Forman-Kay, 2001; Svergun et al, 2001; Burgi et al, 2001; Clore and Schwieters, 2004; Schroeder et al, 2004; Iwahara et al, 2004; Bertini et al, 2004a; Blackledge, 2005; Lindorff-Larsen et al, 2005; Fragai et al, 2006; Tolman and Ruan, 2006; Boehr et al, 2006; Ryabov and Fushman, 2006; Chen et al, 2007; Bernadò et al, 2007; Bertini et al, 2007; Ryabov and Fushman, 2007; Lange et al, 2008; Hulsker et al, 2008; Korzhnev and Kay, 2008; Nodet et al, 2009; Boehr et al, 2009; Stelzer et al, 2009; Huang and Grzesiek, 2010; Fisher et al, 2010; Bashir et al, 2010; Rinnenthal et al, 2011; Bothe et al, 2011; Fisher and Stultz, 2011; Berlin et al, 2013; Russo et al, 2013; Guerry et al, 2013; Kukic et al, 2014; Ravera et al, 2014; Torchia, 2015). Therefore, it is important to know the information content provided by various experimental methods in order to decide on an optimal set of experiments a priori .…”

Studying dynamics by magic-angle spinning solid-state NMR spectroscopy: Principles and applications to biomolecules

“…An operator Q in the laboratory frame is transformed into the interaction frame according to (3) Here, the notation '~' over an operator indicates that it is in the interaction frame. The modified Liouville-von-Neumann equation in the interaction frame is given by (4) and no longer contains the deterministic part of the Hamiltonian explicitly.…”

“…Over the last decades a wide array of techniques have been developed to study (bio-)molecular dynamics by solution-state NMR spectroscopy. Nowadays, a range of different aspects of dynamics can be probed routinely by solution-state NMR, such as the amplitude of fast (picosecond-to-nanosecond) internal motion, properties of overall rotational tumbling as well as exchange processes occurring on millisecond time scales, often involving a small number of distinct states [1][2][3][4][5]. In addition to these equilibrium experiments, kinetic off-equilibrium approaches are available to study processes such as slow folding/unfolding and binding [6][7][8].…”

X-ray crystallography over the past decade for novel drug discovery – where are we heading next?

“…Solution NMR, however, provide information about the dynamics of the molecules studied, represented as an ensemble of structures with varying conformations. The incorporation of NMR data to evaluate the flexibility of various regions of a macromolecule, especially at substrate binding sites, is of particular interest for examining drug binding and release mechanisms [50]. EPR also provides additional information about different conformation states of the protein [51,52].…”