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Frameworks for understanding long-range intra-protein communication.

ABSTRACT: The phenomenon of intra-protein communication is fundamental to such processes as allostery and signaling, yet comparatively little is understood about its physical origins despite notable progress in recent years. This review introduces contemporary but distinct frameworks for understanding intra-protein communication by presenting both the ideas behind them and a discussion of their successes and shortcomings. The first framework holds that intra-protein communication is accomplished by the sequential mechanical linkage of residues spanning a gap between distal sites. According to the second framework, proteins are best viewed as ensembles of distinct structural microstates, the dynamical and thermodynamic properties of which contribute to the experimentally observable macroscale properties. Nuclear magnetic resonance (NMR) spectroscopy is a powerful method for studying intra-protein communication, and the insights into both frameworks it provides are presented through a discussion of numerous examples from the literature. Distinct from mechanical and thermodynamic considerations of intra-protein communication are recently applied graph and network theoretic analyses. These computational methods reduce complex three dimensional protein architectures to simple maps comprised of nodes (residues) connected by edges (inter-residue "interactions"). Analysis of these graphs yields a characterization of the protein's topology and network characteristics. These methods have shown proteins to be "small world" networks with moderately high local residue connectivities existing concurrently with a small but significant number of long range connectivities. However, experimental studies of the tantalizing idea that these putative long range interaction pathways facilitate one or several macroscopic protein characteristics are unfortunately lacking at present. This review concludes by comparing and contrasting the presented frameworks and methodologies for studying intra-protein communication and suggests a manner in which they can be brought to bear simultaneously to further enhance our understanding of this important fundamental phenomenon.

SUBMITTER: Whitley MJ

PROVIDER: S-EPMC2749244 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature

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Frameworks for understanding long-range intra-protein communication.

Whitley Matthew J MJ Lee Andrew L AL

Current protein & peptide science 20090401 2

The phenomenon of intra-protein communication is fundamental to such processes as allostery and signaling, yet comparatively little is understood about its physical origins despite notable progress in recent years. This review introduces contemporary but distinct frameworks for understanding intra-protein communication by presenting both the ideas behind them and a discussion of their successes and shortcomings. The first framework holds that intra-protein communication is accomplished by the se ...[more]

PMID: 19355979

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Project description:Record-breaking magnetic exchange interactions have previously been reported for 3d-metal dimers of the form [M(Pt(SAc)4)(pyNO2)]2 (M = Ni or Co) that are linked in the solid state via metallophilic Pt⋯Pt bridges. This contrasts the terminally capped monomers [M(Pt(SAc)4)(py)2], for which neither metallophilic bridges nor magnetic exchange interactions are found. Computational modeling has shown that the magnetic exchange interaction is facilitated by the pseudo-closed shell d8⋯d8 metallophilic interaction between the filled Pt2+ 5d z 2 orbitals. We present here inelastic neutron scattering experiments on these complexes, wherein the dimers present an oscillatory momentum-transfer-dependence of the magnetic transitions. This allows for the unequivocal experimental assignment of the distance between the coupled ions, which matches exactly the coupling pathway via the metallophilic bridges. Furthermore, we have synthesized and magnetically characterized the isostructural palladium-analogues. The magnetic coupling across the Pd⋯Pd bridge is found through SQUID-magnetometry and FD-FT THz-EPR spectroscopy to be much weaker than via the Pt⋯Pt bridge. The weaker coupling is traced to the larger radial extent of the 5d z 2 orbitals compared to that of the 4d z 2 orbitals. The existence of a palladium metallophilic interaction is evaluated computationally from potential surface cuts along the metal stretching direction. Similar behavior is found for the Pd⋯Pd and Pt⋯Pt-systems with clear minima along this coordinate and provide estimates for the force constant for this distortion. The estimated M⋯M stretching frequencies are found to match experimental observed, polarized bands in single-crystal Raman spectra close to 45 cm-1. This substantiates the existence of energetically relevant Pd⋯Pd metallophilic interactions. The unique properties of both Pt2+ and Pd2+ constitutes an orthogonal reactivity, which can be utilized for steering both the direction and strength of magnetic interactions.

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Frameworks for understanding long-range intra-protein communication.

Publications

Frameworks for understanding long-range intra-protein communication.

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