Structure Determination of Protein−Protein Complexes Using NMR Chemical Shifts: Case of an Endonuclease Colicin−Immunity Protein Complex

Montalvao, Rinaldo W.; Cavalli, Andrea; Salvatella, Xavier; Blundell, Tom L.; Vendruscolo, Michele

doi:10.1021/ja805258z

Cited by 57 publications

(63 citation statements)

References 55 publications

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“…To address this problem, we built on recent findings that NMR structure determination of monomers can be greatly accelerated by coupling de novo modeling with backbone chemical shift data without further NOE, scalar coupling, residual dipolar coupling (RDC), or isotope-edited measurements (24,25). The structure of a dimeric complex was recently predicted from models of monomeric components generated using chemical shift fragments (26). We brought together the chemical-shiftderived fragment method with our symmetric folding-and-docking method to model eight complexes under investigation by the Northeast Structural Genomics consortium (NESG; Table 1).…”

Section: Inference Of Oligomeric Protein Structure From Chemical Shifmentioning

confidence: 99%

Simultaneous prediction of protein folding and docking at high resolution

Das

André

Shen

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

148

174

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Interleaved dimers and higher order symmetric oligomers are ubiquitous in biology but present a challenge to de novo structure prediction methodology: The structure adopted by a monomer can be stabilized largely by interactions with other monomers and hence not the lowest energy state of a single chain. Building on the Rosetta framework, we present a general method to simultaneously model the folding and docking of multiple-chain interleaved homo-oligomers. For more than a third of the cases in a benchmark set of interleaved homo-oligomers, the method generates near-native models of large ␣-helical bundles, interlocking ␤ sandwiches, and interleaved ␣/␤ motifs with an accuracy high enough for molecular replacement based phasing. With the incorporation of NMR chemical shift information, accurate models can be obtained consistently for symmetric complexes with as many as 192 total amino acids; a blind prediction was within 1 Å rmsd of the traditionally determined NMR structure, and fit independently collected RDC data equally well. Together, these results show that the Rosetta ''fold-and-dock'' protocol can produce models of homo-oligomeric complexes with nearatomic-level accuracy and should be useful for crystallographic phasing and the rapid determination of the structures of multimers with limited NMR information.homo-oligomers ͉ molecular replacement ͉ NMR structure inference ͉ protein structure prediction ͉ symmetry T he majority of expressed proteins function within symmetrical homomeric complexes (1-3). Although a boon for evolving functional diversity (4), this ubiquity of oligomeric structures poses numerous challenges for modern structural biology. The phasing of crystallographic data by molecular replacement and NMR structural inference are complicated by the increasing number of degrees of freedom and spectral degeneracy, respectively, in multimeric systems. The ability to predict de novo the structures of multiple interacting molecular chains would potentially alleviate these problems, allowing unphased diffraction measurements or ambiguously assigned NMR spectra to be resurrected as constraints or as independent validation for in silico structural inference.Accurate modeling of previously unseen homomeric structures has not been demonstrated at high resolution. Significant progress has occurred in modeling the folds of individual monomeric soluble proteins (5-7) and the docking arrangements of predefined monomers (8, 9). However, as proteins interact with other proteins, nucleic acids, or smaller molecules, their lowest free-energy backbone conformations typically shift in response to their partners. These often dramatic structural changes have been a persistent and unsolved issue in blind prediction trials of recent years (8).In this report, we show how two different methods developed for de novo conformational sampling (for folding and for docking) can be melded into a more general procedure that permits the blind prediction of intertwined complexes of proteins at near-atomic resolution. Some of th...

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Section: Inference Of Oligomeric Protein Structure From Chemical Shifmentioning

confidence: 99%

Simultaneous prediction of protein folding and docking at high resolution

Das

André

Shen

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

148

174

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“…65 We have developed a computer code called CamDock to enable the structures of protein-protein complexes to be determined by combining advanced docking methods 53 with the information provided by chemical shifts 53 and residual dipolar couplings. 66 It is then of very great importance to be able to relate the principles that emerge from studies in the test tube to analogous events occurring in the cell.…”

Section: Multiple Forms Of Protein Structurementioning

confidence: 99%

Quantitative approaches to defining normal and aberrant protein homeostasis

Vendruscolo

2009

Faraday Discuss.

Self Cite

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Protein homeostasis refers to the ability of cells to generate and regulate the levels of their constituent proteins in terms of conformations, interactions, concentrations and cellular localisation. We discuss here an approach in which physico-chemical properties of proteins and their environments are used to understand the underlying principles governing this process, which is crucial in all living systems. By adopting the strategy of characterising the origins of specific diseases to inform us about normal biology, we are bringing together methods and concepts from chemistry, physics, engineering, genetics and medicine. In particular, we are using a combination of in vitro, in silico and in vivo approaches to study protein homeostasis through the analysis of the effects that result from its perturbation in a select group of specific proteins, from either amino acid mutations, or changes in concentration and solubility, or interactions with other molecules. By developing a coherent and quantitative description of such phenomena, we are finding that it is possible to shed new light on how the physical and chemical properties of the cellular components can provide an understanding of the normal and aberrant behaviour of living systems. Through such an approach it is possible to provide new insights into the origin and consequences of the failure to maintain homeostasis that is associated with neurodegenerative diseases, in particular, and the phenomenon of ageing, in general, and hence provide a framework for the rational design of therapeutic approaches.

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“…An important consequence of exosite binding is that much of the sequence diversity in these proteins is found at the protein-protein interface, 23 a result of the positive selection for novel colicin DNase-Im variants between competing bacterial populations. These properties, along with the extensive characterization of colicin DNase-Im protein complexes reported in the literature, have led to their being adopted as a model system for investigating the coevolution of PPIs, 24 the development of NMR-based methods for structure determination of PPIs, 25 testing of the latest methodologies for computational docking of PPIs, 26 molecular dynamics simulations to follow PPI association, 27 and the directed evolution and design of PPI specificity. 4,[28][29][30] Cognate colicin DNase-Im protein complexes are high-affinity PPIs, exhibiting K d values of ∼10 − 14 -10 − 16 M, while noncognate complexes, which also inhibit nuclease activity, display binding that is 6-10 orders of magnitude weaker.…”

Section: Introductionmentioning

confidence: 99%