Evaluation of Energetic and Dynamic Coupling Networks in a PDZ Domain Protein

Fuentes, Ernesto J.; Gilmore, Stephen; Mauldin, Randall V.; Lee, Andrew L.

doi:10.1016/j.jmb.2006.08.076

Cited by 117 publications

(197 citation statements)

References 51 publications

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“…A well-studied example for systems showing ligand-induced allostery are modular domains for protein-protein interactions denoted as PSD95/Discs large/ZO-1 (PDZ) domains. [11][12][13][14][15][16][17][18][19][20] These domains occur in a set of proteins typically associated with cell junctions and mediate the clustering of membrane ion channels by binding to their C-termini. [15][16][17] PDZ domains share a common fold which consists of two α-helices and six β -strands, with the second α-helix and the second β -strand forming the canonical binding groove ( Figure Figure 1).…”

Section: Introductionmentioning

confidence: 99%

Long-Range Conformational Transition of a Photoswitchable Allosteric Protein: Molecular Dynamics Simulation Study

et al. 2014

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A local perturbation of a protein may lead to functional changes at some distal site. An example is the PDZ2 domain of human tyrosine phosphatase 1E which shows an allosteric transition upon binding to a peptide ligand. Recently Buchli et al. presented a time-resolved study of this transition by covalently linking an azobenzene photoswitch across the binding groove and using a femtosecond laser pulse that triggers the cis-trans photoisomerization of azobenzene. To aid the interpretation of these experiments, in this work seven microsecond runs of all-atom molecular dynamics simulations each for the wild-type PDZ2 in the ligandbound and -free state, as well as the photoswitchable protein (PDZ2S) in the cis and the trans state of the photoswitch, in explicit water. First the theoretical model is validated by recalculating the available NMR data from the simulations. By comparing the results for PDZ2 and PDZ2S, it is analyzed to what extent the photoswitch indeed mimics the free-bound transition. A detailed description of the conformational rearrangement following the cis-trans photoisomerization of PDZ2S reveals a series of photoinduced structural changes, that propagate from the anchor residues of the photoswitch via intermediate secondary structure segments to the C-terminus of PDZ2S. The changes of the conformational distribution of the C-terminal region is considered as the distal response of the isolated allosteric protein. October 9, 2014 * To whom correspondence should be addressed 1 Abstract A local perturbation of a protein may lead to functional changes at some distal site. An example is the PDZ2 domain of human tyrosine phosphatase 1E which shows an allosteric transition upon binding to a peptide ligand. Recently Buchli et al. presented a time-resolved study of this transition by covalently linking an azobenzene photoswitch across the binding groove and using a femtosecond laser pulse that triggers the cis-trans photoisomerization of azobenzene. To aid the interpretation of these experiments, in this work seven microsecond runs of all-atom molecular dynamics simulations each for the wild-type PDZ2 in the ligandbound and -free state, as well as the photoswitchable protein (PDZ2S) in the cis and the trans state of the photoswitch, in explicit water. First the theoretical model is validated by recalculating the available NMR data from the simulations. By comparing the results for PDZ2 and PDZ2S, it is analyzed to what extent the photoswitch indeed mimics the free-bound transition. A detailed description of the conformational rearrangement following the cis-trans photoisomerization of PDZ2S reveals a series of photoinduced structural changes, that propagate from the anchor residues of the photoswitch via intermediate secondary structure segments to the C-terminus of PDZ2S. The changes of the conformational distribution of the C-terminal region is considered as the distal response of the isolated allosteric protein.

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Section: Introductionmentioning

confidence: 99%

Long-Range Conformational Transition of a Photoswitchable Allosteric Protein: Molecular Dynamics Simulation Study

et al. 2014

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“…More accurate modeling of side-chain conformational flexibility may also be important for structure-based drug design, when a target protein changes its binding site in response to binding different small molecules 11 . Work by Ranganathan and others [12][13][14][15][16][17][18] has provided intriguing evidence for the existence of "communication pathways" in proteins to facilitate the transmission of signals between allosteric and active sites. NMR experiments on several systems suggest that side-chains may play an important role in mediating this conformational coupling 19 .…”

Section: Introductionmentioning

confidence: 99%

A Simple Model of Backbone Flexibility Improves Modeling of Side-chain Conformational Variability

Friedland

Linares

Smith

et al. 2008

Journal of Molecular Biology

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The considerable flexibility of side-chains in folded proteins is important for protein stability and function, and may play a role in mediating pathways of energetic connectivity between allosteric sites. While sampling side-chain degrees of freedom has been an integral part of several successful computational protein design methods, the predictions of these approaches have not been directly compared to experimental measurements of side-chain motional amplitudes. In addition, protein design methods generally keep the backbone fixed, an approximation that may substantially limit the ability to accurately model side-chain flexibility. Here we describe a Monte Carlo approach to modeling side-chain conformational variability and validate our method against a large dataset of methyl relaxation order parameters derived from Nuclear Magnetic Resonance experiments (17 proteins and a total of 530 data points). We also evaluate a model of backbone flexibility based on Backrub motions, a type of conformational change frequently observed in ultra-high resolution Xray structures that accounts for correlated side-chain backbone movements. The fixed-backbone model performs reasonably well with an overall rmsd between computed and predicted side-chain order parameters of 0.26. Notably, including backbone flexibility leads to significant © 2008 Elsevier Ltd. All rights reserved. * Corresponding author: Kortemme@cgl.ucsf.edu. AUTHOR CONTRIBUTIONSGDF and TK conceived and designed the experiments. GDF and AJL performed the experiments. GDF, TK, and AJL analyzed the data and wrote the paper. CAS contributed reagents/materials/analysis tools. SUPPORTING INFORMATION AVAILABLEOne figure with population distributions of ubiquitin I13 and L15 chi 1 and chi 2. One table with detailed results from Model 1; one table with results from Models 2 and 3 for nonpolar methyl groups only; and one table with detailed parameter sensitivity results from Model 2.Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. NIH Public Access

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“…Although the PDZ domain family has served as a prime model system for these studies, experimental data that detect intramolecular allosteric pathways are scarce and sometimes conflicting (16,20,21).…”

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confidence: 99%

Sequence-specific Long Range Networks in PSD-95/Discs Large/ZO-1 (PDZ) Domains Tune Their Binding Selectivity

Gianni

Haq

Montemiglio

et al. 2011

Journal of Biological Chemistry

113

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Protein-protein interactions mediated by modular protein domains are critical for cell scaffolding, differentiation, signaling, and ultimately, evolution. Given the vast number of ligands competing for binding to a limited number of domain families, it is often puzzling how specificity can be achieved. Selectivity may be modulated by intradomain allostery, whereby a remote residue is energetically connected to the functional binding site via side chain or backbone interactions. Whereas several energetic pathways, which could mediate intradomain allostery, have been predicted in modular protein domains, there is a paucity of experimental data to validate their existence and roles. Here, we have identified such functional energetic networks in one of the most common protein-protein interaction modules, the PDZ domain. We used double mutant cycles involving site-directed mutagenesis of both the PDZ domain and the peptide ligand, in conjunction with kinetics to capture the fine energetic details of the networks involved in peptide recognition. We performed the analysis on two homologous PDZ-ligand complexes and found that the energetically coupled residues differ for these two complexes. This result demonstrates that amino acid sequence rather than topology dictates the allosteric pathways. Furthermore, our data support a mechanism whereby the whole domain and not only the binding pocket is optimized for a specific ligand. Such cross-talk between binding sites and remote residues may be used to fine tune target selectivity.Several studies on protein-protein interaction modules (1), such as SH2, SH3, and PDZ 5 domains, have highlighted the apparent problem of how selectivity is achieved in a cellular context (2-4). For example, the synapse contains several PDZ proteins (5) with apparently overlapping specificity, and yet they have distinct roles in scaffolding and signaling (6). One mechanism that could modulate specificity is intradomain allostery (7). Multisubunit proteins such as hemoglobin are well known for their allosteric behavior whereby the oxygen binding is cooperative because ligation of one subunit will modulate the affinity in the other subunits of the tetramer (8). But allostery is also present within monomeric proteins (9), and it may be invoked even in the absence of a detectable conformational change (10 -15).Previous studies on monomeric globular proteins have predicted allosteric pathways on an amino acid residue level based on analysis of co-evolution (16, 17), molecular dynamics simulations (18), or NMR-constrained molecular dynamics (19). Although the PDZ domain family has served as a prime model system for these studies, experimental data that detect intramolecular allosteric pathways are scarce and sometimes conflicting (16,20,21).In protein folding studies, it proved illuminating to compare homologous proteins to unravel basic determinants of the underlying mechanism (22). Here, we employ the same strategy to assess the structural pattern of intradomain allostery by looking at the coupling fr...

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Evaluation of Energetic and Dynamic Coupling Networks in a PDZ Domain Protein

Cited by 117 publications

References 51 publications

Long-Range Conformational Transition of a Photoswitchable Allosteric Protein: Molecular Dynamics Simulation Study

Long-Range Conformational Transition of a Photoswitchable Allosteric Protein: Molecular Dynamics Simulation Study

A Simple Model of Backbone Flexibility Improves Modeling of Side-chain Conformational Variability

Sequence-specific Long Range Networks in PSD-95/Discs Large/ZO-1 (PDZ) Domains Tune Their Binding Selectivity

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