The role of backbone motions in ligand binding to the c-Src SH3 domain

Wang, Chunyu; Pawley, Norma H.; Nicholson, Linda

doi:10.1006/jmbi.2001.5083

Cited by 91 publications

(125 citation statements)

References 72 publications

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“…The free state is estimated to have τ m of 7.57 ± 0.08 nsec with D ∥ /D⊥ = 0.81 ± 0.07 (oblate) and the pT868-bound state to have τ m of 10.70 ± 0.07 with D ∥ /D⊥ = 1.21 ± 0.06 (prolate). (Note that a prolate to oblate shift was reported for peptide binding to an SH3 domain (13).) For the free and bound states, both oblate and prolate axially symmetric fits are acceptable with high statistical confidence and have χ 2 similar to within 10%.…”

Section: Hydrodynamics Of Ki-fha Free and Bound To Clv1 Pt868 Peptidementioning

confidence: 77%

“…This could provide part of the compensating favorable enthalpy driving the association of pThr peptides to KI-FHA (Ding et al, to be published) and to another FHA domain (3). Peptide binding was also observed to rigidify and stabilize an SH3 domain both near and far from the interface (13). Precedent for enthalpic stabilization at long-range was suggested by antibody binding to lysozyme increasing its hydrogen exchange protection to the distal side (80).…”

Section: Significance Of Pthr Peptide Binding-dependent Flexibility Cmentioning

confidence: 99%

“…Phosphopeptide binding does not appear to alter the structure of FHA domains significantly (4,6,(24)(25)(26). This suggests that FHA domains may use a rigid, pre-formed surface for recognizing phosphoprotein partners.Many protein-protein interaction sites do, however, have some flexibility revealed by NMR relaxation, often fluctuating over the µsec to msec range (12,13,(27)(28)(29)(30)(31)(32)(33). NMR relaxation rates result from the density of motions that reorient the bond probed, described by spectral density functions that are Fourier transforms of time correlation functions of the bond reorientation.…”

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confidence: 99%

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PhosphoThr Peptide Binding Globally Rigidifies Much of the FHA Domain from Arabidopsis Receptor Kinase-Associated Protein Phosphatase^,

et al. 2005

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A net increase in the backbone rigidity of the kinase-interacting FHA domain (KI-FHA) from the Arabidopsis receptor kinase-associated protein phosphatase (KAPP) accompanies the binding of a phosphoThr peptide from its CLV1 receptor-like kinase partner, according to 15 N NMR relaxation at 11.7 and 14.1 T. All of the loops of free KI-FHA display evidence of nsec-scale motions. Many of these same residues have residual dipolar couplings that deviate from structural predictions. Binding of the CLV1 pT868 peptide seems to reduce nsec-scale fluctuations of all loops, including half of the residues of recognition loops. Residues important for affinity are found to be rigid, i.e. conserved residues and residues of the subsite for the key pT+3 peptide position. -This behavior parallels SH2 and PTB domain recognition of pTyr peptides. PhosphoThr peptide binding increases KI-FHA backbone rigidity (S 2 ) of three recognition loops, a loop nearby, seven strands from the β-sandwich, and a distal loop. Compensating the trend of increased rigidity, binding enhances fast mobility at a few sites in four loops on the periphery of the recognition surface and in two loops on the far side of the β-sandwich. Line broadening evidence of µsec to msec-scale fluctuations occurs across the six-stranded β-sheet and nearby edges of the β-sandwich; this forms a network connected by packing of interior side chains and H-bonding. A patch of the slowly fluctuating residues coincides with the site of segment-swapped dimerization in crystals of the FHA domain of human Chfr. Phosphopeptide binding introduces µsec to msec-scale fluctuations to more residues of the long 8/9 *To whom correspondence should be addressed, E-mail: vandorens@missouri.edu, Phone: 1 (573) 882-5113, FAX: 1 (573) 884-4812. † These authors contributed equally to this work. ‡ Current address: Department of Chemistry, 225 Prospect St., Yale University, New Haven, CT 06520The NMR relaxation data and their model-free interpretation are available for free and bound KI-FHA under BMRB accession codes 5841 and 6474 at www.bmrb.wisc.edu. NIH Public Access Author ManuscriptBiochemistry. Author manuscript; available in PMC 2010 January 29. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript recognition loop of KI-FHA. The rigidity of this FHA domain appears to couple as a whole to pThr peptide binding. KeywordsFHA domain; phosphoThr-binding module; protein-protein interactions; NMR relaxation; relaxation dispersion; dynamics; residual dipolar couplings FHA domains bind phosphothreonine-and phosphoserine-containing partners in diverse eukaryotic signaling pathways that include DNA damage repair, cell proliferation, pre-mRNA splicing, forkhead transcription factors, Ring-finger proteins, and kinesins (1). Several highresolution structures of FHA domains have appeared (2-8), but no detailed studies of their dynamics. Flexibility often appears to correlate with binding events, including affinity of protein modules for peptides (9-11). Residue-specific effects on...

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Section: Hydrodynamics Of Ki-fha Free and Bound To Clv1 Pt868 Peptidementioning

confidence: 77%

Section: Significance Of Pthr Peptide Binding-dependent Flexibility Cmentioning

confidence: 99%

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confidence: 99%

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PhosphoThr Peptide Binding Globally Rigidifies Much of the FHA Domain from Arabidopsis Receptor Kinase-Associated Protein Phosphatase^,

et al. 2005

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“…Pseudo-3D versions of the inversion recovery and CPMG pulse sequences modified to include a water flip-back pulse and sensitivity enhancement were used to measure T 1 and T 2 rates, respectively (52,53). Both experiments included 1024 complex points with a spectral width of 14.28 ppm in the t 2 dimension and 256 complex points with a spectral width of 31.82 ppm in the t 1 dimension.…”

Section: Nmr Spin Relaxation Measurements and Reduced Spectral Densitmentioning

confidence: 99%

Free energy landscape remodeling of the cardiac pacemaker channel explains the molecular basis of familial sinus bradycardia

Boulton¹,

Akimoto

Akbarizadeh

et al. 2017

Journal of Biological Chemistry

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Edited by Norma AllewellThe hyperpolarization-activated and cyclic nucleotide-modulated ion channel (HCN) drives the pacemaker activity in the heart, and its malfunction can result in heart disorders. One such disorder, familial sinus bradycardia, is caused by the S672R mutation in HCN, whose electrophysiological phenotypes include a negative shift in the channel activation voltage and an accelerated HCN deactivation. The outcomes of these changes are abnormally low resting heart rates. However, the molecular mechanism underlying these electrophysiological changes is currently not fully understood. Crystallographic investigations indicate that the S672R mutation causes limited changes in the structure of the HCN intracellular gating tetramer, but its effects on protein dynamics are unknown. Here, we utilize comparative S672R versus WT NMR analyses to show that the S672R mutation results in extensive perturbations of the dynamics in both apo-and holo-forms of the HCN4 isoform, reflecting how S672R remodels the free energy landscape for the modulation of HCN4 by cAMP, i.e. the primary cyclic nucleotide modulator of HCN channels. We show that the S672R mutation results in a constitutive shift of the dynamic auto-inhibitory equilibrium toward inactive states of HCN4 and broadens the free-energy well of the apo-form, enhancing the millisecond to microsecond dynamics of the holo-form at sites critical for gating cAMP binding. These S672R-induced variations in dynamics provide a molecular basis for the electrophysiological phenotypes of this mutation and demonstrate that the pathogenic effects of the S672R mutation can be rationalized primarily in terms of modulations of protein dynamics.

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“…Nonetheless, all thermodynamic studies of SH3 ligand binding reported to date have surprisingly revealed an invariantly negative binding enthalpy that is partially compensated by unfavorable entropic contributions (12)(13)(14)(15)(16)(17). This thermodynamic behavior, which cannot be rationalized exclusively in terms of direct interactions between hydrophobic surfaces, reveals an underlying complexity in the recognition of proline-rich ligands by SH3 domains.…”

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confidence: 96%

Role of Interfacial Water Molecules in Proline-rich Ligand Recognition by the Src Homology 3 Domain of Abl

Palencia

Cámara-Artigas

Pisabarro

et al. 2010

Journal of Biological Chemistry

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The interaction of Abl-Src homology 3 domain (SH3) with the high affinity peptide p41 is the most notable example of the inconsistency existing between the currently accepted description of SH3 complexes and their binding thermodynamic signature. We had previously hypothesized that the presence of interfacial water molecules is partially responsible for this thermodynamic behavior. We present here a thermodynamic, structural, and molecular dynamics simulation study of the interaction of p41 with Abl-SH3 and a set of mutants designed to alter the water-mediated interaction network. Our results provide a detailed description of the dynamic properties of the interfacial water molecules and a molecular interpretation of the thermodynamic effects elicited by the mutations in terms of the modulation of the water-mediated hydrogen bond network. In the light of these results, a new dual binding mechanism is proposed that provides a better description of proline-rich ligand recognition by Abl-SH3 and that has important implications for rational design.The recognition of proline-rich sequences by protein-protein interaction modules, such as SH3 3 or WW domains, is one of the most common mechanisms by which specific, transient protein-protein interactions are established within the cell. SH3 domains are found in oncoproteins and proteins overexpressed in deregulated signaling pathways during cancer development and are also associated with other pathologies such as AIDS, osteoporosis, or inflammatory processes (1-2). Inhibitors of the interactions between SH3 domains and their partners have proved to be promising therapeutic agents, validating these domains as attractive targets for drug design (3-6). Nevertheless, despite the wealth of structural and functional information collected during the last 2 decades, the forces driving proline-rich ligand recognition by SH3 domains are still not fully understood.SH3 domains fold into a ␤-barrel structure composed of two orthogonal anti-parallel three-stranded ␤-sheets connected by three main loops (RT, n-Src, and distal loops). The binding site is a relatively flat, hydrophobic surface that consists of three shallow pockets. SH3 ligands typically contain the PpP motif (where and p are frequently hydrophobic and proline residues, respectively) and bind in a PPII conformation so that each of the P moieties packs tightly into one hydrophobic pocket formed by highly conserved aromatic residues on the surface of the domain. Additional interactions, which have been proposed to confer increased affinity and specificity, are established between residues flanking the core motif in the ligand and a third pocket delimited by the RT and n-Src loops, whose sequences vary among different SH3 domains (7-9).According to this description, the recognition of proline-rich sequences by SH3 domains, based primarily in the burial of hydrophobic surfaces in the ligand and SH3-binding site (7, 9), would be expected to present a thermodynamic signature dominated by the hydrophobic effect, with the main dr...

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The role of backbone motions in ligand binding to the c-Src SH3 domain

Cited by 91 publications

References 72 publications

PhosphoThr Peptide Binding Globally Rigidifies Much of the FHA Domain from Arabidopsis Receptor Kinase-Associated Protein Phosphatase^,

PhosphoThr Peptide Binding Globally Rigidifies Much of the FHA Domain from Arabidopsis Receptor Kinase-Associated Protein Phosphatase^,

Free energy landscape remodeling of the cardiac pacemaker channel explains the molecular basis of familial sinus bradycardia

Role of Interfacial Water Molecules in Proline-rich Ligand Recognition by the Src Homology 3 Domain of Abl

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The role of backbone motions in ligand binding to the c-Src SH3 domain

Cited by 91 publications

References 72 publications

PhosphoThr Peptide Binding Globally Rigidifies Much of the FHA Domain from Arabidopsis Receptor Kinase-Associated Protein Phosphatase,

PhosphoThr Peptide Binding Globally Rigidifies Much of the FHA Domain from Arabidopsis Receptor Kinase-Associated Protein Phosphatase,

Free energy landscape remodeling of the cardiac pacemaker channel explains the molecular basis of familial sinus bradycardia

Role of Interfacial Water Molecules in Proline-rich Ligand Recognition by the Src Homology 3 Domain of Abl

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PhosphoThr Peptide Binding Globally Rigidifies Much of the FHA Domain from Arabidopsis Receptor Kinase-Associated Protein Phosphatase^,

PhosphoThr Peptide Binding Globally Rigidifies Much of the FHA Domain from Arabidopsis Receptor Kinase-Associated Protein Phosphatase^,