Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: implications for the entropy of association with DNA

Bracken, Clay; Carr, Peter A.; Cavanagh, John; Palmer, Arthur G.

doi:10.1006/jmbi.1998.2429

Cited by 213 publications

(301 citation statements)

References 71 publications

Supporting

Mentioning

270

Contrasting

Unclassified

Order By: Relevance

“…The difference in R 2 rates at 850 and 700 MHz was then computed, and significant changes in microsecond to millisecond dynamics were identified using an approach similar to the one described above for the reduced spectral density analysis. The S 2 order parameters were calculated from J(0) and J( N ϩ H ) as described previously (54,55). The S 2 distributions were modeled through non-linear fitting with both one and two Gaussian curves.…”

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

View full text Add to dashboard Cite

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.

show abstract

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

View full text Add to dashboard Cite

show abstract

“…(1). 36,37 s c;i ¼ 1=x N fðJð0Þ i À Jðx N Þ i Þ=Jðx N Þ i g 1=2 (1) Furthermore, an approximate order parameter (S 2 ) has been obtained directly from J(0) and J(x N ) using Eq. (2).…”

Section: Spectral Density Functions and Order Parametersmentioning

confidence: 99%

Dynamics of a truncated prion protein, PrP(113–231), from ¹⁵N NMR relaxation: Order parameters calculated and slow conformational fluctuations localized to a distinct region

et al. 2009

View full text Add to dashboard Cite

Prion diseases are associated with the misfolding of the prion protein (PrP C ) from a largely a-helical isoform to a b-sheet rich oligomer (PrP Sc ). Flexibility of the polypeptide could contribute to the ability of PrP C to undergo the conformational rearrangement during PrP C -PrP Sc interactions, which then leads to the misfolded isoform. We have therefore examined the molecular motions of mouse PrP C , residues 113-231, in solution, using 15 N NMR relaxation measurements. A truncated fragment has been used to eliminate the effect of the 90-residue unstructured tail of PrP C so the dynamics of the structured domain can be studied in isolation. 15 N longitudinal (T 1 ) and transverse relaxation (T 2 ) times as well as the proton-nitrogen nuclear Overhauser effects have been used to calculate the spectral density at three frequencies, 0, x N, and 0.87x H . Spectral densities at each residue indicate various time-scale motions of the main-chain. Even within the structured domain of PrP C , a diverse range of motions are observed. We find that removal of the tail increases T 2 relaxation times significantly indicating that the tail is responsible for shortening of T 2 times in full-length PrP C . The truncated fragment of PrP has facilitated the determination of meaningful order parameters (S 2 ) from the relaxation data and shows for the first time that all three helices in PrP C have similar rigidity. Slow conformational fluctuations of mouse PrP C are localized to a distinct region that involves residues 171 and 172. Interestingly, residues 170-175 have been identified as a segment within PrP that will form a steric zipper, believed to be the fundamental amyloid unit. The flexibility within these residues could facilitate the PrP C -PrP Sc recognition process during fibril elongation.

show abstract

“…Alternatively, 15 N relaxation data are occasionally interpreted by the reduced spectral density approach. Examples of its application in molecular recognition are refs (33,37). Without explicit modeling of protein tumbling, this approach suggests frequency distribution of amide bond reorientations at 1 H and 15 N Larmor precession frequencies, as well as much lower frequencies (38)(39)(40)(41).…”

mentioning

confidence: 99%

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

et al. 2005

View full text Add to dashboard Cite

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...

show abstract

Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: implications for the entropy of association with DNA

Cited by 213 publications

References 71 publications

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

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

Dynamics of a truncated prion protein, PrP(113–231), from ¹⁵N NMR relaxation: Order parameters calculated and slow conformational fluctuations localized to a distinct region

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

Contact Info

Product

Resources

About

Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: implications for the entropy of association with DNA

Cited by 213 publications

References 71 publications

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

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

Dynamics of a truncated prion protein, PrP(113–231), from 15N NMR relaxation: Order parameters calculated and slow conformational fluctuations localized to a distinct region

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

Contact Info

Product

Resources

About

Dynamics of a truncated prion protein, PrP(113–231), from ¹⁵N NMR relaxation: Order parameters calculated and slow conformational fluctuations localized to a distinct region

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