Conformational exchange on the microsecond time scale in alpha-helix and beta-hairpin peptides measured by 13C NMR transverse relaxation

Molecular basis for impaired DNA damage response function associated with the RAP80 ΔE81 defect

Signal transduction within the DNA damage response is driven by the flux of protein-protein interaction cascades that ultimately recruit repair complexes to sites of damage. The protein RAP80 plays a central role in the damage response by targeting BRCA1/BRCA2 tumor suppressors to DNA damage foci through multivalent binding of Lys-63-linked polyubiquitin chains. Mutations within the high penetrance BRCA1/BRCA2 genes account for ∼20% of familial breast cancers. The genetic basis for the remaining cancers remains unknown, but may involve defects in binding partners for BRCA1 and BRCA2 that lead to impaired targeting to foci and a concomitant role in the pathogenesis of cancer. Recently, an in-frame deletion mutation (ΔE81) in a conserved region from the first ubiquitin interaction motif of RAP80 has been linked to an increase in chromosomal abnormalities. Using NMR spectroscopy, we demonstrate that the N-cap motif within the α-helix of the first ubiquitin interaction motif from ΔE81 undergoes a structural frameshift that leads to abolishment of multivalent binding of polyubiquitin chains. Loss of this single glutamate residue disrupts favorable electrostatic interactions between RAP80 and ubiquitin, establishing a plausible molecular basis for a potential predisposition to cancer unrelated to mutations within BRCA1/BRCA2 genes.

α-helix formation rate of oligopeptides at subzero temperatures

In 1999, Clarke et al. ((1999) Proc. Natl. Acad. Sci. USA 96, 7232–7237) reported that the nucleation rate of α-helix of oligopeptide AK16 is as slow as 60 ms. In the present study, we measured the nucleation rate of oligopeptide, C17 (DLTDDIMCVKKILDKVG, corresponding to α-helical region of 84th to 100th amino acids of bovine α-lactalbumin) using the same method as Clarke et al. We found only initial bursts of the increase of α-helices at temperatures higher than −50°C in the presence of 70% methanol. The result with AK16 was the same as Clarke et al. reported. We also found that the folding rate of polyglutamic acid is too fast to be detected by the stopped-flow apparatus at 4°C. These results demonstrate that the α-helix formation rates in C17, AK16 and polyglutamic acid are shorter than the dead time of the stopped-flow apparatus (6 ms).

Mechanism for recognition of polyubiquitin chains: balancing affinity through interplay between multivalent binding and dynamics

RAP80 plays a key role in signal transduction in the DNA damage response by recruiting proteins to DNA damage foci by binding K63-polyubiquitin chains with two tandem ubiquitin-interacting motifs (tUIM). It is generally recognized that the typically weak interaction between ubiquitin (Ub) and various recognition motifs is intensified by themes such as tandem recognition motifs and Ub polymerization to achieve biological relevance. However, it remains an intricate problem to develop a detailed molecular mechanism to describe the process that leads to amplification of the Ub signal. A battery of solution-state NMR methods and molecular dynamics simulations were used to demonstrate that RAP80-tUIM employs mono- and multivalent interactions with polyUb chains to achieve enhanced affinity in comparison to monoUb interactions for signal amplification. The enhanced affinity is balanced by unfavorable entropic effects that include partial quenching of rapid reorientation between individual UIM domains and individual Ub domains in the bound state. For the RAP80-tUIM-polyUb interaction, increases in affinity with increasing chain length are a result of increased numbers of mono- and multivalent binding sites in the longer polyUb chains. The mono- and multivalent interactions are characterized by intrinsically weak binding and fast off-rates; these weak interactions with fast kinetics may be an important factor underlying the transient nature of protein-protein interactions that comprise DNA damage foci.

Probing Methyl Dynamics from 13C Autocorrelated and Cross-Correlated Relaxation

An understanding of side-chain motions in protein is of great interest since side chains often play an important role in protein folding and intermolecular interactions. A novel method for measuring dipole-dipole cross-correlated relaxation in methyl groups of uniformly 13C-labeled proteins without deuteration has been developed by our group. The excellent agreement between dynamic parameters of methyl groups in ubiquitin obtained from the cross-correlated relaxation and 13C spin-lattice relaxation and those derived previously from 2H relaxation data demonstrates the reliability of the method. This method was applied to the study of side-chain dynamics of human intestinal fatty acid binding protein (IFABP) with and without its ligand. Binding of oleic acid to the protein results in decreased mobility of most of the methyl groups in the binding region, whereas no significant change in mobility was observed for methyl groups in the nonbinding region.

NMR chemical shift and relaxation measurements provide evidence for the coupled folding and binding of the p53 transactivation domain

The interaction between the acidic transactivation domain of the human tumor suppressor protein p53 (p53TAD) and the 70 kDa subunit of human replication protein A (hRPA70) was investigated using heteronuclear magnetic resonance spectroscopy. A 1H-15N heteronuclear single quantum coherence (HSQC) titration experiment was performed on a 15N-labeled fragment of hRPA70, containing the N-terminal 168 residues (hRPA701-168) and p53TAD. HRPA701-168 residues important for binding were identified and found to be localized to a prominent basic cleft. This binding site overlapped with a previously identified single-stranded DNA-binding site, suggesting that a competitive binding mechanism may regulate the formation of p53TAD-hRPA70 complex. The amide 1H and 15N chemical shifts of an uniformly 15N-labeled sample of p53TAD were also monitored before and after the addition of unlabeled hRPA701-168. In the presence of unlabeled hRPA701-168, resonance lineshapes increased and corresponding intensity reductions were observed for specific p53TAD residues. The largest intensity reductions were observed for p53TAD residues 42-56. Minimal binding was observed between p53TAD and a mutant form of hRPA701-168, where the basic cleft residue R41 was changed to a glutamic acid (R41E), demonstrating that ionic interactions play an important role in specifying the binding interface. The region of p53TAD most affected by binding hRPA701-168 was found to have some residual alpha helical and beta strand structure; however, this structure was not stabilized by binding hRPA701-168. 15N relaxation experiments were performed to monitor changes in backbone dynamics of p53TAD when bound to hRPA701-168. Large changes in both the transverse (R2) and rotating frame (R1) relaxation rates were observed for a subset of the p53TAD residues that had 1H-15N HSQC resonance intensity reductions during the complex formation. The folding of p53TAD upon complex formation is suggested by the pattern of changes observed for both R2 and R1. A model that couples the formation of a weak encounter complex between p53TAD and hRPA701-168 to the folding of p53TAD is discussed in the context of a functional role for the p53-hRPA70 complex in DNA repair.

Foldon, the natural trimerization domain of T4 fibritin, dissociates into a monomeric A-state form containing a stable beta-hairpin: atomic details of trimer dissociation and local beta-hairpin stability from residual dipolar couplings

The C-terminal domain of T4 fibritin (foldon) is obligatory for the formation of the fibritin trimer structure and can be used as an artificial trimerization domain. Its native structure consists of a trimeric beta-hairpin propeller. At low pH, the foldon trimer disintegrates into a monomeric (A-state) form that has similar properties as that of an early intermediate of the trimer folding pathway. The formation of this A-state monomer from the trimer, its structure, thermodynamic stability, equilibrium association and folding dynamics have been characterized to atomic detail by modern high-resolution NMR techniques. The foldon A-state monomer forms a beta-hairpin with intact and stable H-bonds that is similar to the monomer in the foldon trimer, but lacks a defined structure in its N and C-terminal parts. Its thermodynamic stability in pure water is comparable to designed hairpins stabilized in alcohol/water mixtures. Details of the thermal unfolding of the foldon A-state have been characterized by chemical shifts and residual dipolar couplings (RDCs) detected in inert, mechanically stretched polyacrylamide gels. At the onset of the thermal transition, uniform relative changes in RDC values indicate a uniform decrease of local N-HN and Calpha-Halpha order parameters for the hairpin strand residues. In contrast, near-turn residues show particular thermal stability in RDC values and hence in local order parameters. This coincides with increased transition temperatures of the beta-turn residues observed by chemical shifts. At high temperatures, the RDCs converge to non-zero average values consistent with predictions from random chain polymer models. Residue-specific deviations above the unfolding transition reveal the persistence of residual order around proline residues, large hydrophobic residues and at the beta-turn.

Expected and unexpected results from combined β-hairpin design elements

A model beta-hairpin dodecapeptide [EFGWVpGKWTIK] was designed by including a favorable D-ProGly Type II' beta-turn sequence and a Trp-zip interaction, while also incorporating a beta-strand unfavorable glycine residue in the N-terminal strand. This peptide is highly folded and monomeric in aqueous solution as determined by combined analysis with circular dichroism and 1H NMR spectroscopy. A peptide representing the folded conformation of the model beta-hairpin [cyclic(EFGWVpGKWTIKpG)] and a linear peptide representing the unfolded conformation [EFGWVPGKWTIK] yield unexpected relative deviations between the CD and 1H NMR spectroscopic results that are attributed to variations in the packing interactions of the aromatic side chains. Mutational analysis of the model beta-hairpin indicates that the Trp-zip interaction favors folding and stability relative to an alternate hydrophobic cluster between Trp and Tyr residues [EFGYVpGKWTIK]. The significance of select diagonal interactions in the model beta-hairpin was tested by rearranging the cross-strand hydrophobic interactions to provide a folded peptide [EWFGIpGKTYWK] displaying evidence of an unusual backbone conformation at the hydrophobic cluster. This unusual conformation does not appear to be a result of the glycine residue in the beta-strand, as replacement with a serine results in a peptide [EWFSIpGKTYWK] with a similar and seemingly characteristic CD spectrum. However, an alternate arrangement of hydrophobic residues with a Trp-zip interaction in a similar position to the parent beta-hairpin [EGFWVpGKWITK] results in a folded beta-hairpin conformation. The differences between side chain packing of these peptides precludes meaningful thermodynamic analysis and illustrates the caution necessary when interpreting beta-hairpin folding thermodynamics that are driven, at least in part, by aromatic cross strand interactions.

Platelet factor 4 promotes adhesion of hematopoietic progenitor cells and binds IL-8: novel mechanisms for modulation of hematopoiesis

Platelet factor 4 (PF4) is an abundant platelet alpha-granule C-X-C chemokine that has weak chemotactic potency but strongly inhibits hematopoiesis through an unknown mechanism. We find that PF4 binds to human CD34+ hematopoietic progenitor cells (HPCs) with a median effective concentration of 1 microg/mL but not after exposure to chondroitinase ABC. PF4 enhances adhesion of HPCs to intact stroma. Committed progenitors also adhere avidly to immobilized PF4. This adhesion is time-dependent, requires metabolic activity, causes cytoskeletal rearrangement, and induces cell-cycle inhibition. Using extracellular acidification rate to indicate transmembrane signaling, we find that interleukin-8 (IL-8), but not PF4, activates CD34+ progenitors, and PF4 blocks IL-8-mediated activation. Surface plasmon resonance analysis shows that PF4 binds IL-8 with high (dissociation constant [Kd] = 42 nM) affinity. Nuclear magnetic resonance analysis of IL-8 and PF4 in solution confirms this interaction. We conclude that PF4 has the capacity to influence hematopoiesis through mechanisms not mediated by a classical high-affinity, 7-transmembrane domain chemokine receptor. Instead, PF4 may modulate the hematopoietic milieu both directly, by promoting progenitor adhesion and quiescence through interaction with an HPC chondroitin sulfate-containing moiety, and indirectly, by binding to or interfering with signaling caused by other, hematopoietically active chemokines, such as IL-8.

Expanding the frequency range of the solid-state T1rho experiment for heteronuclear dipolar relaxation

Solid-state spin-lattice relaxation in the rotating frame permits the investigation of dynamic processes with correlation times in the range of microseconds. The relaxation process in organic solids is driven by the fluctuation of the local magnetic field due to the dipole-dipole interaction of the probe nuclei (13C,15N) with 1H in close proximity. However, its effect is often hidden by a competing relaxation process due to the contact between the rotating frame 13C/15N Zeeman and 1H dipolar reservoirs. In most cases the latter process becomes superior for the commonly applied low and moderate spin-lock fields and practically does not provide information about the molecular dynamics. To suppress this undesired process and to expand the dynamic range of T1rho experiments, we present two approaches. The first one uses a resonance offset of the frequency of the spin-lock irradiation, which leads to a significant enhancement of the effective spin-lock frequency without the application of destructive high transmitter powers. We derive the theory and demonstrate the applicability of the method on various model compounds. The second approach utilizes heteronuclear 1H decoupling during the 13C/15N spin-lock irradiation which disrupts the contact between the 13C/15N Zeeman and 1H dipolar reservoirs. We demonstrate the method and discuss the results qualitatively.

Helix formation via conformation diffusion search

The helix-coil transition kinetics of an alpha-helical peptide were investigated by time-resolved infrared spectroscopy coupled with laser-induced temperature-jump initiation method. Specific isotope labeling of the amide carbonyl groups with 13C at selected residues was used to obtain site-specific information. The relaxation kinetics following a temperature jump, obtained by probing the amide I' band of the peptide backbone, exhibit nonexponential behavior and are sensitive to both initial and final temperatures. These data are consistent with a conformation diffusion process on the folding energy landscape, in accord with a recent molecular dynamics simulation study.

Temperature-dependent helix-coil transition of an alanine based peptide

The helix-coil transition of a synthetic alpha-helical peptide (the D-Arg peptide), Ac-YGG(KAAAA)(3)-CO-D-Arg-CONH(2), was studied by static far-UV circular dichroism (CD) and time-resolved infrared spectroscopy coupled with the laser-induced temperature-jump technique for rapid relaxation initiation. Equilibrium thermal unfolding measurements of the D-Arg peptide monitored by CD spectroscopy reveal an apparent two-state helix-coil transition, with a thermal melting temperature around 10 degrees C. Time-resolved infrared (IR) measurements following a laser-induced temperature jump, however, reveal biphasic (or multiphasic) relaxation kinetics. The fast phase rises within the 20 ns response time of the detection system. The slow phase has a decay lifetime of approximately 140 ns at 300 K and exhibits monotonic temperature dependence with an apparent activation energy around 15.5 kcal/mol.

A new approach to visualizing spectral density functions and deriving motional correlation time distributions: applications to an alpha-helix-forming peptide and to a well-folded protein

A new approach to visualizing spectral densities and analyzing NMR relaxation data has been developed. By plotting the spectral density function, J(omega), as F(omega)=2 omega J(omega) on the log-log scale, the distribution of motional correlation times can be easily visualized. F(omega) is calculated from experimental data using a multi-Lorentzian expansion that is insensitive to the number of Lorentzians used and allows contributions from overall tumbling and internal motions to be separated without explicitly determining values for correlation times and their weighting coefficients. To demonstrate the approach, (15)N and (13)C NMR relaxation data have been analyzed for backbone NH and C(alpha)H groups in an alpha-helix-forming peptide 17mer and in a well-folded 138-residue protein, and the functions F(omega) have been calculated and deconvoluted for contributions from overall tumbling and internal motions. Overall tumbling correlation time distribution maxima yield essentially the same overall correlation times obtained using the Lipari-Szabo model and other standard NMR relaxation data analyses. Internal motional correlational times for NH and C(alpha)H bond motions fall in the range from 100 ps to about 1 ns. Slower overall molecular tumbling leads to better separation of internal motional correlation time distributions from those of overall tumbling. The usefulness of the approach rests in its ability to visualize spectral densities and to define and separate frequency distributions for molecular motions.