Three highly conserved aromatic residues in RNA recognition motifs (RRM) participate in stacking interactions with RNA bases upon binding RNA. We have investigated the contribution of one of these aromatic residues, Phe56, to the complex formed between the N-terminal RRM of the spliceosomal protein U1A and stem-loop 2 of U1 snRNA. Previous work showed that the aromatic group is important for high affinity binding. Here we probe how mutation of Phe56 affects the kinetics of complex dissociation, the strength of the hydrogen bonds formed between U1A and the base that stacks with Phe56 (A6) and specific target site recognition. Substitution of Phe56 with Trp or Tyr increased the rate of dissociation of the complex, consistent with previously reported results. However, substitution of Phe56 with His decreased the rate of complex association, implying a change in the initial formation of the complex. Simultaneous modification of residue 56 and A6 revealed energetic coupling between the aromatic group and the functional groups of A6 that hydrogen bond to U1A. Finally, mutation of Phe56 to Leu reduced the ability of U1A to recognize stem-loop 2 correctly. Taken together, these experiments suggest that Phe56 contributes to binding affinity by stacking with A6 and participating in networks of energetically coupled interactions that enable this conserved aromatic amino acid to play a complex role in target site recognition.
A theoretical analysis of dipolar recoupling with a windowless multipulse irradiation ͑DRAWS͒ is presented. Analytical expressions that describe the degree to which the DRAWS pulse sequence recouples the dipolar interaction as a function of offset and spinning rate are derived using Floquet theory. Numerical methods are used to assess the performance of DRAWS in the preparation and detection of multiple quantum coherence. Simulations indicate that the mutual orientation of two or more CSA tensors can be obtained with high accuracy from double quantum spectra prepared and detected by DRAWS irradiation ͑DQDRAWS͒. These expectations are born out by experiment and in particular, the mutual orientation of three 13 C CSA tensors in selectively labeled 2Ј-deoxythymidine are determined from DQDRAWS data. The results of the DQDRAWS analysis of CSA tensor orientation in 2Ј-deoxythymidine are shown to be in excellent agreement with results obtained by conventional methods. Using these CSA tensor orientations and an independent measurement of internuclear distance, a practical strategy is proposed and executed for deriving the mutual orientation of purine and pyrimidine bases in a DNA dodecamer from DQDRAWS data. The DQDRAWS method for determining the mutual orientation of rigid bodies in macromolecules is compared and contrasted to distance-based methods.
We present a two-dimensional NMR technique for the
measurement of dipolar couplings in polycrystalline
solids. This experiment is fully transverse and uses a windowless
dipolar recoupling pulse sequence (DRAWS,
described in Gregory, D. M.; et al. Chem. Phys.
Lett.
1995, 246, 654−663) to effect coherence
transfer.
Direct, internuclear coherence transfer produces negative
cross-peaks in the 2D spectrum. Cross-peak
development and experimental requirements for obtaining distances from
the two-dimensional solid-state
NMR spectra of two- and three-spin systems are discussed, and
demonstrations are shown for thymidine-2,4-13
C
2 and
l-alanine-13
C
3.
Internuclear distances are derived by comparison of experimental
cross-peak
buildup curves with numerical simulations. In the three-spin
system, indirect coherence-transfer mechanisms
prohibit the interpretation of buildup curves as due to isolated spin
pair interactions and limit the accuracy of
some distance measurements. This 2D technique can also be used for
spectral assignment, as demonstrated
by an application to
l-arginine·HCl-U-13
C,
N.
The RNA recognition motif (RRM) binds to single-stranded RNA target sites of diverse sequences and structures. A conserved mode of base recognition by the RRM involves the simultaneous formation of a network of hydrogen bonds with the base functional groups and a stacking interaction between the base and a highly conserved aromatic amino acid. We have investigated the energetic contribution of the functional groups involved in the recognition of an essential adenine, A6, in stem-loop 2 of U1 snRNA by the N-terminal RRM of the U1A protein. Previously, we found that elimination of individual hydrogen bond donors and acceptors on A6 destabilized the complex by 0.8-1.9 kcal/mol, while mutation of the aromatic amino acid (Phe56) that stacks with A6 to Ala destabilized the complex by 5.5 kcal/mol. Here we continue to probe the contribution of A6 to complex stability through mutation of both the RNA and protein. We have removed two hydrogen-bonding functional groups by introducing a U1A mutation, Ser91Ala, and replacing A6 with tubercidin, purine, or 1-deazaadenine. We find that the complex is destabilized an additional 1.2-2.6 kcal/mol by the elimination of the second hydrogen bond donor or acceptor. Surprisingly, deletion of all of the functional groups involved in hydrogen bonds with the U1A protein by substituting adenine with 4-methylindole reduced the binding free energy by only 2.0 kcal/mol. Experiments with U1A proteins containing mutations of Phe56 suggested that improved stacking interactions due to the greater hydrophobicity of 4-methylindole than adenine may be partly responsible for the small destabilization of the complex upon substitution of 4-methylindole for A6. The data imply that hydrophobic interactions can compensate energetically for the disruption of the complex hydrogen-bonding network between nucleotide and protein.
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