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Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs.

Yildirim I, Stern HA, Sponer J, Spackova N, Turner DH - J Chem Theory Comput (2009)

Bottom Line: Restraining the structures with hydrogen bond restraints did not improve the predictions.The calculations using positional restraints and a nonplanar amino group reproduce the signs of DeltaG degrees from the experimental results and are, thus, capable of providing useful qualitative insights complementing the NMR experiments.The results suggest that a better description of the backbone is key to reproducing the experimental free energy results with computational free energy predictions.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics and Astronomy, Department of Chemistry and Department of Pediatrics, University of Rochester, Rochester, New York, 14627, and Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 61265 Brno, Czech Republic.

ABSTRACT
Guanine-adenine (GA) base pairs play important roles in determining the structure, dynamics, and stability of RNA. In RNA internal loops, GA base pairs often occur in tandem arrangements and their structure is context and sequence dependent. Calculations reported here test the thermodynamic integration (TI) approach with the amber99 force field by comparing computational predictions of free energy differences with the free energy differences expected on the basis of NMR determined structures of the RNA motifs (5'-GCGGACGC-3')(2), (5'-GCiGGAiCGC-3')(2), (5'-GGCGAGCC-3')(2), and (5'-GGiCGAiGCC-3')(2). Here, iG and iC denote isoguanosine and isocytidine, which have amino and carbonyl groups transposed relative to guanosine and cytidine. The NMR structures show that the GA base pairs adopt either imino (cis Watson-Crick/Watson-Crick A-G) or sheared (trans Hoogsteen/Sugar edge A-G) conformations depending on the identity and orientation of the adjacent base pair. A new mixing function for the TI method is developed that allows alchemical transitions in which atoms can disappear in both the initial and final states. Unrestrained calculations gave DeltaG degrees values 2-4 kcal/mol different from expectations based on NMR data. Restraining the structures with hydrogen bond restraints did not improve the predictions. Agreement with NMR data was improved by 0.7 to 1.5 kcal/mol, however, when structures were restrained with weak positional restraints to sample around the experimentally determined NMR structures. The amber99 force field was modified to partially include pyramidalization effects of the unpaired amino group of guanosine in imino GA base pairs. This provided little or no improvement in comparisons with experiment. The marginal improvement is observed when the structure has potential cross-strand out-of-plane hydrogen bonding with the G amino group. The calculations using positional restraints and a nonplanar amino group reproduce the signs of DeltaG degrees from the experimental results and are, thus, capable of providing useful qualitative insights complementing the NMR experiments. Decomposition of the terms in the calculations reveals that the dominant terms are from electrostatic and interstrand interactions other than hydrogen bonds in the base pairs. The results suggest that a better description of the backbone is key to reproducing the experimental free energy results with computational free energy predictions.

No MeSH data available.


5′iCG3′/3′iGA5′, imino GA stacked on iCiG in 5′GGiCGAiGCC3′/3′CCiGAGiCGG5′ (2O83) after minimization with amber99 force field. The distance between the cross-strand hydrogen bond of H21−O6 is 4.01 Å. With the modified amber99 force field, this distance is 2.60 Å. The figure was created with VMD.(56)
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fig8: 5′iCG3′/3′iGA5′, imino GA stacked on iCiG in 5′GGiCGAiGCC3′/3′CCiGAGiCGG5′ (2O83) after minimization with amber99 force field. The distance between the cross-strand hydrogen bond of H21−O6 is 4.01 Å. With the modified amber99 force field, this distance is 2.60 Å. The figure was created with VMD.(56)

Mentions: Both the amber99 and modified amber99 force fields give a free energy difference of −0.6 ± 0.1 kcal/mol for ΔG°3 − ΔG°2 (Table 1). In the iCGAiG system, the cross-strand distance between the amino group (H21) of G of the GA base pair and the carbonyl group (O4) of iC of the iCiG base pair is longer than in iGGAiC (compare Figures 7 and 8). As a result, the prediction of modified amber99 is similar to the prediction of amber99. The magnitude of ΔG°3 − ΔG°2 is smaller than suggested by experiments. Again, neither amber99 nor the modified amber99 force fields accurately take into account all the interactions responsible for the observed structures.


Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs.

Yildirim I, Stern HA, Sponer J, Spackova N, Turner DH - J Chem Theory Comput (2009)

5′iCG3′/3′iGA5′, imino GA stacked on iCiG in 5′GGiCGAiGCC3′/3′CCiGAGiCGG5′ (2O83) after minimization with amber99 force field. The distance between the cross-strand hydrogen bond of H21−O6 is 4.01 Å. With the modified amber99 force field, this distance is 2.60 Å. The figure was created with VMD.(56)
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2807739&req=5

fig8: 5′iCG3′/3′iGA5′, imino GA stacked on iCiG in 5′GGiCGAiGCC3′/3′CCiGAGiCGG5′ (2O83) after minimization with amber99 force field. The distance between the cross-strand hydrogen bond of H21−O6 is 4.01 Å. With the modified amber99 force field, this distance is 2.60 Å. The figure was created with VMD.(56)
Mentions: Both the amber99 and modified amber99 force fields give a free energy difference of −0.6 ± 0.1 kcal/mol for ΔG°3 − ΔG°2 (Table 1). In the iCGAiG system, the cross-strand distance between the amino group (H21) of G of the GA base pair and the carbonyl group (O4) of iC of the iCiG base pair is longer than in iGGAiC (compare Figures 7 and 8). As a result, the prediction of modified amber99 is similar to the prediction of amber99. The magnitude of ΔG°3 − ΔG°2 is smaller than suggested by experiments. Again, neither amber99 nor the modified amber99 force fields accurately take into account all the interactions responsible for the observed structures.

Bottom Line: Restraining the structures with hydrogen bond restraints did not improve the predictions.The calculations using positional restraints and a nonplanar amino group reproduce the signs of DeltaG degrees from the experimental results and are, thus, capable of providing useful qualitative insights complementing the NMR experiments.The results suggest that a better description of the backbone is key to reproducing the experimental free energy results with computational free energy predictions.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics and Astronomy, Department of Chemistry and Department of Pediatrics, University of Rochester, Rochester, New York, 14627, and Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 61265 Brno, Czech Republic.

ABSTRACT
Guanine-adenine (GA) base pairs play important roles in determining the structure, dynamics, and stability of RNA. In RNA internal loops, GA base pairs often occur in tandem arrangements and their structure is context and sequence dependent. Calculations reported here test the thermodynamic integration (TI) approach with the amber99 force field by comparing computational predictions of free energy differences with the free energy differences expected on the basis of NMR determined structures of the RNA motifs (5'-GCGGACGC-3')(2), (5'-GCiGGAiCGC-3')(2), (5'-GGCGAGCC-3')(2), and (5'-GGiCGAiGCC-3')(2). Here, iG and iC denote isoguanosine and isocytidine, which have amino and carbonyl groups transposed relative to guanosine and cytidine. The NMR structures show that the GA base pairs adopt either imino (cis Watson-Crick/Watson-Crick A-G) or sheared (trans Hoogsteen/Sugar edge A-G) conformations depending on the identity and orientation of the adjacent base pair. A new mixing function for the TI method is developed that allows alchemical transitions in which atoms can disappear in both the initial and final states. Unrestrained calculations gave DeltaG degrees values 2-4 kcal/mol different from expectations based on NMR data. Restraining the structures with hydrogen bond restraints did not improve the predictions. Agreement with NMR data was improved by 0.7 to 1.5 kcal/mol, however, when structures were restrained with weak positional restraints to sample around the experimentally determined NMR structures. The amber99 force field was modified to partially include pyramidalization effects of the unpaired amino group of guanosine in imino GA base pairs. This provided little or no improvement in comparisons with experiment. The marginal improvement is observed when the structure has potential cross-strand out-of-plane hydrogen bonding with the G amino group. The calculations using positional restraints and a nonplanar amino group reproduce the signs of DeltaG degrees from the experimental results and are, thus, capable of providing useful qualitative insights complementing the NMR experiments. Decomposition of the terms in the calculations reveals that the dominant terms are from electrostatic and interstrand interactions other than hydrogen bonds in the base pairs. The results suggest that a better description of the backbone is key to reproducing the experimental free energy results with computational free energy predictions.

No MeSH data available.