Hydrogen bonding and packing density are factors most strongly connected to limiting sites of high flexibility in the 16S rRNA in the 30S ribosome

Huggins, Wayne; Ghosh, Sujit K; Wollenzien, Paul

doi:10.1186/1472-6807-9-49

Table 3 Comparison of B factors, hydrogen bonding and neighbor atom count around reactive and unreactive nucleotide pairs

From: Hydrogen bonding and packing density are factors most strongly connected to limiting sites of high flexibility in the 16S rRNA in the 30S ribosome

UV reactions					Statistics³
	Nucleotide Pairs Reactive		Unreactive
Parameter	n¹	Ave. ± S.D.	n²	Ave. ± S.D.	z value	p value
B factor for both nt.	42	65.8 ± 26.8	2156	58.0 ± 26.1	1.917	0.0553
Value of larger B factor of pair	42	77.8 ± 36.1	2156	67.3 ± 28.0	2.392	0.0168
H bonds/nt. for both nt.	42	1.13 ± 1.2	523	1.70 ± 0.85	-4.038	< 0.0001
H bonds in lesser H-bonded nt.	42	0.47 ± 0.73	523	0.97 ± 1.04	-3.055	0.0024
Atom count around both nt.	42	21.8 ± 8.9	2156	28.0 ± 9.3	-4.282	< 0.0001
Atom count – lower-packed nt.	42	15.6 ± 11.0	2156	23.2 ± 9.5	-5.249	< 0.0001
UVA-s ⁴ U reactions					Statistics
	Nucleotide Pairs Reactive		Unreactive
Parameter	n⁴	Ave. ± S.D.	n⁵	Ave. ± S.D.	z value	p value
B factor for both nt.	50	66.3 ± 24.9	2761	58.5 ± 28.6	1.915	0.0556
Value of larger B factor of pair	50	74.1 ± 25.7	2761	68.8 ± 31.2	1.194	0.2327
Value of s⁴U B factor	24	72.0 ± 25.4	315	66.3 ± 31.9	0.855	0.3934
H bonds/nt. for both nt.	50	1.27 ± 0.90	844	1.76 ± 0.77	-4.329	< 0.0001
H bonds/s⁴U	24	0.71 ± 0.91	315	1.55 ± 0.96	-4.146	< 0.0001
Atom count around both nt.	50	25.6 ± 11.3	2761	30.8 ± 8.4	-4.431	< 0.0001
Atom count around the s⁴U	24	21.0 ± 11.6	315	30.0 ± 8.8	-4.712	< 0.0001

¹The number of reactive nucleotide pairs evaluated is 14, 13 and 15 in the T. thermophilus [11], E. coli I and E. coli II [13] structures respectively, after removal of observed crosslinks that have > 10.5 Å between reactive bonds and because two crosslinking sites are not present in the T. thermophilus structure. The average and standard deviations here, and in other data, are weighted averages and standard deviations from three sets of measurements.
²The number of measurements of unreactive pairs is 768, 674 and 714 in the T. thermophilus, E. coli I and E. coli II structures respectively, except for the hydrogen bonding frequencies which were evaluated from a representative number of nucleotide pairs in each structure.
³ z-value is the difference of sample means normalized by the standard error of the means. The null hypothesis, that the populations have the same averages, can be rejected at the 5% and 1% level of significance if |z| ≥ 1.96 and |z| ≥ 2.56, respectively. p-value is the probability that random sampling would lead to a difference between sample means as large (or larger) than that has been observed, if the null hypothesis is true, i.e., if the populations have the same true mean.
⁴The number of reactive nucleotide pairs evaluated is 18, 16 and 16 in the T. thermophilus, E. coli I and E. coli II structures, after removal of observed crosslinks that have > 18 Å between reactive bonds. For evaluation of H bonds/s⁴U and atom count around the s⁴U, there are eight s⁴Us that are involved in the 18 photocrosslinks that are evaluated in each of the three structures.
⁵The number of measurements of unreactive pairs is 893, 928 and 940 in the T. thermophilus, E. coli I and E. coli II structures respectively, except for the hydrogen bonding frequencies which were evaluated manually on a representative number of nucleotide pairs in each structure and for the value of the s⁴U B factor, H bonds/s⁴U, and atom count around the s⁴U which were evaluated just once on each of the 105 substituted s⁴U positions in each structure.

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ISSN: 1472-6807

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