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Neighborhood 1 was initially designed with studies of the 530-loop in mind. As this project progressed, the CAR surface was discovered and found to interact with the mRNA. N1 was used to generate all of the data used in Scopino et al., 2020 (CAR Surface Discovery) as well as supplementary information for Scopino et al., 2021 (R146 Methylation). However, in order to optimize our subsystem for studying the CAR interaction surface we designed Neighborhood 2 in August 2020. Major changes include changing the residues included in the subsystem and changing from Na+ ions to achieve electroneutrality to using K+ ions, as is more common among other groups doing ribosome MD.

N1 consists of 495 residues and was created by selecting a 40 angstrom sphere around G530 of the 530 loop. The rRNA and protein chains within this sphere were extended in cases where the number of artificial chain breaks could be reduced (with a total of 23 chains in the subsystem).

The initial subsystem structures have 5' phosphates removed for compatibility with t-LEaP. They also have the +2 codon mRNA substituted from:
5' -- CCU (A-site codon) -- GCU (+1 codon) -- AAC (+2 codon) -- 3' to
5' -- CCU (A-site codon) -- GCU (+1 codon) -- GCC (+2 codon) -- 3' in order to conform to the observed GCN pattern.

All Neighborhood 1 data has now been stripped of solvent (not ions) and moved into long-term storage at:

rstore6.wesleyan.edu:/data/1/weirlab/MD_backup/kscopino/N1/
   530_LOOP_DATA: unpublished data from the 530 loop project
   SCOPINO_2020_STAGE_C2SUB_DATA: all data for the 2020 CAR Surface Discovery paper
   PLUSONE_CODON_SUBS_N1_DATA: unpublished +1 C2 substitution data with piggybacking (see below)
   SCOPINO_2021_MR146_DATA: supplementary data for the 2021 R146 Methylation paper

After publishing the 2020 paper, we set about trying to address why the N1 5JUP simulations were fairly unstable. To fix this, a 50ps Piggybacking protocol was implemented between equilibration and neutral dynamics in order to give the system more time to evolve before fixing the onion shell. N2 does not show the same instability and therefore does not use a piggybacking step.

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