the bound crystal structure of the sam - ii riboswitch ( pdb id:2qwy ; chain a ) solved by gilbert et al . all md simulations were carried out using the amber 10 suite of programs ( 70 ) . in order to obtain the unbound form of the riboswitch , the structure was edited to remove the ligand . the modified nucleic acid parameters ( parmbsc0 ) ( 71 ) of the cornell et al . these parameters along with the structure of the unbound riboswitch were loaded into the leap module in amber . the system was placed in an explicit tip3p ( 73 ) truncated octahedron water box consisting of 11 257 water molecules , and 50 na+ counter ions were added to bring the system to neutrality . after minimizing the system , a 10 ns equilibration was carried out using the pmemd module . the langevin thermostat was used during the equilibration in order to bring the system from 100k to 300k using a collision frequency of 1.0 /ps . following the 10 ns equilibration , particle mesh ewald ( 74 ) method was used to treat long range electrostatics . a 2 fs time - step was used to solve newton s equations of motion at a constant pressure of 1 bar and a constant temperature of 300k using the ntp ensemble . all bonds involving hydrogen atoms were restrained using the shake algorithm ( 75 ) , and a 9  cutoff was applied to all long ranged non - bonded interactions . starting with the sam ligand previously removed from the crystal structure of the riboswitch , the gaussview program ( 76 ) was used to add hydrogens to the ligand and the structure was quantum mechanically optimized using the gaussian program at the hf/6 - 31-g(d ) level of theory . force field parameters were obtained using the antechamber module in amber , and partial charges were generated with the resp ( 77 ) method from the electrostatic potential calculated using the gaussian program , also at the hf/6 - 31g(d ) level of theory . these force field parameters and charges were loaded into leap along with the default nucleic acid parameters in order to prepare the sam - ii riboswitch complex . the complex was also solvated in a truncated octahedron tip3p water box consisting of 11 254 water molecules . the positive charge of the ligand resulted in the addition of only 49 na+ counter ions to the system in order to bring it to neutrality . equilibration and dynamics were carried out from this point on under the same conditions and for the same length of time ( 200 ns ) as for the free riboswitch . the residue residue cross - correlation coefficients were calculated using the trajectories of the entire simulation of the unbound form of the sam - ii riboswitch . the cross - correlation coefficient   for the displacement of any two atoms i and j , where ri is the displacement from the average position of i. the cross - correlation coefficients , cij , is therefore a 2d matrix with the value of each coefficient between + 1.0 and 1.0 , where + 1.0 signifies perfect positive correlated motions , and 1.0 signifies perfect negative correlated motions . the cross - correlation coefficients were averaged over each residue , such that there was only one cij per residue . the cross - correlation coefficients are then plotted using a color - coded 2d matrix from red ( + 1 ) to blue ( 1 ) . the bound crystal structure of the sam - ii riboswitch ( pdb id:2qwy ; chain a ) solved by gilbert et al . all md simulations were carried out using the amber 10 suite of programs ( 70 ) . in order to obtain the unbound form of the riboswitch , the structure was edited to remove the ligand . the modified nucleic acid parameters ( parmbsc0 ) ( 71 ) of the cornell et al . these parameters along with the structure of the unbound riboswitch were loaded into the leap module in amber . the system was placed in an explicit tip3p ( 73 ) truncated octahedron water box consisting of 11 257 water molecules , and 50 na+ counter ions were added to bring the system to neutrality . after minimizing the system , a 10 ns equilibration was carried out using the pmemd module . the langevin thermostat was used during the equilibration in order to bring the system from 100k to 300k using a collision frequency of 1.0 /ps . following the 10 ns equilibration , particle mesh ewald ( 74 ) method was used to treat long range electrostatics . a 2 fs time - step was used to solve newton s equations of motion at a constant pressure of 1 bar and a constant temperature of 300k using the ntp ensemble . all bonds involving hydrogen atoms were restrained using the shake algorithm ( 75 ) , and a 9  cutoff was applied to all long ranged non - bonded interactions . starting with the sam ligand previously removed from the crystal structure of the riboswitch , the gaussview program ( 76 ) was used to add hydrogens to the ligand and the structure was quantum mechanically optimized using the gaussian program at the hf/6 - 31-g(d ) level of theory . force field parameters were obtained using the antechamber module in amber , and partial charges were generated with the resp ( 77 ) method from the electrostatic potential calculated using the gaussian program , also at the hf/6 - 31g(d ) level of theory . these force field parameters and charges were loaded into leap along with the default nucleic acid parameters in order to prepare the sam - ii riboswitch complex . the complex was also solvated in a truncated octahedron tip3p water box consisting of 11 254 water molecules . the positive charge of the ligand resulted in the addition of only 49 na+ counter ions to the system in order to bring it to neutrality . equilibration and dynamics were carried out from this point on under the same conditions and for the same length of time ( 200 ns ) as for the free riboswitch . the residue  residue cross - correlation coefficients were calculated using the trajectories of the entire simulation of the unbound form of the sam - ii riboswitch . the cross - correlation coefficient   for the displacement of any two atoms i and j , where ri is the displacement from the average position of i. the cross - correlation coefficients , cij , is therefore a 2d matrix with the value of each coefficient between + 1.0 and 1.0 , where + 1.0 signifies perfect positive correlated motions , and 1.0 signifies perfect negative correlated motions . the cross - correlation coefficients were averaged over each residue , such that there was only one cij per residue . the cross - correlation coefficients are then plotted using a color - coded 2d matrix from red ( + 1 ) to blue ( 1 ) . this work was supported by georgia state 's ; ibm system p5 supercomputer , acquired through a partnership of the southeastern universities research association and ibm supporting the suragrid initiative . this work was supported in part by research initiation grant from georgia state university , the department of chemistry at georgia state university , and the georgia cancer coalition .
many bacterial genes are controlled by metabolite sensing motifs known as riboswitches , normally located in the 5 un - translated region of their mrnas . 
 small molecular metabolites bind to the aptamer domain of riboswitches with amazing specificity , modulating gene regulation in a feedback loop as a result of induced conformational changes in the expression platform . here , we report the results of molecular dynamics simulation studies of the s - adenosylmethionine ( sam)-ii riboswitch that is involved in regulating translation in sulfur metabolic pathways in bacteria . we show that the ensemble of conformations of the unbound form of the sam - ii riboswitch is a loose pseudoknot structure that periodically visits conformations similar to the bound form , and the pseudoknot structure is only fully formed upon binding the metabolite , sam . 
 the rate of forming contacts in the unbound form that are similar to that in the bound form is fast . 
 ligand binding to sam - ii alters the curvature and base - pairing of the expression platform that could affect the interaction of the latter with the ribosome .