Table 3

RNAi system with transcription/translation machinery

Reaction Number

Reaction

Rate Constant

Remarks


1

mRNA + siRNA -> gRNA

0.008 hr-1

2

dsRNA -> 10*siRNA

2.0 hr-1

3

mRNA -> dsRNA

0.002 hr-1

4

siRNA ->ϕ

2.0 hr-1

5

mRNA ->ϕ

18 hr-1

6

gRNA ->ϕ

2.8 hr-1

7

O + R -> O_R

12.0 hr-1

Regulatory molecule R binds to the operator region O to form the bound complex O_R

8

O_R -> O + R

0.24 hr-1

O_R dissociates into free R and O

9

P + RNAP -> P_RNAPC

1.2 hr-1

RNAP binds to promoter region P forming closed complex P_RNAPC

10

P_RNAPC -> P + RNAP

0.06 hr-1

P_RNAPC dissociates into free RNAP and P

11

P_RNAPC -> P_RNAPO

48 hr-1

Isomerization of closed to open complex (P_RNAPO)

12

P_RNAPO -> TrRNAP + mRNA + P

54 hr-1

RNAP clears promoter region and mRNA chain synthesis starts. TrRNAP denotes transcribing RNA polymerase.

13

TrRNAP -> RNAP

4.8 hr-1

RNAP completes transcription and is released from DNA.

14

mRNA + Ribosome -> RibRBS

0.6 hr-1

Ribosome binds to mRNA forming bound complex RibRBS

15

RibRBS -> mRNA+ Ribosome

0.06 hr-1

Ribosome dissociation from RibRBS

16

RibRBS -> EIRib + mRNA

18 hr-1

Ribosome EIRib initiates translation of mRNA chain

17

EIRib -> protein

48 hr-1

Protein synthesis by transcribing ribosome

18

protein ->ϕ

0.18 hr-1

Protein product degradation


Ghosh et al. BMC Genomics 2009 10(Suppl 1):S17   doi:10.1186/1471-2164-10-S1-S17

Open Data