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Insight into gene fusion from molecular dynamics simulation of fused and un-fused IGPS (Imidazole Glycerol Phosphate Synthetase).

Yiting Y, Lei L, Sakharkar MK, Kangueane P - Bioinformation (2006)

Bottom Line: Our interest is to document the structure and dynamics differences between fused and un-fused IGPS.Therefore, we probed into the structures of fused IGPS in SC and un-fused IGPS in TT using molecular dynamics simulation for 5ns.Simulation shows that fused IGPS in SC has larger interface area between HisF-HisH and greater radius of gyration compared to un-fused IGPS in TT.

View Article: PubMed Central - PubMed

Affiliation: School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50, Nanyang Avenue, Singapore 639798.

ABSTRACT
Gene fusion produces proteins with novel structural architectures during evolution. Recent comparative genome analysis shows several cases of fusion/fission across distant phylogeny. However, the selection forces driving gene fusion are not fully understood due to the lack of structural, dynamics and kinetics data. Available structural data at PDB (protein databank) contains limited cases of structural pairs describing fused and un-fused structures. Nonetheless, we identified a pair of IGPS (imidazole glycerol phosphate synthetase) structures (comprising of HisF - glutaminase unit and HisH - cyclase unit) from S. cerevisiae (SC) and T. thermophilus (TT). The HisF-HisH structural units are domains in SC and subunits in TT. Hence, they are fused in SC and un-fused in TT. Subsequently, a domain-domain interface is formed in SC and a subunit-subunit interface in TT between HisF and HisH. Our interest is to document the structure and dynamics differences between fused and un-fused IGPS. Therefore, we probed into the structures of fused IGPS in SC and un-fused IGPS in TT using molecular dynamics simulation for 5ns. Simulation shows that fused IGPS in SC has larger interface area between HisF-HisH and greater radius of gyration compared to un-fused IGPS in TT. These structural features for the first time demonstrate the evolutionary advantage in generating proteins with novel structural architecture through gene fusion.

No MeSH data available.


Gap index (ratio of volume to interface area) between HisH and HisF is given for IGPS from SC and TT over a 5 ns molecular           dynamics simulation. The gap index is similar for the interface between HisH and HisF from SC and TT.
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Figure 6: Gap index (ratio of volume to interface area) between HisH and HisF is given for IGPS from SC and TT over a 5 ns molecular dynamics simulation. The gap index is similar for the interface between HisH and HisF from SC and TT.

Mentions: Figure 6 shows the gap index (ratio of gap volume to interface area) between HisH and HisF in SC IGPS and TT IGPS for structures generated over a 5 ns simulation. Unlike interface area and gap volume, gap index is steadily similar throughout the simulation period.


Insight into gene fusion from molecular dynamics simulation of fused and un-fused IGPS (Imidazole Glycerol Phosphate Synthetase).

Yiting Y, Lei L, Sakharkar MK, Kangueane P - Bioinformation (2006)

Gap index (ratio of volume to interface area) between HisH and HisF is given for IGPS from SC and TT over a 5 ns molecular           dynamics simulation. The gap index is similar for the interface between HisH and HisF from SC and TT.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1904513&req=5

Figure 6: Gap index (ratio of volume to interface area) between HisH and HisF is given for IGPS from SC and TT over a 5 ns molecular dynamics simulation. The gap index is similar for the interface between HisH and HisF from SC and TT.
Mentions: Figure 6 shows the gap index (ratio of gap volume to interface area) between HisH and HisF in SC IGPS and TT IGPS for structures generated over a 5 ns simulation. Unlike interface area and gap volume, gap index is steadily similar throughout the simulation period.

Bottom Line: Our interest is to document the structure and dynamics differences between fused and un-fused IGPS.Therefore, we probed into the structures of fused IGPS in SC and un-fused IGPS in TT using molecular dynamics simulation for 5ns.Simulation shows that fused IGPS in SC has larger interface area between HisF-HisH and greater radius of gyration compared to un-fused IGPS in TT.

View Article: PubMed Central - PubMed

Affiliation: School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50, Nanyang Avenue, Singapore 639798.

ABSTRACT
Gene fusion produces proteins with novel structural architectures during evolution. Recent comparative genome analysis shows several cases of fusion/fission across distant phylogeny. However, the selection forces driving gene fusion are not fully understood due to the lack of structural, dynamics and kinetics data. Available structural data at PDB (protein databank) contains limited cases of structural pairs describing fused and un-fused structures. Nonetheless, we identified a pair of IGPS (imidazole glycerol phosphate synthetase) structures (comprising of HisF - glutaminase unit and HisH - cyclase unit) from S. cerevisiae (SC) and T. thermophilus (TT). The HisF-HisH structural units are domains in SC and subunits in TT. Hence, they are fused in SC and un-fused in TT. Subsequently, a domain-domain interface is formed in SC and a subunit-subunit interface in TT between HisF and HisH. Our interest is to document the structure and dynamics differences between fused and un-fused IGPS. Therefore, we probed into the structures of fused IGPS in SC and un-fused IGPS in TT using molecular dynamics simulation for 5ns. Simulation shows that fused IGPS in SC has larger interface area between HisF-HisH and greater radius of gyration compared to un-fused IGPS in TT. These structural features for the first time demonstrate the evolutionary advantage in generating proteins with novel structural architecture through gene fusion.

No MeSH data available.