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Komputer Bantu Rakit 16 Protein Ubur-Ubur

Superkomputer dapat membantu perakitan protein. Dengan supercharging protein ubur-ubur, Anna J. Simon et al (2019) menyusun struktur 16 protein. Metode ini dapat diterapkan dalam teknologi pharmaceutical targeting, artificial energy harvesting, 'smart' sensing dan building materials. (University of Texas (Austin), Texas Advanced Computing Center, 29/3/2019).

Dengan superkomputer, tim ilmuwan itu merancang protein-protein yang terakit (self-assemble) agar tersusun dan menyerupai molekul hemoglobin. Molekul hemoglobin dalam sel darah merah mengambil oksigen dari paru-paru dan membawanya ke seluruh tubuh agar seseorang tetap hidup. Empat salinan protein yang sama dalam hemoglobin terbuka atau tertutup seperti kelopak bunga dengan struktur berpasangan dan saling-respons. Kolaborasi ilmuwan itu menggunakan metode supercharged protein assembly—perakitan protein melalui supercharging yakni memacu interaksi protein tertentu dengan menggabungkan varian desain muatan sangat positif atau negatif yang direkayasa (Science Daily, 29/3/2019).

Melalui cara supercharging protein, tim ilmuwan itu mengubah sub unit-sub unit protein, asam amino, guna memberi muatan sangat positif (protein cerulean fluorescent protein (Ceru) +32) atau negatif (charged protein GFP -17) kepada protein-protein itu. “By giving these proteins all these opportunities, these different places where they could potentially interact, they were able to choose the right ones. There were certain patterns and interactions that were there, available, and energetically favored, that we didn't necessarily predict beforehand that would allow them to assemble into these specific shapes...We found that by taking proteins that don't normally interact with each other, we can make copies that are either highly positively or highly negatively charged. Combining the highly positively and negatively charged copies, we can make the proteins assemble into very specific structured assemblies,” papar Anna J. Simon, Ph.D, postdoctoral researcher di Ellington Lab of UT Austin, Amerika Serikat, dan co-author studi ilmiah ini (University of Texas (Austin), Texas Advanced Computing Center, 29/3/2019).

Kemudian tim ilmuwan itu menggunakan simulasi superkomputer untuk memvalidasi dan menginformasikan hasil eksperimennya. Dengan superkomputer XSEDE Comet di San Diego Supercomputer Center dan Stampede2 Texas Advanced Computing Center di Amerika Serikat,  Anna J. Simon et al (2019) mendesain protein-protein yang merakit-diri (self-assemble) guna menyatukan dan merakit-ulang molekul-molekul hidup (life-giving-molecules) seperti hemoglobin. “When we were first figuring out what kind of model to use and whether this simplified model would give us reasonable results, Comet was a great place to try these simulations. Comet was a great testbed for what we were doing,” ungkap Vyas Ramasubramani, Ph.D, rekayasa kimia di University of Michigan (University of Texas (Austin), Texas Advanced Computing Center, 29/3/2019).

 “The Skylake nodes of the Stampede2 supercomputer were instrumental in achieving the performance that was necessary to compute these electrostatic interactions that act between the oppositely-charged proteins in an efficient manner. The availability of the Stampede2 supercomputer was at just the right point in time for us to perform these simulation,” papar Dr. Jens Glaser, assistant research di Glotzer Group, Department of Chemical Engineering pada  University of Michigan (Amerika Serikat) dan co-author studi ilmiah ini (University of Texas (Austin), Texas Advanced Computing Center, 29/3/2019).

Kolaborasi riset itu melibatkan juga ilmuwan Arti Pothukuchy; Jimmy Gollihar; Barrett Morrow; David Taylor, assistant professor biosains molekul di  UT Austin; dan Yi Zhou dari UT Austin Ellington Lab of UT Austin. Hasil riset itu dirilis oleh jurnal Nature Chemistry, edisi akhir Maret 2019 (Anna J. Simon, Yi Zhou, Vyas Ramasubramani, Jens Glaser, Arti Pothukuchy, Jimmy Gollihar, Jillian C. Gerberich, Janelle C. Leggere, Barrett R. Morrow, Cheulhee Jung, Sharon C. Glotzer, David W. Taylor, Andrew D. Ellington, “Supercharging enables organized assembly of synthetic biomolecules”, Nature Chemistry, 2019).

Perihal hasil riset itu, Anna J. Simon, Ph.D, berpandangan : “We think supercharged protein assembly is an easier way to develop the kind of materials that have exciting synthetic properties without having to spend so much time or having to know exactly how they're going to come together beforehand. We think that will accelerate the ability to engineer synthetic materials and for discovery and exploration of these nanostructured protein materials.” (University of Texas (Austin), Texas Advanced Computing Center, 29/3/2019).

Riset itu didanai oleh US Army Research Laboratory, US Army Research Office, Welch Foundation, Cancer Prevention and Research Institute of Texas, program postdoctoral fellowship Arnold O. Beckman dari AJS dan grant principal investigators melibatkan Sharon Glotzer,  Anthony C. Lembke Department Chair of Chemical Engineering pada University of Michigan, dan  Andy Ellington, associate director  pada Center for Systems and Synthetic Biology, UT Austin. Sumber daya XSEDE didanai oleh National Science Foundation. 

Oleh: Servas Pandur