Potensi Sinamaldehid sebagai Anti Hiperpigmentasi secara In Silico

Permasalahan kulit yang sering ditemui yaitu hiperpigmentasi yang terjadi akibat adanya sintesis melanin berlebihan yang menyebabkan penggelapan warna kulit. Hiperpigmentasi dapat diatasi dengan agen anti hiperpigmentasi yang beraktivitas dalam menghambat proses sintesis melanin. Sintesis melanin dapat dihambat dengan berbagai cara salah satunya dengan menghambat aktivitas tyrosinase. Tyrosinase merupakan enzim yang berperan dalam mengkatalisis proses biosintesis melanin. Sinamaldehid merupakan senyawa bahan alam banyak ditemukan pada tanaman Cinnamomum burmanni mempunyai aktivitas sebagai antioksidan. Penelitian ini bertujuan untuk mengetahui potensi sinamaldehid dalam menghambat tyrosinase yang akan dibandingkan dengan native liganya secara in silico. Uji in silico dilakukan secara docking molecular dengan tahapan yaitu preparasi dan optimasi sinamaldehid, preparasi tyrosinase serta validasi dan docking. Metode docking molecular telah dinyatakan valid karena RMSD (root mean square distance) yang diperoleh tidak lebih dari 3 Å. Analisis data dilakukan dengan melihat energi ikatan yang dihasilkan dan ikatan yang terbentuk antara senyawa dengan residu asam amino pada protein. Nilai energi ikatan yang diperoleh antara ikatan sinamaldehid dengan tyrosinase adalah-6,21 kkal/mol. Sedangkan energi ikatan antara tyrosinase dengan native ligandnya -4,79 kkal/mol. Hal tersebut menunjukkan afinitas dari sinamaldehid pada protein tyrosinase lebih besar dibandingkan native ligandnya, sehingga sinamaldehid dikatakan memiliki potensi sebagai anti hiperpigmentasi dengan mekanisme molecular berupa inhibitor protein target tyrosinase sehingga dapat menghambat aktivitas enzim tyrosinase.

Percentile-based spread: a more accurate way to compare crystallographic models

The comparison of biomacromolecular crystal structures is traditionally based on the root-mean-square distance between corresponding atoms. This measure is sensitive to the presence of outliers, which inflate it disproportionately to their fraction. An alternative measure, the percentile-based spread (p.b.s.), is proposed and is shown to represent the average variation in atomic positions more adequately. It is discussed in the context of isomorphous crystal structures, conformational changes and model ensembles generated by repetitive automated rebuilding.

How root-mean-square distance (r.m.s.d.) values depend on the resolution of protein structures that are compared

The most popular estimator of structural similarity is the root-mean-square distance (r.m.s.d.) between equivalent atoms, computed after optimal superposition of the two structures that are compared. It is known that r.m.s.d. values do not depend only on conformational differences but also on other features, for example the dimensions of the structures that are compared. An open question is how they might depend on the accuracy of the experimentally determined protein structures. Given that the accuracy of the protein crystal structures is generally estimated through the crystallographic resolution, it is important to know the dependence of the r.m.s.d. on the crystallographic resolution of the two structures that are compared. 14458 protein structure pairs of identical sequence were compared and the resulting r.m.s.d. values were normalized to 100-residue length to avoid the bias introduced by the dependence of the r.m.s.d. values on the protein-pair dimensions. On average, smaller r.m.s.d. values are associated with protein structure pairs at better resolution and the r.m.s.d. values tend to increase if the two proteins that are compared have been refined at different resolutions. For crystallographic resolutions ranging between 1.6 and 2.9 Å, both relationships appear to be linear: r.m.s.d. = −0.73 + 0.48 resolution and delta_r.m.s.d. = 0.20 + 0.30 delta_resolution (`delta' indicating difference). Although the linearity of these relationships is not expected to hold outside the 1.6–2.9 Å resolution range, they are useful in making the r.m.s.d. values more reliable.