S-Stem Scholar Anthony Luna's Blog

 Hello, Today I familiarized myself with iTASSER, which is a platform that uses algorithms to construct models of specific proteins that are being investigated. The protein I requested a model of belonged to Deinococcus Radiodurans, D. rad, and had the following locus tag Ga0133345_1136. Below are four images of the protein rotating through space.  

Hello everyone,  Below you will find some more information I was able to discover about my protein, alpha-amylase 1B. Locus tag : NM_001008218 Size : 1838 bp Accession number : NM_001008218 Version : NM_001008218.1 Comment : REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from CB958705.1, CB957894.1, CB958435.1, and AI627716.1.   Comparing the information from NCBI and the information I used for the first assignment, the only discrepancy I can note is that NCBI gives the length in “base pairs” while the website protein atlas gives the length in “amino acids”. Graphic summary of my BLAST run                                                                            My first two sets of primers

09/09/2020 Anthony Luna Today I finished the first assignment of the bioinformatics project focusing on proteins .  My assigned protein is Q5T084 AMY1B , also known as alpha-amylase 1B polypeptide (Reactome.org). It is found in Homo sapiens and aids in the bodily function of digestion and absorption. Specifically, digestion and absorption of branched starch, amylopectin, and linear starch, amylose (Reactome.org). All of which takes place in the extracellular region of various cells. Moving onto the size, mass, and structure of alpha-amylase 1B. The protein alpha-amylase is folded into three distinct domains, A, B, and C. Yet, my primary focus is on domain B, which has a length of 105 amino acids, aa, and a mass of 12.4 kilo Daltons, kDa (Proteinatlas.org). Alpha-amylase 1B is described as projecting off of domain A in a loop like fashion. However, when a calcium ion binds to domain B, it is then described as relatively rigid (Schutte) . As for diseases involving alpha-amylase 1B, ...