Liyana Azmi

20 Questions 21 Answers 0 Followers

Questions related from Liyana Azmi

Why aren't my protein growing in optimisation conditions?

I've set up some screening trays with my protein and got crystals after two days. After shooting this crystals at the synchroton, I am sure that these crystals are protein crystals. I've set up my...

06 April 2017 5,156 5 View

Does anyone have a good protocol for flagella preparation/purification?

I need a protocol to shear flagella off E.coli O157:H7. I have been using a protocol online that is basically resuspending an overnight culture in a syringe and then, spinning it down to acquire...

30 March 2017 609 2 View

How does one crystallise a protein with the presence of TCEP as the reducing agent, and with it's co-factors (NAD+ and Fe2+)?

I have a protein which I know is stable with the presence of co-factors (NAD+ and Fe2+). Recently i have been trying to purify it with the TCEP as a reducing agent since my protein is known to...

23 November 2016 7,642 2 View

Are there any websites that can be used to predict small-molecule binding interactions with proteins?

I am looking for a computing way to predict where a small molecule will bind to a protein; at residual level.

12 August 2016 1,298 3 View

How do I check for steric clashes and how to I filter them?

I amrunning DMD modelling to model possible conformations of my proteins. However when I submit my proteins for DMD modelling, it came back to me reporting that it had steric clashes.. How do I...

17 March 2016 2,819 2 View

Does protein crystallize better at lower concentrations?

Hi, previously I've crystallized a protein at 15mg/ml and have obtaind diamond shaped crystals. however, the second time i tried growing these crystals using the same protein with lower...

27 October 2015 7,349 3 View

Why can't I run my data on Sedfit?

I did an analysis of a protein on AUC and did a sedimentation velocity and equilibrium experimetn. after acquiring the data, I stored in in a USB stick and tried to run it on Sedfit. I'm currently...

14 September 2015 8,728 2 View

Why are there no protein expressed even under different expressing conditions?

I am purifying AdhE (96 kDa) protein which is bifunctional and ontains 2 functional domains; (acetaldehyde dehydrogenase and Alcohol dehydrogenase). Before purification, I did a small scale...

28 August 2015 4,438 6 View

How can I validate whether my cross-linking or de-cross linking works?

I am doing Chip-seq, but at the end of the experiment I have obtained a clear DNA background for my negative samples but absolutely no DNA from my tested samples. I think there might be something...

04 August 2014 5,512 7 View

Why is there no DNA after DNA purification in Chip-seq?

I've done chip seq for bacterial cells. My shearing was done to 200bp and I've confirmed it by running a DNA gel after shearing them. I've then immunoprecipitate them with antibodies at 1:200...

01 August 2014 7,304 5 View

Is 5% glycerol okay in a buffer for isothermal titration calorimetry?

My protein stays in solution in 250mM imidazole, 5mM MgSO4 and 5% glycerol. However, I'm trying to make a simpler buffer to reduce the 'noise' in ITC analysis. I'm wondering on using 2.5% glycerol...

05 June 2014 5,638 3 View

Does anybody know any easy online websites for protein structure prediction?

I have a protein sequence which I want to see in 3D. I tried Pymol and Cn3D, but the protein files that they have don't have the sequence which I want to see. I have to predict the protein...

18 March 2014 8,861 21 View

Why do my colonies grow all over the plate?

I made ampicillin plates (1:1000 ampicillin dilution that is 400ul in 4 mls of LB broth) and grew my transformants (dh5 alpha + vector pT7-FLAG2 + DNA inserts)into the agar overnight at 37 celsius...

10 March 2014 2,161 10 View

Why do I keep getting multiple bands for my plasmid extraction even after using QIAGEN miniprep?

My vector is pT7 FLAG2 sized 4.8kbp and my insert is roughly 2-3kbp. I grew them in BL21 and sub-cultured them overnight with ampicilin before extracting them. After that I digested them with my...

25 February 2014 3,306 14 View

Is it normal to have multiple bands after doing birnboim and doly prep?

I did my birnboim and doly prep and received multiple bands everytime. I compared the bands with samples using Qiagen miniprep kits and still I have multiple clean bands. When I added RNase to my...

21 February 2014 979 3 View

Why won't my DNA precipitate dissolve in my TE buffer in Birnboim and Doly method?

I'm screening for my plasmids which are pT7-FLAG2 with inserts approximately 1000-3000 bp each. My plasmid is 4.8kbp. I've cultured them in BL21 and tried extracting them using Birnboim and Doly...

20 February 2014 3,958 2 View

Why is there a huge blob of band following my birnboim and doly plasmid prep?

I did a Birnboim and Boly plasmid Prep for my plasmid and insert which are grown on BL21. After that, I digested them with my restriction enzymes and run the samples on the gel. What I got was a...

19 February 2014 3,926 3 View

Does anyone know any good anti-fliD (HAP2) antibodies?

Specifically, I'm looking for anti-FliD (also known as HAP2) for Escherichia coli O157:H7, the capping protein at the end of the filament.

01 January 1970 2,262 2 View

Why is there a secondary band on my SDS-PAGE gel?

I'm purifying a protein that has a functional cysteine residue at the active site. In the file below, on the left is the SDS of the protein post-IMAC purification. These fractions are then...

01 January 1970 1,834 3 View

Is there an interactive metabolic pathway map available for use?

Roche provides an intereactive complete metabolic pathway map online however, I can't seem to be able to search for the metabolie/enzyme/anything on the map using the options provided. (here's the...

01 January 1970 718 2 View