Protein dropcaps

To make a webpage stylish does not mean that it cannot be biochemically themed. In fact, to can have both thanks to protein dropcaps! using the protein alphabet made by Prof. Mark Howarth in Nature Structural and Molecular Biology in May 2015(available Here) in combination with a wee JS script I wrote you can be a stylish biochemist. The script along with documentation is available in my GitHub page: https://github.com/matteoferla/protein_alphabet_dropcaps.

A fully suicidal enzyme follows a second order equation

That a fully suicidal enzyme follows a second order equation is a rather intuitive statement, but it is nice to have formal proof, which is as follows.

The curious case of fluorescein and implicit waters

I recently was asked a straightforward task: get the energy scores of a given protein by itself, conjugated with fluorescein maleimide and its ring opened form. Despite that, I failed miserably because of implicit waters playing odd tricks.
Given that it is of no real use, I am happy to share so to give a tutorial of how to do that in Rosetta (ligand docking), which I found taxing the first time.

GFP is technically a suicide enzyme

GFP has an oxygen dependent maturation step to form its cofactor. Therefore, it could be farcically considered a suicide enzyme... It performs a reaction: it converts oxygen to peroxide —doing a single turnover.

Skewed mutational biases: English scrabble with Klingon tiles

Skewed mutational biases: English scrabble with Klingon tiles

In a game of Scrabble one draws seven tiles from a bag and the best results are found when a bag and the language used match. In library making with error-prone PCR one does not have that luxury, but different methods differing degrees of fairness. Mutazyme is like playing in English with a Latin tile set, while manganese Taq with equal nucleotides is like playing in English with a Klingon tile set.

Pi projects: a new year's resolutions

2018 is here. I have papers that I want to or have to write and endless tasks I want to complete, but life is not all about career-driven self-sacrifice, it is also about having fun and what better way than with physical computing. And more time passes the more Rasberry pi projects I find I want to do. So I thought I'd share my shortlist of what I think are the most useful.

Hacking PDBs for fusion protein

This is a How-to guide to make structures of fusion protein —the shoddy way.
NB. This assumes medium–advanced PyMol competency.

Introduction

Representing the structures of fusion protein is a rather annoying task. There are many ways of doing this.
Contrary to expectations, submitting the sequence of a fusion protein to the Phyre server (threading/ab initio predictor) or similar will return spaghetti, just as happens with circular permutations (for which you get a cracked half open domain with spaghetti attached). But give it a go nevertheless —it may save you a lot of time!
Rosetta can be used, but the domains will not be photogenic and it is truly overkill.
So the best way is to simply hack the PDB files and some PyMol ninjutsu.

As an example I will make phusion, i.e. Pyrococcus furiosus DNA polymerase fused to Sulfolobus solfataricus 7D domain (Sso7), because its name basically says it is a fusion.