Plausible Accuracy

I’ve got about 70 pages written on a document that I call “my thesis”. The problem is, I hate it. I’ve written it all in fits and spurts, jumping around from one section to the next. Some days I’ll write pages and pages and it seems like it’s going really well, and other days I’ll spend all day staring at emacs and not getting anything down. Lately it’s been much more of the latter.

I decided to give something a shot. I fired up OpenOffice and set it to full screen web view. This gives you a glorious screen of space to write in, without any distractions. I just started writing, trying as hard as I could to keep things like formatting, citations, paragraph structure, and above all sections out of my mind. I want to write something that flows.  Maybe it’s a crazy idea.  A thesis is a really large document to write from start to finish, and the nature of research (especially my research) makes combining the whole thing into a fluid narrative tough.  Call me stupid, but I’m going to take a stab at it.

I’m not sure what this document is yet, to be honest.  It may become part of my thesis.  It may just be a convenient way to help me organize my thoughts before I write them into the official document.  It’s just as likely (more likely in some ways) that I’ll give up on this a week from now.  Until then, I’ll be posting it here on Plausible Accuracy for you to read and comment on.  Any feedback is greatly appreciated.

I’m planning on just posting chunks whenever they get to some modiucm of “done” - that is to say more or less when one train of thought has been laid down.  I’m not editing this as I go (besides the most obvious of typos), not including citations or figures.  The idea is just to write.  I’ll post links to all the sections somewhere as I add on.

It is often cited by those who work in the field that 30% of the proteins in the human organism are associated with the membrane in some way.   Of all of the functions that a cell may have - replicating DNA, transcribing RNA messages, generating new proteins, altering the internal conditions, etc – fully one in every three proteins it deems necessary to produce have some function to perform which requires at least a transient interaction with a membrane.  The functions these proteins perform are as varied as the macromolecules themselves.  Many of them are components of signal transduction vital for communicating messages which pass between cells.  Others are environmental sensors which can stimulate the cell to open itself to certain molecules or close to others.
In spite of their prevalence and functional significance, membrane-associated proteins have not been studied as well as their more soluble counterparts.  Mostly this is due to the various restrictions imposed by experimental methods.  Most of the methods employed by biochemists, including heterologous expression in microorganisms, chromatography for purification, and spectrographic analysis are most efficacious on highly concentrated samples in aqueous buffers.  These are conditions that are not typically accessible to membrane-associated proteins, as they tend to have large hydrophobic regions which allow them to form complexes with the alkyl chains found in the interior of lipid bilayers.  These same hydrophobic regions of course make the proteins insoluble in the very conditions that we tend to use.  In the last couple of decades, we have begun to realize that the importance of understanding the structure and function of these proteins is worth the effort it takes to do so.
This document is the accounting of my own research into several membrane-associated proteins.  Initially I worked on an integral membrane protein, the NK1 receptor.  This is a member of the G Protein-coupled Receptor (GPCR) superfamily  and is involved in signal transduction.  Specifically, the receptor is activated by binding to a small peptide found in the extracellular medium.  A signal is then propagated via the protein through the cellular membrane, activating a bound G protein inside.  This G protein then activates a variety of second messengers which eventually cause a physiological response.  The goal of my work with the receptor was to design and produce a model system which we could use to gain insights into the precise chemistry involved in binding to the peptide ligand.  This process involved comparative modeling and  custom gene synthesis in addition to the expression and analysis of the native protein.  Following my work with the NK1 receptor, I moved to structural investigations of some members of the phospholipase A2 family.  Unlike the GPCR family to which NK1 belongs, the PLA2s are interfacial proteins – soluble to some degree in aqueous conditions, but able to bind membranes and undertake catalysis.  The small secreted PLA2s carry out several functions in the body, some of which are unclear.  One of the central problems in teasing out specific roles for the different family members is that these proteins adopt a similar fold and have overlapping binding affinity for the inhibitors which have been developed.  The primary thrust of my research was to obtain a crystal structure of one family member thought to be a critical player in the early stages of inflammation in humans.
Throughout the course of this research, I've tried to do what I can to expand the body of knowledge we have on membrane proteins.  Often this came in the form of purification or expression techniques; data that is hard to publish.  This is precisely the type of data that we need to share, however, if we are to maximize and combine our efforts in gaining a larger comprehension of what a third of our proteins are actually doing.

This entry was posted on Wednesday, May 7th, 2008 at 1:14 pm and is filed under Biochemistry, open science. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site.