ESR Blog

The RAMP ESRs will first introduce themselves on this page each at a time, then they will post regular articles on their activity within RAMP all throughout their PhD.


This month Jannik, ESR 4 tells us about the difference between an industrial and academia secondment.

This year I have been on two secondments, so I have spent very little time in Leeds. Both secondments have been great and added value to my personal development and to the development of my project: “Novel Approaches to Membrane-bound Pyrophosphatase Structures”.

-Whom did you visit and what did you do? First, I went to Arwen Pearson’s Group at the University of Hamburg to do time-resolved crystallography experiments … read full blog here


This time, My, ESR9 shares with us some PhD Life experiences.

PhD Life – What I am doing while waiting for my crystals to grow.

Being involved in other projects.

We have a strong RAMP presence in Maynooth right now, with Jessica having just joined the lab and Cristina here on secondment.

I also have a helping hand this year, with a 4th year undergraduate student doing his final year project and we’re characterising different detergent systems. I’m working alongside Cristina and Jessica on their projects and we’re all learning new things together.

Giant Unilamellar vesicles (GUV) are a type of liposomes, microscopic vesicles, which are formed by phospholipid bilayers with a size above 1 µm. They differ from small unilamellar vesicles (SUV, 20-100nm) and large unilamellar vesicles (LUV, > 100 nm) only by the size. Due to their size range, GUVs can serve as ideal artificial cells to study membrane protein insertion and activity in the phospholipid bilayer. Based on previous work on GUVs for protein self-assembling studies in our lab, Cristina wants to establish a protocol for reconstitution of her membrane transporters in this system during her secondment in Maynooth. read full blog here


Cristina, ESR7 tells us about the outreach activity all ESRs organised during the summer workshop.

Why did you take part in this event? (Describe your participation)

“Crystals made of tears: from misery to cheer”  is an outreach event that took place at “The Devereux” pub in central London. The outreach event had the purpose of presenting our network and giving an overview of membrane protein crystallography. What is best than having all the ESRs from RAMP in London to talk about that?

I believe that outreach activities are quite important in science, to promote awareness and trust in scientific research, and, why not, hopefully, inspire a new generation of scientists. 

Some of us already had experience with going to schools or science exhibitions, but this event allowed us to try something new, a different kind of “public outreach”. The purpose was to show what science is, try to interest people in our field and attempt all this in an informal and chilled out environment. So, we thought, why not having science with wine/beer and pizza in a pub on a Friday night? read full blog


Virginia, ESR 10 is working with molecular dimension on a web tool. Learn about it on her blog-post.

What is the purpose of this secondment?
For my secondment in Molecular Dimensions, we came up with an idea to build a web tool that will help crystallographers to optimise crystallisation plates, especially in the initial crystallisation trials. The project was inspired by one of the most common feedback MDL gets from the users of their crystallisation plates.
A common issue many crystallographers have is that once an initial crystallisation hit has been obtained from a commercial screen, the optimisation of the hit conditions is not trivial it could be quite challenging. The task becomes even more challenging when users try to optimise some of the newest, more sophisticated screens. These screens have many complex conditions and a large number of variables (salts, buffers, precipitant, additives, pH, temperature…). The drawback of these screens is that as the complexity increases, read full blog


This month, Elham gives us an update on her Phd and on her progress.

Can you remind us briefly what your project is about?

The topic of my PhD thesis is “Optimisation of crystal growth using a microfluidic technology-based crystallisation bench”

Three main objectives for this PhD are 1. Adapting crystallization bench (OptiCrys) to crystallize membrane proteins 2. Doing a statistical study to compare diffraction resolution of crystals of model membrane proteins, which are obtained using different crystallization techniques 3. Growing large enough crystals for Neutron Macromolecular Crystallography.

OptiCrys (shown in figure 1) was designed in our lab several years ago for crystallizing soluble proteins. This machine uses dialysis method (figure 1b) to crystallize proteins by changing temperature and reservoir composition during the experiment in order to optimize crystallization conditions. It will help us explore different conditions with the same protein sample since the sample is not consumed during the experiment. By using the dialysis method and controlling the temperature and composition of the crystallization solution, we are able to control the crystallization process to have crystals with the appropriate size and good diffraction qualities for X-ray or Neutron Crystallography.

Figure1. a. Crystallization Bench. b. Temperature-controlled flowing reservoir dialysis setup [1]. full article here

Sam is on secondment in Grenoble for two months. Read all about hissecondment here.

– What is the purpose of this secondment?

The purpose of my secondment at the Institute for Structural Biology in Grenoble, France is to try to grow large crystals of SERCA for NMX studies using some of the specialised equipment they have here, in particular an apparatus which allows the temperature of the crystallisation mixture to be finely controlled. The idea is to alter the protein solubility of the mixture by changing the temperature – this means that you can adjust the conditions to the point where the protein contained within the solution will be added to the mass of the existing crystal (or crystals) instead of coming out of the solution as new crystals. The result is a few very large crystals instead of many smaller crystals. read full blog here


After two weeks of training in the UK, Sofia Jaho tells us about this experience!

Sofia Jaho’s experience of the RAMP “Professional Development and Leadership Training” in UK

What did you learn during the workshop?

Recently, I participated at the RAMP’s workshop held in UK, concerning professional development and leadership. The courses for Professional Development were organized by the Graduate School at Imperial College London and the training on Leadership skills was implemented by the Doctoral College of the University of Surrey. Almost 2 weeks of intense training on what is known as “soft skills”. Many scientists (myself included!) consider that scientific skills or lab skills, as for example methods, techniques,… read full blog here


Sofia Trampari also spent some time on secondment at NOVARTIS, read abot her experince down below.

My secondment at Novartis

What is the purpose of this secondment?

The purpose of my secondment in NOVARTIS was first of all to experience the industrial point of view of research and also to apply the HiLiDe method to a GPCR target. GPCRs are membrane proteins and therefore hard to crystallize and study their structure read full article here.


This month Claudia tells us about her latest secondmentys at Novartis.

– What is the purpose of this secondment?

I’m working on the A2A adenosine receptor (A2AR), trying to elucidate the nature of the interaction with some of its binding partners. The understanding of these interactions will hopefully provide novel tools to modulate the receptor’s signalling output and thereby help to develop novel drugs. A more direct way of modulating A2AR signalling is to block the binding site for its natural ligand, adenosine. This can be achieved by using a specific set of molecules called antagonists. Novartis has developed new sets of antagonists for the A2AR. In my secondment I tried to crystallise the A2AR in complex with some of these molecules to better understand the molecular mechanisms involved in binding. This information will help to generate better, more potent and more specific drugs. read full article


Could you remind us briefly what your project is about?

As mentioned earlier in my previous post, I will be studying three membrane proteins; bacteriorhodopsin (BR), Leucine Transporter (LeuT) and outer membrane protein F (OmpF) using neutron macromolecular crystallography (NMX) technique.

One can study the diffraction pattern of a protein in different ways, be it X-rays, electron or neutron. I chose neutron diffraction studies for my proteins. This is because I would like to determine the hydrogen positions and understand the protonated state of different chemical groups in proteins which is otherwise not possible by X-Ray diffraction. But, why it is difficult to locate hydrogen by X-Ray crystallography? read full article


This month Diogo teaches us about how crystals are formed and about the difference between diamond, water and protein crystals.

Last post we talked about how we could go from a protein crystal to a structure (Fig. 1 shows the protein crystal size). But what about the protein crystal itself? Getting the protein crystals formed in the first place is often a major bottle neck in this field of research. I thought: scientists struggle a great deal in this procedure, why wouldn’t I share the burden with you? So off we go to see how protein crystals are made. read full article


– Could you remind us briefly what your project is about?

I am following novel approaches to solve high resolution structures of membrane-bound pyrophosphatases (mPPase) using a technique called x-ray crystallography (many of us have already talked about that previously, just check out earlier blog posts). For the proteins I am working on, the most commonly used methods for crystallisation and structure solution have failed so far. Therefore, we are currently trying to generate stabilised versions of one mPPase by introducing mutations. In a number of cases, this has been shown to improve the protein expression, simplify the protein handling and purification and/or aid in crystallisation. A second approach we are following to improve the diffraction properties of our crystals read full article


This month My shares with us her latest secondment experience and gives us a very fresh insight of secondments!


The mobility scheme of each ITN requires us ESRs to have secondments in different institutions within the network. Allowing us the chance to acquire new knowledge and to develop professional network. Here, I am happy to share with you my first experience during my secondment at Imperial College London in the lab of Prof. Bernadette Byrne, whose whole lab I want to thank for the great help and support during my secondment.

What is the purpose of this secondment?

Beside the general purpose of secondments as mentioned above, my project specific purpose was to find optimal conditions to crystallize OmpG (Outer membrane protein G), a model membrane protein I am working with, and to increase the previous crystallization volume for the application of a phase diagram setup. read full article


This month, Sam tells us about his work so far.

– Could you remind us briefly what your project is about?

As mentioned in my first post, my project is about studying the sarcoplasmic reticulum Ca2+-ATPase (SERCA) using neutron macromolecular crystallography (NMX). NMX is similar to the X-ray diffraction technique that Diogo explained previously, except we observe how a protein crystal produces a neutron diffraction pattern. As neutrons scatter off atomic nuclei instead of electrons as with X-rays, hydrogens – which have very few electrons for X-rays to scatter off – are more easily revealed.

In the case of SERCA, we are interested in how protons move through the protein during its functional cycle. The protein performs the vital function of controlling intracellular calcium levels by pumping Ca2+ from the cytoplasm into to the sarco/endoplasmic reticulum (SER). At the same time, SERCA also counter-transports protons from the SER into the cytoplasm. While we have a good understanding of Ca2+ transport, we are unsure of the exact pathway these protons take through the protein. We hope that by mapping hydrogens in SERCA using NMX, we will be able to identify this proton pathway.

However, NMX experiments also present significant challenges, in particular the requirement read full article


This month, Diogo, ESR 8 updates us on his work and explains us how we get proteins strucutre from crystals

– Could you remind us briefly what your project is about?

As I explained in my first post my project is about obtaining many successive 3-D protein pictures over a wide rande of time-scales (down to every 0.000 000 000 000 001 seconds – femtoseconds). We can then pool the pictures together following the timeline, in the end obtaining a movie of the protein in action. Bird figure.

At the time I gave an analogy of taking pictures of a bird versus a protein, in the end having a movie of the bird flying, or the protein performing its function, but bear in mind the different size scales (Fig. 1): the protein I work with is only 90 angstroms in its largest dimension (or 0, 000 000 009 meters)! read full article


This years first publication if from our new ESR, Jessica Ames. Welcome to RAMP Jessica!

Please tell us about yourself

I was born and raised in a small, rural town in central Illinois in the USA. I studied chemical engineering at a Rose-Hulman Institute of Technology in Indiana for a couple of years before transferring to the University of Oklahoma. I graduated from the University of Oklahoma in August 2018 with a BS degree in chemical biosciences. When I’m not in lab, I love traveling, listening to and making music, and catching up with friends. read full article here



This years last blog entry is an update on Sofia Trampari’s PhD experience.

SofiaTrampariCut

– Could you remind us briefly what your project is about?

My project is about investigating the dynamics and behavior of lipid-detergent-protein micelles. It is a biophysical study on the phase behavior of membrane proteins in the presence of lipids and detergent by a crystallographic and electron microscopy (EM) perspective.

Proteins are fundamental for life and for most of its functions. Membrane proteins are part of the membranes of the cells and between many functions that they have, they can control the flow of nutrients in and out of the cells. Ion transporters such as the Na,K-ATPase generate inward Na+ and outward K+ concentration gradients. Neurotransmitter transporters of the SLC6 family (also referred to as neurotransmitter-sodium symporters, NSS) terminate synaptic signal transmission by Na+ dependent reuptake of released neurotransmitters… read full article


This month, Cristina shares with us her experience at Molecular Dimesions where she spent two months on sedondmenet.

Screenshot 2018-11-20 at 15.26.47

– What is the purpose of this secondment?

As part of my PhD project I had the chance to spend two months at Molecular Dimensions Ltd (MDL) in Newmarket, Suffolk, UK.

This secondment had the purpose of developing a new product that could be useful in my and the other ESRs research projects. I found interesting and exciting to work on an idea with the perspective of make it take shape and become real.

Furthermore, I had always been on the customers’ side, buying and using MDL products, whereas for two months I had to change my perspective and put myself in the supplier’s shoes. This helped me consider the different and most practical aspects of the implementation of an idea and think about many details, such as: the most suitable materials, the most convenient solution for shipment… read full article here


This month, is Virginia Apostolopoulos turn to share with us her experience as a RAMP-ITN ESR and to give us an update of her work.

Picture virginia

Could you remind us briefly what your project is about?

My project revolves around the theoretical study of the crystallisation of membrane proteins. Instead of doing an experimental study on how membrane proteins crystallise, I will try to create computational models to understand the physics of the crystallisation of such complex biological systems. That means studying nucleation and the growth of crystals, in correlation with phenomena such as diffusion and flow, that play an important role in the crystallisation process.

The experimental ESRs will help me to achieve my goal, by providing experimental data that they collected during their experiments. Then by analysing their data, I will be able to find patterns and trends that will help to better understand how membrane proteins crystallise read full article here


This month, Jofia Jaho gives us an update on her research and she shares with us her experience so far as a RAMP-ITN ESR.

– Could you remind us briefly what your project is about?

S. Jaho_ESR2

My thesis is about the crystallization of membrane proteins with an automated microfluidic pipeline. But what do these fancy words really mean? They simply describe that my work is associated with the process of crystallizing membrane proteins on microfluidic devices.

What are membrane proteins and why we need to study them? Membrane proteins are proteins located on the membranes of the cell. Depending on their structure, they are involved in a plethora of biological functions. For example, there is a family of membrane proteins (transporters) that are responsible for transporting molecules across the cellular membrane. They transport for example ferric iron ions (Fe+3)… read full article


picture claudia rognee

This month Claudia ESR3 shares with us her experice as a RAMP ESR student and an update on her research.

“- Could you remind us briefly what your project is about?

I am working on one of the adenosine receptors. This is a membrane receptor translating signals from the outside into the interior of the cell. It belongs to the family of G protein coupled receptors (GPCRs). The different receptors in this family recognize a large variety of signals, ranging from light to neurotransmitters and hormones, but they all have very similar way of translating these signals into the cell.

Interestingly, there are many different signalling outputs for these receptors. One way to modulate these outputs is though the binding of different proteins to the receptor. However, currently very little is known about these interactions. The aim of my project is to determine the structure of the adenosine receptor together…read full article


Jannik ESR4 tells us about his experience in the “in meso in depht” workshop that took place in May 2018 in Dublin and Maynooth.

Passbild-Jannik

“What did you learn during the workshop?

During our two weeks in sunny Ireland, we learnt a lot about the fundamental theory behind crystallisation and got hands-on experience on measuring protein solubility curves and protein-protein interactions. As a network that works on RAtionalising Membrane Protein crystallisation, this was very important for us. The second part of the workshop focused on in meso crystallisation as an alternative to the commonly used in surfo crystallisation of membrane proteins. The in meso method takes advantage …” read full article here.


elham rognée 2

Elham, ESR1, tells us about her experience in the “Advanced methods in macromolecular crystallization VIII” course held in Nove Hrady in Czech Republic.

” Why did you take part in this event? (Describe your participation)

“Methods in macromolecular crystallization” is one of the FEBS advanced courses that is held in Nove Hrady, Czech Republic. This course was about different methods in crystallization and in crystallography studies. It was completely related to my thesis and gave me a general understanding of various methods…” read full article


IMG_9125

Swati, ESR11, tells us about her experience in the recent RAMP research workshop “in meso in depth” that took place in May 2018 in Dublin and Maynooth

“What did you learn during the workshop?

Biological membranes mostly consist of lipids and proteins. These lipids and proteins form a complex that is required for protein stability and folding. So, this workshop was all about how we crystallize membrane proteins (MP) in presence of lipids and make the in vitro niche most suitable for the crystallization of a protein. In order to achieve this, we gained the expertise in Hi-LiDe and Lipidic cubic phase (LCP) …” read full article


My - Blog post picture

My, ESR9, tells us about her experience in the recent RAMP research workshop “in meso in depth” that took place in May 2018 in Dublin and Maynooth

“The workshop enabled me to gain an insight into important crystallisation methods, which I had not used before and covered a theoretical understanding of nucleation and crystallisation processes. I learned why protein-protein interactions have a huge impact on crystallisation and more about the importance of protein phase diagrams…” read full article


Picture virginia

Virginia  Apostolopoulou is ESR10, works in the Department of Physics at the University of Surrey, UK. Her PhD subject is  “Modelling crystal formation in complex systems”.

“I graduated from University of Crete, Greece, in 2014 with a bachelor degree in Applied Mathematics. I continued my studies at the University of Crete, and in 2017 I got my master degree in Applied and Computational Mathematics. I am passionate about many areas of applied mathematics…” read full article


SofiaTrampariCut

Sofia Trampari is ESR5, works in Aarhus University, Denmark. Her PhD subject is “Crystallization and phase behavior of membrane transporters in lipid-detergent micelles

“I was born and raised in Athens, Greece. Being an excited and naturally curious person, I consider Physics to be the most intriguing field of research as it addresses a huge range of phenomena, from the nanoscale physics to the laws of the infinite universe. My innate passion to discover the world and my need to work towards finding ways to improve people’s wellbeing led me to pursue my studies in biophysics….” read full article


picture claudia rognee

Claudia Stohrer is ESR3, works at University of Leeds, United Kingdom. Her PhD subject is “Structure determination of the Adenosine receptor A2A in complex with intracellular binding partners”.

“I grew up in Switzerland near the city of Basel. Biology was always my favourite subject, and during high school I could follow up my interests. With “Schweizer Jugend Forscht”, I got my first opportunity to get to know research work at University level by carrying out a little research project at the University of Geneva. I absolutely loved it…” read full article


Passbild-Jannik

Jannik Strauss is ESR4, works at University of Leeds, United Kingdom. His subject is “Novel Approaches to Proton Pumping Pyrophosphatases”.

“I grew up in a small town close to Hannover in Germany. After I finished school, I worked at the Institute of Microbiology and Hospital Hygiene of Nordstadt Hospital in Hannover for one year, where I helped identifying disease-causing microbes in patient samples. It was during that time that I found my passion for infectious disease research…” – read full article


Cristina picture-final-final

Cristina Cecchetti is ESR7, works at Imperial College London, United Kingdom. Her subject is “Structural and functional studies of plant and fungal secondary active transporters”.

“I come from Nemi, a small town close to Rome in Italy. I grew up in a family with a scientific background: my father used to teach physics and chemistry in high school and my uncle is a chemist and teaches chemistry and maths. I got a Bachelor Degree in Chemistry at Sapienza University of Rome, thanks to a deep interest in chemistry developed during high school…” – read full article


Picture Sam rognée

Samuel Hjorth-Jensen is ESR 12 and is completing his PhD at Aarhus University in Denmark. His PhD subject is “proton pumping in sarcoplasmic reticulum Ca2+-ATPase studied by neutron crystallography “.

“I grew up in Pittsworth, a small country town in Queensland, Australia. Growing up in Australia has provided me with a love of the outdoors – I enjoy being in the sun while kayaking, hiking or swimming in the ocean. Education wise, I have completed a Bachelor degree in Exercise Science from James Cook University in tropical far-north Queensland…” – read full article


elham rognée 2

Elham Vahdatahar is ESR1, she works at the University of Grenoble Alpes, France. Her subject is “Optimisation of crystal growth using a microfluidic technology-based crystallisation bench”.

“I was born in Ahwaz, Iran. I studied cellular and molecular biology (genetics) at Isfahan University and then I chose to study biophysics at the University of Tehran. My master thesis was about the effect of potassium sorbate and vitamin C on fibrillation of bovine serum albumin. I really like to know more about proteins;…” – read full article


My - Blog post picture

Thi Thanh My Nguyen is ESR 9, works at Maynooth University, Ireland. Her PhD subject is “experimental phase diagrams to optimise membrane protein crystallization”. 

“I come from a small fishing village in Vietnam and grew up near the North Sea in Germany. Living close to the sea my whole life, I enjoy being at the coast in any kind of weather. I did my Bachelor’s and Master’s degrees in Industrial Biology at the Bremen University of Applied Sciences…” – read full article


Swati picture final

Swati Aggarwal is ESR 11, works at European Spallation Source (ESS) ERIC in Lund, Sweden. Her PhD subject: Elucidating the function of proton pumps with neutron crystallography.

“I come from a small valley surrounded by Himalayas known as Dehradun in India. I completed my Master’s in Biotechnology from National Institute of Technology, Rourkela, India. I spend my leisure time in painting…” – read full article.


Cromarte Rogers

Marty Rogers is ESR 6, works at Trinity College Dublin, Ireland. His subject: Novel lipid environments for use in lipid cubic phase (in meso) crystallization of membrane proteins.

“I was born and raised in South Carolina in the USA. I played the French horn in school bands and orchestras since I was 10 years old, and music of all forms is still one of my passions. I completed an undergrad degree in Chemistry at the University of Oxford before….” – read full article.


photo-Sofia-Jaho-finale

Sofia Jaho is ESR 2, works at the Institute for Structural Biology in Grenoble, France. Her subject : Crystallization of membrane proteins with an automated microfluidic pipeline.

“I come from Fier, a small city in Albania but I grew up in Argos, a town in South-East of Greece. While being a high school student, I used to work during summer at different half-time jobs. I studied at the Department of Chemical Engineering at University of Patras…” – read full article.


Diogo is the first to go, and accepted to answer a few questions to present himself!

foto cortada

Diogo Melo is ESR 8, works at the Center for Free Electron Laser Science (CFEL) in Hamburg, Germany. His subject : Controlled growth of uniformly sized microcrystals, optimised for time-resolved crystallographic experiments

“I come from Alguber, a small village in Portugal that mostly lives off agriculture, in which I used to work most of the summers. I studied biochemistry for four years in the University of Algarve and two years in NOVA University of Lisbon…” – read full article