Author: ElenaInSingapore

How to Elucidate the Structure of Peptide Monolayers on Gold Nanoparticles?

I have recently submitted my PhD thesis and we have now pre-printed on bioRxiv the work constituting its major chapter. Together with the pre-print, the data have been made publicly available in an online repository of the University of Liverpool. Well isn’t it perfect timing that this week is open access week? 😉

This work has been conducted nearly entirely during the 2 years of my PhD spent at the A*STAR Institute of Materials Research and Engineering (IMRE) and at the A*STAR Institute of High Performance Computing (IHPC) in Singapore.

In this study, peptide-capped gold nanoparticles are considered, which offer the possibility of combining the optical properties of the gold core and the biochemical properties of the peptides.

In the past, short peptides have been specifically designed to form self-assembled monolayers on gold nanoparticles. Thus, such approach was described as constituting a potential route towards the preparation of protein-like nanosystems. In other words, peptide-capped gold nanoparticles can be depicted as building-blocks which could potentially be assembled to form artificial protein-like objects using a “bottom-up” approach.

However, the structural characterization of the peptide monolayer at the gold nanoparticles’ surface, essential to envision the design of building-blocks with well-defined secondary structure motifs and properties, is poorly investigated and remains challenging to assess experimentally.

In the pre-printed manuscript, we present a molecular dynamics computational model for peptide-capped gold nanoparticles, which was developed using systems characterized by mean of IR spectroscopy as a benchmark. In particular, we investigated the effect of the peptide capping density and the gold nanoparticle size on the structure of self-assembled monolayers constituted of either CALNN or CFGAILSS peptide.

The computational results were found not only to well-reproduce the experimental ones, but also to provide insights at the molecular level into the monolayer’s structure and organization, e.g., the peptides’ arrangement within secondary structure domains on the gold nanoparticle, which could not have been assessed with experimental techniques.

Overall, we believe that the proposed computational model will not only be used to predict the structure of peptide monolayers on gold nanoparticles, thus helping in the design of bio-nanomaterials with well-defined structural properties, but will also be combined to experimental findings, in order to obtain a compelling understanding of the monolayer’s structure and organization.

In this sense, we would like to stress that, in order to improve data reproducibility, enable further analysis and the use of the proposed computational model for peptide-capped gold nanoparticles, we are making the data and the custom-written software to assemble and analyse the systems publicly available.

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Snapshots of the final structure of the simulated 5 (left) and 10 (right) nm CFGAILSS-capped gold nanoparticle, illustrating different content and organization of secondary structure motifs.

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April in Singapore – First Month, First Impressions

I am PhD student in Raphaël’s group, now in Singapore, where I will spend two years of my PhD working at the Institute of Materials Research and Engineering (IMRE).

In a couple of days it will be a month since I moved here. On my farewell night out in Liverpool, Raphaël asked me if I was going to write a post for his blog once in Singapore, I thought, why not! The idea of a blog post from Singapore then became a monthly blog from Singapore and I am now writing about my April in Singapore.

The first thing I want to talk about is quite obvious: the food. The food is great and inexpensive. According to The Economist, Singapore is the most expensive city in the world, but I am sure they haven’t considered the food prices when they came to this conclusion (they might have considered the cheese prices though 😉 ). Here there are food courts, which are food centers with stalls selling food ranging from pig’s organ soups to the five different types of Chinese noodles, from Indian fish head curry served with paratha to Singaporean chicken rice and Japanese tempura. The food courts can be fancy ones when inside air-conditioned shopping malls or open-air with more traditional dishes. And when I said that the food is inexpensive I meant that with £2 you can eat a proper dish! I am then not surprised that people here do not use to cook!
The Institute where I am working is inside the National University of Singapore campus and so far I have been in three different canteens that are basically food courts inside different departments (almost as it is in Liverpool 😉 ).
Also, the first time I went to the supermarket I was surprised to see all the products that Singapore imports from Europe; I found many Italian and French brands that I have never found in Liverpool. Huge modern shopping malls are everywhere with quite impressive lists of restaurant/fast food chains inside. I have also found the French bakery Paul and it brought back nice memories of when I used to live in Paris.
On one hand I find Singapore deeply Westernized, the number of shopping malls is something unbelievable (and somehow scary) and in each of them  there are the same fast food chains and more or less the same shops, but on the other hand I think that the culture of  food here is great and different from any other place! The food traditions of the different ethnic groups who migrated and live here (Singapore is 74% Chinese, 13% Malay, 9% Indian, and 3% Eurasian) have resisted the westernization of the country and made the Singaporean food very unique; I would even say that Singaporean cuisine is the coexistence of other Asian countries cuisines over 710 km²!

The Parkroyal Hotel Garden in Singapore. I found it very suggestive with gardens and plants merged in the glass and steel.

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