Spare time fun: protein structure analysis of mutations causing inheritable diseases

Most people I know would not consider protein structure analysis of mutations causing inheritable diseases “spare time fun”. Then again, most people I know don’t think I am like most people they know.

This week I’m a “single-dad”, since my wife is traveling. So my spare time right now is almost non existent. Nevertheless, the thought of mutating a Proline into a Glycine at position 22 intrigued me, so I spent a few minutes simulating it. Here is what I found out:

Method

The 3D-structure of my protein of interest was obtained from the UniProt database using Reprof. The structural information was obtained from the analysis of PDB: 3NIR. Annotations were obtained from UniProt entry CRAM_CRAAB.

Amino Acids

I was interested in the mutation of a Proline into a Glycine at position 22.

The figure below shows the schematic structures of the original (left) and the mutant (right) amino acid. The backbone, which is the same for each amino acid, is colored red. The side chain, unique for each amino acid, is colored black.

 mutates into 

Each amino acid has its own specific size, charge, and hydrophobicity-value. The original wild-type residue and newly introduced mutant residue differ in these properties: the mutant residue is smaller than the wild-type residue, while the wild-type residue is more hydrophobic than the mutant residue.

Variants

A mutation to “S” was found at this position, which differs from the mutation I was simulating. The effect of this variant is annotated as: In isoform SI.

Conservation

The wild-type residue is not conserved at this position. Another residue type was observed more often at this position in other homologous sequences. This means that other homologous proteins exist with that other residue type than with the wild-type residue in my protein sequence, but the other residue type is not similar to my mutant residue. Therefore, the mutation is possibly damaging.

Domains

This residue is part of an interpro domain named: Thionin IPR001010

The mutated residue is located on the surface of a domain with unknown function. The residue was not found to be in contact with other domains of which the function is known within the used structure. However, contact with other molecules or domains is still possible and might be affected by this mutation.

Amino Acid Properties

The wild-type and mutant amino acids differ in size. The mutant residue is smaller than the wild-type residue. This will cause a possible loss of external interactions.

The hydrophobicity of the wild-type and mutant residue differs. The mutation might cause loss of hydrophobic interactions with other molecules on the surface of the protein.

Images

Overview of the protein in ribbon-presentation. The protein is coloured by element; α-helix=blue, β-strand = red, turn=green, and random coil=cyan.

Overview of the protein in ribbon-presentation. The protein is coloured grey, the side chain of the mutated residue is coloured magenta and shown as small balls.

Close-up of the mutation. The protein is coloured grey, the side chains of both the wild-type and the mutant residue are shown and coloured green and red respectively.

Close-up of the mutation (seen from a slightly different angle). The protein is coloured grey, the side chains of both the wild-type and the mutant residue are shown and coloured green and red (not show from this angle) respectively.

Close-up of the mutation (seen from a slightly different angle). The protein is coloured grey, the side chains of both the wild-type and the mutant residue are shown and coloured green and red respectively.

Movies

Close-up of the mutation. Both the wild-type and mutant side chain are shown in green and red respectively. The rest of the protein is show in grey.

Close-up of the mutation, same colours as animation 1. The animation shows alternating the wild-type side chain and the mutant side chain.

Citation

Protein structure analysis of mutations causing inheritable diseases. DOI: 10.1186/1471-2105-11-548. PubMed: 21059217.

Visiting the London Design Museum

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Yesterday I visited the Design Museum (“The world’s leading museum devoted to contemporary design in every form from architecture and fashion to graphics, product and industrial design”) in its spectacular new location on High Street Kensington (London), with my son.

The #newdesignmuseum opened its doors in its new location only 5 days ago. The building and renovation are great, and in a nice location: on the edge of Holland Park, with the added bonus of being near the Kyoto Garden, Muji, and not far from the Serpentine Gallery.

I was expecting more from the shop(s) and I felt the exhibitions lacked a more daring curating, and more compelling communication. Although the loose “Designer, Maker, User” theme was not bad, they could have definitely dug more into the concept.

Additionally, it felt the collection was not comprehensive enough, with an overwhelming majority of consumer electronic devices, and not enough from other disciplines like fashion, architecture, or even manufacturing.

All in all, a nice evening in a nice museum, but plenty of room for improvement.

Valencia (Spain) VC flows

Adam Gilfix, Brian de Luna, and Luke Heine, with the help of Dealroom.co, have created a very interesting data visualization tool for Venture Capital (VC) flows.

I know for a fact and from experience that VC activity in places like Silicon Valley, NY, Boston, or London is big. But even when I go back home (Valencia – Spain) for the holidays, there are all kinds of “VC” events, news, meetings, spaces… which, given the conservative and provincial nature of the “Valencian Investors” I have met, surprises me.

So I decided to check out Valencia (Spain) VC flows. Unsurprisingly, those “flows” (both inbound and outbound) are quite recent, very very small, extremely limited in geographical reach, and conservative in industries. See for yourself:

View post on imgur.com

View post on imgur.com

View post on imgur.com

Several caveats, though:

  • The data may not cover ALL VC activity in the region
  • Some activity may be wrongly identified (for example, there is a transaction coming from “Valencia – Venezuela”, which could be a coincidence, or most likely a data collection error)

4 days in Asuncion (Paraguay)

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From Sunday 20 to Wednesday 23 November I have been in Asunción (Paraguay) for several business meetings.

Regardless of the very interesting business projects and meetings at the highest level ( in a single day I met with three “Secretaries” or “Ministers”: Industry and Commerce, Technology, and Health), it was a pleasure to know one of the few countries that I had yet to visit in South America. Now I only have Bolivia left.

Asunción is a rapidly changing city. You can already see the first mega-malls, luxury urban condos, and some modern office buildings, but for the most part it is still a low-height city, full of single-family dwellings of all kinds (from palaces to shantytowns), with many cobblestone roads in the city center, next to perfectly well paved avenues with several lanes, which act as a constant reminder and testament of the great and growing inequalities that exist, not only in the region, but unfortunately worldwide.

My hotel was the excellent La Misión, very adorable and well located, and with a pool on the terrace, which given a temperature of 38ºC, and especially coming from a hail in London the day before, was very appreciated. In the morning, breakfast was a not very extensive buffet, but it had delicious local options (from the “Paraguayan soup” which is a dry soup, to the “cocido”: herbal infusion of used tereré and sugar). A particular highlight was the freshly squeezed natural fruit juices at my disposal, which has allowed me to experiment with blends like carrot-guava, passion fruit-mango-strawberry, etc. A true gourmet pleasure, which, together with live harp music, was a perfect way to start the day.

For work, I had the opportunity to visit three very different hospitals (Pediatric, National, and Cancer). There I realized that although there are perfectly qualified professionals, political will, seemingly adequate management, and resources (scarce but existent), there is much to be done. However, that is the paradox: that lagging in many areas puts them in a position of privilege to be able to implement the latest technologies without going through legacy systems, rejection and friction to change, pre-existing interests and structures, and endless other circumstances than act as barriers to technology adoption in many other countries with greater resources and level of technological penetration.

Of course, I can not fail to mention the food. Although, generally, I prefer Asian food, and despite being “not so elaborate” or “sophisticated”, Paraguayan food has interesting dishes (such as Paraguayan soup, chipa guasú, vorí-vorí … ), excellent meat, and a wide variety of delicious fruits (in fact the fruit trees are everywhere, so much so that children play in the street with mangoes), although I was looking forward to trying the Araticú.

Speaking of meat, on my various trips to the outskirts of “Greater Asunción”, I saw so many cows along the road that it reminded me of India (except they were not famished, quite the contrary). I also saw areas specializing in various handicrafts (such as straw objects, chairs, or balls), people of many different backgrounds and opinions, and an overwhelmingly green and leafy landscape.

The people I have met have been very pleasant, and as always, it allows me to know more closely the reality of a country that I did not know too much about. Especially interesting was to experience the long working hours (where have you seen a Government high official schedule a meeting at 7:00 am?), learn about the War of the Triple Alliance, and about indigenous natives and the Guaraní language . As icing on the cake, the last day there was a party at my client’s house, attended by a dozen executives from large companies, and where we enjoyed a “gourmet” grill. Something tells me that I will soon be back with my new friends.

Invited to speak at GIANT Health event in London

Right after I returned from Germany, and before departing for Paraguay, I was invited to speak at the GIANT Health event (the “global innovation and new technology health event), health in The Coronet, London.

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The event run for 3 days, November 16-18, with 3 parallel tracks, and it included over 200 speakers. I spoke November 18, in the main auditorium.

There was an exhibition area, with several companies and organizations showing their innovations and technologies.

The venue was quite “grunge”, and it made you feel more like you were performing in a rock concert, rather than speaking at a healthcare event. All in all a massive, interesting, and fun event (except for the poor kamikaze organizers 😉 ).

Düsseldorf Museums

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Last week I spent 3 days in Düsseldorf, attending the Medica trade show. But I do not want to bore you with that. I’d rather tell you what I did after the trade show closed every day.

Since Düsseldorf is a city that I know well, I decided to concentrate in its museums and art galleries. I could not have picked a more perfect time!

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At the Kunsthalle I attended the excellent exhibition titled “Wool and water”, wi­th: Li­li Du­jou­rie, Isa Genz­ken, As­trid Klein, Mi­scha Ku­ball, Aron Meh­zi­on, Rein­hard Mu­cha, Stur­te­vant, Ro­se­ma­rie Tro­ckel, and Ger­hard Rich­ter; cu­ra­ted by Gre­gor Jan­sen. An absolutely “can’t miss” exhibition. Alluring and exciting. I could not remember the last time I was so excited about an exhibition. I felt like clapping, like calling the curator and the artists and showing my respect and admiration.

I also visited both the K20 and K21 at the Kunstsammlung Nordrhein-Westfalen (KNW).

The K20 Grabbeplatz was exhibiting “Cloud and Crystal: The Dorothee and Konrad Fischer Collection”. Quite an amazing collection including works by: Carl Andre, Richard Artschwager, Lothar Baumgarten, Bernd and Hilla Becher, Joseph Beuys, Marcel Broodthaers, Stanley Brouwn, Daniel Buren, Alan Charlton, Hanne Darboven, Jan Dibbets, Dan Flavin, Gilbert & George, Douglas Huebler, Stephen Kaltenbach, On Kawara, Harald Klingelhöller, Jannis Kounellis, Jim Lambie, Sol LeWitt, Richard Long, Konrad Lueg, Robert Mangold, Piero Manzoni, John McCracken, Mario Merz, Juan Muñoz, Bruce Nauman, Giuseppe Penone, Manfred Pernice, Ulrich Rückriem, Robert Ryman, Gregor Schneider, Thomas Schütte, Niele Toroni, Paloma Varga Weisz, and Lawrence Weiner.

But the complete shock was at the K21 Ständehaus, a very special venue for young international artists and for the contemporary portions of the KNW permanent collection.

The underground level was showing “My Phantasies”, with works by: Gerhard Altenbourg, Katharina Fritsch, Julian Göthe, Sabine Groß, Nan Hoover, Axel Hütte, Jürgen Klauke, Alicia Kwade, Kris Martin, Pauline M’Barek, Gerhard Merz, Dieter Roth, Wilhelm Sasnal, Wael Shawky, Nancy Spero, Thomas Struth, Rosemarie Trockel and Gillian Wearing. Only OK. Some interesting pieces, but not worth going out of your way for. BUT the Artist’s Rooms in the three above ground levels were just absolutely stunning.

Traversing three levels, 22 rooms offer intensive up-close encounters with painting, sculpture, photography, film, and in particular with spatially-oriented art. Selected contemporary artists are invited to display works for a period of one year, thereby engaging in dialogue with other works in the collection. What I was privileged enough to enjoy was:

1st floor

  • Imi Knoebel
  • Christian Jankowski
  • Bill Viola
  • James Turrell

2nd floor

  • Ibrahim Mahama
  • Antonia Low [until end of October, 2016]
  • Alexandra Bircken [from end of November, 2016]
  • Hans-Peter Feldmann
  • Diango Hernández
  • Bertold Stallmach / Nina Fischer & Maroan el Sani

3rd floor

  • Tomás Saraceno
  • Franz West [under construction]
  • Janet Cardiff/George Bures Miller
  • Chiharu Shiota
  • Anna Oppermann [temporarily closed]
  • Christian Boltanski

Please, if you can go to Düsseldorf, or you’re already there, do make sure to visit “Wool and water” at the Kunsthalle and the Artist’s Rooms at K21 Ständehaus. Absolutely awesome.

Invited to participate in PA Consulting event

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A few days ago I was invited to participate in a Healthcare Innovation workshop at PA Consulting in London.

Beyond the cute venue, and spectacular list of attendees from the healthcare, industry, and political spaces (“Don’t waste time talking to someone with ‘Lord’ in his title, they are not there to really work”, one of my colleagues advises me), what impressed me was the extremely well organized, choreographed, and disciplined approach to innovation they had. Quite a learning experience!

I acquired a David Shrigley piece from the Ludwig Museum

November 9 I acquired from the Ludwig Museum “I collect records”, a 27 cm ø 175gr. professional vinyl frisbee piece that the Turner Prize-nominated artist and occasional DJ David Shrigley created in 2012.

“I collect records” is based on a drawing he did for a record cover featured in his exhibition Life and Life Drawing.

3 days in Cologne November 2016 for BioEurope

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November 6-9 I had to travel to Cologne (Germany) to attend the BioEurope trade show, along with a UK delegation. I have been in Cologne several times before, so I was not particularly surprised. But as with every trip, here are a few remarkable things I would like to comment:

  • The hotel was right next to the train station and the Cathedral, quite convenient
  • It rained every frigging day. It was cold and dark
  • Where there are trees, Autumn is quite a spectacle
  • Rheinpark is very nice, but has too many walls. They have a “beach club” (I guess some sand by the river could be considered a “beach”), which closed and very sad in the winter
  • The “locker bridge” (Hohenzollernbrücke) is amusing. Herd mentality, symbols, the power of love, the risk of too much additional weight on the bridge…
  • The cathedral is tall and dark. Very tall and very dark. And it has a really cool “pixellated” stain glass window. I like to think of it as a Matrix glitch
  • The Ludwig Museum is very nice. I should write a post about it. And it has a great store: mostly books. No ties or watches. Thank you
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  • Pharma Industry is a lot of mirrors and smoke. Speculation riding on the back of a few blockbusters, the greed of executives, and the commercial naivety of researchers. It reminds me of the circus VCs and entrepreneurs put together in every single TechCrunch and similar events

What am I doing here? Sometimes in order to find yourself, when you are not where you want to be, you have to get lost. But I have a plan. And it’s a good one 😉

Invited by the Duque of York to have dinner at Windsor Castle November 3

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The other day I received a letter from Buckingham Palace, inviting me to have dinner with the Duke of York (Prince Andrew) on Thursday at Windsor Castle.

I was curious to see the castle from the inside: it is a medieval style fortress, filled with military memorabilia (guns, swords, lances, armors…), banners and crests. It was more Game of Thrones than Harry Potter.

The reception was held at the Grand Reception Room. Then the delicious dinner was impeccably served at Waterloo Chamber. One thing I noticed is that all serving staff was a member of a minority, yet none of the guests except two, were.

After dinner, tea (and delicious bonbons) was served at St. George’s Hall, where I had a chance to chat with the Duke.

Honestly, I was surprised. I guess many of us have seen his picture, when married to Sarah Ferguson. They seemed like quite a lively and smily couple. He seemed so human and fun. Yet the man I spoke to the other day was a stern, strict, strong man. One that transmitted “statesmanship”. Is it because Brexit? Because the Queen is 90? Talking about the Queen, he mentioned an amusing anecdote about this very particular woman: just the day before she wanted to try a new water nebulizer for the toilet bathroom, so she headed to the first one (nevermind it was the gents’) with her entourage. As she was wearing gloves, instead of removing her gloves, she asked her staff to wash their hands using the new nebulizer, and to tell her what they thought 0_0

When I pointed out the anachronism of the monarchy in XXI century Europe, the duque talked, in no uncertain terms, about leadership. He said (if I remember the quote correctly):

“No. 10 [UK’s Prime Minister Cabinet] is good at following. We [Did he mean the UK Royal Family? Did he mean him and me? Did he mean his guests?] are good at leading. That’s what we have to do”.

I will not comment on that quote, as I am not absolutely sure I interpreted it correctly, and I do not even want to start a “royal-political-especulation” post, particularly in post-Brexit UK.

One thing I will comment, though, is that it was a true pleasure to be able to meet and chat with the rest of the technology-focused guests:

  • Tim Berners-Lee, Director, World Wide Web Consortium
  • Andrew Eland, Engineering Director, Google Deep Mind
  • Christopher Bishop, Director, Microsoft Research Cambridge
  • Corinna Zarek, Deputy US Chief Technology Office, The White House
  • Natalie Black, Deputy Director No. 10 Policy Unit, UK Prime Minister’s Office
  • David Cleevely, Chairman, Raspberry Pi Foundation
  • Liam Maxwell, National Technology Adviser, Her Majesty’s Government
  • John Simmons, Minister Counselor, US Embassy

Then again, this kind of concentration of power and behind-the-door petit-comitee gathering is something I have often decried as a toxic byproduct of a system (be it representative democracy, monarchy, or consumerist capitalism) that we desperately need to change.