Category Archives: Proteins

Mol2vec: Finding Chemical Meaning in 300 Dimensions

Embeddings of Amino Acids

2D projections (t-SNE) of Mol2vec vectors of amino acids (bold arrows). These vectors were obtained by summing the vectors of the Morgan substructures (small arrows) present in the respective molecules (amino acids in the present example). The directions of the vectors provide a visual representation of similarities. Magnitudes reflect importance, i.e. more meaningful words. [Figure from Ref. 1]

Natural Language Processing (NLP) algorithms are usually used for analyzing human communication, often in the form of textual information such as scientific papers and Tweets. One aspect, coming up with a representation that clusters words with similar meanings, has been achieved very successfully with the word2vec approach. This involves training a shallow, two-layer artificial neural network on a very large body of words and sentences — the so-called corpus — to generate “embeddings” of the constituent words into a high-dimensional space. By computing the vector from “woman” to “queen”, and adding it to the position of “man” in this high-dimensional space, the answer, “king”, can be found.

A recent publication of one of my former InhibOx-colleagues, Simone Fulle, and her co-workers, Sabrina Jaeger and Samo Turk, shows how we can embed molecular substructures and chemical compounds into a similarly high-dimensional, continuous vectorial representation, which they dubbed “mol2vec“.1 They also released a Python implementation, available on Samo Turk’s GitHub repository.

 

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Protein Structure Classification: Order in the Chaos

The number of known protein structures has increased exponentially over the past decades; there are currently over 127,000 structures deposited in the PDB [1]. To bring order to this large volume of data, and to further our understanding of protein function and evolution, these structures are systematically classified according to sequence and structural similarity. Downloadable classification data can be used for annotating datasets, exploring the properties of proteins and for the training and benchmarking of new methods [2].

Yearly growth of structures in the PDB (adapted from [1])

Typically, proteins are grouped by structural similarity and organised using hierarchical clustering. Proteins are sorted into classes based on overall secondary structure composition, and grouped into related families and superfamilies. Although this process could originally be manually curated, as with Structural Classification of Proteins (SCOP) [3] (last updated in June 2009), the growing number of protein structures now requires semi- or fully-automated methods, such as SCOP-extended (SCOPe) [4] and Class, Architecture, Topology, Homology (CATH) [5]. These resources are comprehensive and widely used, particularly in computational protein research. There is a large proportion of agreement between these databases, but subjectivity of protein classification is to be expected. Variation in methods and hierarchical structure result in differences in classifications.  For example, different criteria for defining and classifying domains results in inconsistencies between CATH and SCOPe.

The arrangements of secondary structure elements in space are known as folds. As a result of evolution, the number of folds that exist in nature is thought to be finite, predicted to be between 1000-10,000 [6]. Analysis of currently known structures appears to support this hypothesis, although solved structures in the PDB are likely to be a skewed sample of all protein structures space. Some folds are extremely commonly observed in protein structures.

In his ‘periodic table for protein structures’, William Taylor went one step further in his goal to find a comprehensive, non-hierarchical method of protein classification [7]. He attempted to identify a minimal set of building blocks, referred to as basic Forms, that can be used to assemble as many globular protein structures as possible. These basic Forms can be combined systematically in layers in a way analogous to the combination of electrons into valence shells to form the periodic table. An individual protein structure can then be described as the closest matching combination of these basic Forms.  Related proteins can be identified by the largest combination of basic Forms they have in common.

The ‘basic Forms’ that make up Taylor’s ‘periodic table of proteins’. These secondary structure elements accounted for, on average, 80% of each protein in a set of 2,230 structures (all-alpha proteins were excluded from the dataset) [7]

The classification of proteins by sequence, secondary and tertiary structure is extensive. A relatively new frontier for protein classification is the quaternary structure: how proteins assemble into di-, tri- and multimeric complexes. In a recent publication by an interdisciplinary team of researchers, an analysis of multimeric protein structures in combination with mass spectrometry data was used to create a ‘periodic table of protein complexes’ [8]. Three main types of assembly steps were identified: dimerisation, cyclisation and heteromeric subunit addition. These types are systematically combined to predict many possible topologies of protein complexes, within which the majority of known complexes were found to reside. As has been the case with tertiary structure, this classification and exploration of of quaternary structure space could lead to a better understanding of protein structure, function and evolutionary relationships. In addition, it may inform the modelling and docking of multimeric proteins.

 

  1. RCSB PDB Statistics
  2. Fox, N.K., Brenner, S.E., Chandonia, J.-M., 2015. The value of protein structure classification information-Surveying the scientific literature. Proteins Struct. Funct. Bioinforma. 83, 2025–2038.
  3. Murzin AG, Brenner SE, Hubbard T, Chothia C., 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 247, 536–540.
  4. Fox, N.K., Brenner, S.E., Chandonia, J.-M., 2014. SCOPe: Structural Classification of Proteins–extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Res. 42, 304-9.
  5. Dawson NL, Lewis TE, Das S, et al., 2017. CATH: an expanded resource to predict protein function through structure and sequence. Nucleic Acids Research. 45, 289-295.
  6. Derek N Woolfson, Gail J Bartlett, Antony J Burton, Jack W Heal, Ai Niitsu, Andrew R Thomson, Christopher W Wood,. 2015. De novo protein design: how do we expand into the universe of possible protein structures?, Current Opinion in Structural Biology, 33, 16-26.
  7. Taylor, W.R., 2002. A “periodic table” for protein structures. Nature. 416, 657–660.
  8. Ahnert, S.E., Marsh, J.A., Hernandez, H., Robinson, C. V., Teichmann, S.A., 2015. Principles of assembly reveal a periodic table of protein complexes. Science. 80, 350

Start2Fold: A database of protein folding and stability data

Hydrogen/deuterium exchange (HDX) experiments are used to probe the tertiary structures and folding pathways of proteins. The rate of proton exchange between a given residue’s backbone amide proton and the surrounding solvent depends on the solvent exposure of the residue. By refolding a protein under exchange conditions, these experiments can identify which regions quickly become solvent-inaccessible, and which regions undergo exchange for longer, providing information about the refolding pathway.

Although there are many examples of individual HDX experiments in the literature, the heterogeneous nature of the data has deterred comprehensive analyses. Start2Fold (Start2Fold.eu) [1] is a curated database that aims to present protein folding and stability data derived from solvent-exchange experiments in a comparable and accessible form. For each protein entry, residues are classified as early/intermediate/late based on folding data, or strong/medium/weak based on stability data. Each entry includes the PDB code, length, and sequence of the protein, as well as details of the experimental method. The database currently includes 57 entries, most of which have both folding and stability data. Hopefully, this database will grow as scientists add their own experimental data, and reveal useful information about how proteins refold.

The folding data available in Start2Fold is visualised in the figure below, with early, intermediate and late folding residues coloured light, medium and dark blue, respectively.

start2foldpng

[1] Pancsa, R., Varadi, M., Tompa, P., Vranken, W.F., 2016. Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability. Nucleic Acids Res. 44, D429-34.

Seventh Joint Sheffield Conference on Cheminformatics Part 1 (#ShefChem16)

In early July I attended the the Seventh Joint Sheffield Conference on Cheminformatics. There was a variety of talks with speakers at all stages of their career. I was lucky enough to be invited to speak at the conference, and gave my first conference talk! I have written two blog posts about the conference: part 1 briefly describes a talk that I found interesting and part 2 describes the work I spoke about at the conference.

One of the most interesting parts of the conference was the active twitter presence. #ShefChem16. All of the talks were live tweeted which provided a summary of each talk and also included links to software or references. It also allowed speakers to gain insight and feedback on their talk instantly.

One of the talks I found most interesting presented the Protein-Ligand Interaction Profiler (PLIP). It is a method for the detection of protein-ligand interactions. PLIP is open-source and has a web-based online tool and a command-line tool. Unlike PyMol which only calculates polar contacts, and not the type of interaction, PLIP calculates 8 different types of interactions: hydrogen bonding, hydrophobic, π-π stacking, π-cation interactions, salt bridges, water bridges, halogen bonds, metal complexes. For a given pdb file the interactions are calculated and shown in a publication quality figure shown here.

Screen Shot 2016-07-20 at 14.16.23

The display can also be downloaded as a PyMol session so the display can be modified. 

This tool is an extremely useful way to calculate protein-ligand interactions and can be used to find the types of interactions formed by the protein-ligand complex.

PLIP can be found here: https://projects.biotec.tu-dresden.de/plip-web/plip/

A program to aid primary protein structure determination -1962 style.

This year, OPIG have been doing series of weekly lectures on papers we considered to be seminal in the field of protein informatics. I initially started looking at “Comprotein: A computer program to aid primary protein structure determination” as it was one of the earliest (1960s) papers discussing a computational method of discovering the primary structure of proteins. Many bioinformaticians use these well-formed, tidy, sterile arrays of amino acids as the input to their work, for example:

MGLSDGEWQL VLNVWGKVEA DIPGHGQEVL IRLFKGHPET LEKFDKFKHL KSEDEMKASE DLKKHGATVL TALGGILKKK GHHEAEIKPL AQSHATKHKI PVKYLEFISE CIIQVLQSKH PGDFGADAQG AMNKALELFR KDMASNYKEL GFQG
(For those of you playing at home, that’s myoglobin.)

As the OPIG crew come from a diverse background and frequently ask questions well beyond my area of expertise, if for nothing other than posterior-covering, I needed to do some background reading. Though I’m not a researcher by trade any more, I began to realise despite the lectures/classes/papers/seminars I’d been exposed to, regarding all the clever things you do with a sequence when you have it, I didn’t know how you would actually go from a bunch of cells expressing (amongst a myriad of other molecules) the protein you were interested in, to the neat array of characters shown above. So without further ado:

The first stage in obtaining your protein is: cell lysis and there’s not much in it for the cell.
Mangle your cell using chemicals, enzymes, sonification or a French press (not your coffee one).

The second stage is producing a crude extract by centrifuging the above cell-mangle. This, terrifyingly, appears to be done between 10,000G and 100,000G and removes the cellular debris leaving it as a pellet in the bottom of the container, with the supernatant containing little but a mix of the proteins which were present in the cytoplasm along with some additional macromolecules.

Stage three is to purify the crude extract. Depending on the properties of the protein you’re interested in, one or more of the following stages are required:

  • Reverse-phase chromatography to separate based on hydrophobicity
  • Ion-exchange to separate based on the charge of the proteins
  • Gel-filtration to separate based on the size of the proteins

If all of the above are preformed, whilst the sequence of these variously charged/size-sorted/polar proteins will still be still unknown, they will now be sorted into various substrates based upon their properties. This is where the the third stage departs from science and lands squarely in the realm of art. The detergents/protocols/chemicals/enzymes/temperatures/pressures of the above techniques all differ depending on the hydrophobicity/charge/animal source of the type of protein one is aiming to extract.

Since at this point we still don’t know their sequence, working out the concentrations of the various constituent amino acids will be useful. One of the simplest methods of determining the amino acid concentrations of a protein is follow a procedure similar to:

Heat the sample in 6M HCL at at a temperature of 110C for 18-24h (or more) to fully hydrolyse all the peptide bonds. This may require an extended period (over 72h) to hydrolyse peptide bonds which are known to be more stable, such as those involving valine, isoleucine and leucine. This however can degrade Ser/Thr/Tyr/Try/Gln and Cys which will subsequently skew results. An alternative is to raise the pressure in the vessel to allow temperatures of 145-155C to for 20-240 minutes.

TL;DR: Take the glassware that’s been lying about your lab since before you were born, put 6M hydrochloric acid in it and bring to the boil. Take one difficultly refined and still totally unknown protein and put it in your boiling hydrochloric acid. Seal the above glassware in order to use it as a pressure vessel. Retreat swiftly whilst the apparatus builds up the appropriate pressure and cleaves the protein as required. -What could go wrong?

At this point I wondered if the almost exponential growth in PDB entries was due to humanity’s herd of biochemists now having been thinned to those which remained simply being several generations worth of lucky.

Once you have an idea of how many of each type of amino acid comprise your protein, we can potentially rebuild it. However at this point it’s like we’ve got a jigsaw puzzle and though we’ve got all the pieces and each piece can only be one of a limited selection of colours (thus making it a combinatorial problem) we’ve no idea what the pattern on the box should be. To further complicate matters, since this isn’t being done on but a single copy of the protein at a time, it’s like someone has put multiple copies of the same jigsaw into the box.

Once we have all the pieces, to determine the actual sequence, a second technique needs to be used. Though invented in 1950, Edman degradation appears not to have been a particularly widespread protocol, or at least it wasn’t in the National Biomedical Research Foundation from which the above paper emerged. This means of degradation tags the N-terminal amino acid and cleaves it from the rest of the protein. This can then be identified and the protocol repeated. Whilst this would otherwise be ideal, it suffers from a few issues in that it takes about an hour per cycle, only works reliably on sequences of about 30 amino acids and doesn’t work at all for proteins which have their n-terminus bonded or buried.

Instead, the refined protein is cleaved into a number of fragments at known points using a single enzyme. For example, Trypsin will cleave on the carboxyl side of arginine and lysine residues. A second copy of the protein is then cleaved using a different enzyme at a different point. These individual fragments are then sorted as above and their individual (non-sequential) components determined.

For example, if we have a protein which has an initial sequence ABCDE
Which then gets cleaved by two different enzymes to give:
Enzyme 1 : (A, B, C) and (D, E)
Enzyme 2 : (A, B) and (C, D)

We can see that the (C, D) fragment produced by Enzyme 2 overlaps with the (A, B, C) and (D, E) fragments produced by Enzyme 1. However, as we don’t know the order in which the amino acid appear within in each fragment, thus there are a number of different sequences which can come to light:

Possibility 1 : A B C D E
Possibility 2 : B A C D E
Possibility 3 : E D C A B
Possibility 4 : E D C B A

At this point the paper comments that such a result highlights to the biochemist that the molecule requires further work for refinement. Sadly the above example whilst relatively simple doesn’t include the whole host of other issues which plague the biochemist in their search for an exact sequence.

Protein Interaction Networks

Proteins don’t just work in isolation, they form complex cliques and partnerships while some particularly gregarious proteins take multiple partners. It’s becoming increasingly apparent that in order to better understand a system, it’s insufficient to understand its component parts in isolation, especially if the simplest cog in the works end up being part of system like this.

So we know what an individual protein looks like, but what does it actually do?

On a macroscopic scale, a cell doesn’t care if the glucose it needs comes from lactose, converted by lactase into galactose and glucose, or from starch converted by amalase, or from glycogen, or from amino acids converted by gluconeogenesis. All it cares about is the glucose. If one of these multiple pathways should become unavailable, as long as the output is the same (glucose) the cell can continue to function. At a lower level, by forming networks of cooperating proteins, these increase a system’s robustness to change. The internal workings may be rewired, but many systems don’t care where their raw materials come from, just so long as they get them.

Whilst sequence similarity and homology modelling can explain the structure and function of an individual protein, its role in the greater scheme of things may still be in question. By modelling interaction networks, higher level questions can be asked such as: ‘What does this newly discovered complex do’? – ‘I don’t know, but yeast’s got something that looks quite like it.’ Homology modelling therefore isn’t just for single proteins.

Scoring the similarity of proteins in two species can be done using many non-exclusive metrics including:

  • Sequence Similarity – Is this significantly similar to another protein?
  • Gene Ontology – What does it do?
  • Interaction Partners – What other proteins does this one hang around with?


    • Subsequently clustering these proteins based on their interaction partners, highlights the groups of proteins which form functional units. These are highly connected internally whilst having few edges to adjacent clusters. This can provide insight into previously un-investigated proteins which by virtue of being in a cluster of known purpose, their function can be inferred.