HOME

TheInfoList



OR:

Macromolecular docking is the computational modelling of the quaternary structure of complexes formed by two or more interacting biological macromolecules.
Protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
–protein complexes are the most commonly attempted targets of such modelling, followed by protein–
nucleic acid Nucleic acids are large biomolecules that are crucial in all cells and viruses. They are composed of nucleotides, which are the monomer components: a pentose, 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nuclei ...
complexes. The ultimate goal of docking is the prediction of the three-dimensional structure of the macromolecular complex of interest as it would occur in a living organism. Docking itself only produces plausible candidate structures. These candidates must be ranked using methods such as scoring functions to identify structures that are most likely to occur in nature. The term "docking" originated in the late 1970s, with a more restricted meaning; then, "docking" meant refining a model of a complex structure by optimizing the separation between the interactors but keeping their relative orientations fixed. Later, the relative orientations of the interacting partners in the modelling was allowed to vary, but the internal geometry of each of the partners was held fixed. This type of modelling is sometimes referred to as "rigid docking". With further increases in computational power, it became possible to model changes in internal geometry of the interacting partners that may occur when a complex is formed. This type of modelling is referred to as "flexible docking".


Background

The biological roles of most proteins, as characterized by which other macromolecules they interact with, are known at best incompletely. Even those proteins that participate in a well-studied
biological process Biological processes are those processes that are necessary for an organism to live and that shape its capacities for interacting with its environment. Biological processes are made of many chemical reactions or other events that are involved in ...
(e.g., the Krebs cycle) may have unexpected interaction partners or functions which are unrelated to that process. In cases of known protein–protein interactions, other questions arise. Genetic diseases (e.g.,
cystic fibrosis Cystic fibrosis (CF) is a genetic disorder inherited in an autosomal recessive manner that impairs the normal clearance of Sputum, mucus from the lungs, which facilitates the colonization and infection of the lungs by bacteria, notably ''Staphy ...
) are known to be caused by misfolded or
mutated In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA replication, DNA or viral rep ...
proteins, and there is a desire to understand what, if any, anomalous protein–protein interactions a given mutation can cause. In the distant future, proteins may be designed to perform biological functions, and a determination of the potential interactions of such proteins will be essential. For any given set of proteins, the following questions may be of interest, from the point of view of technology or natural history: * Do these proteins bind ''
in vivo Studies that are ''in vivo'' (Latin for "within the living"; often not italicized in English) are those in which the effects of various biological entities are tested on whole, living organisms or cells, usually animals, including humans, an ...
''? If they do bind, * What is the spatial configuration which they adopt in their
bound state A bound state is a composite of two or more fundamental building blocks, such as particles, atoms, or bodies, that behaves as a single object and in which energy is required to split them. In quantum physics, a bound state is a quantum state of a ...
? * How strong or weak is their interaction? If they do not bind, * Can they be made to bind by inducing a mutation? Protein–protein docking is ultimately envisaged to address all these issues. Furthermore, since docking methods can be based on purely physical principles, even proteins of unknown function (or which have been studied relatively little) may be docked. The only prerequisite is that their
molecular structure Molecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that det ...
has been either determined experimentally, or can be estimated by a
protein structure prediction Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its Protein secondary structure, secondary and Protein tertiary structure, tertiary structure ...
technique. Protein–nucleic acid interactions feature prominently in the living cell. Transcription factors, which regulate
gene expression Gene expression is the process (including its Regulation of gene expression, regulation) by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, proteins or non-coding RNA, ...
, and
polymerase In biochemistry, a polymerase is an enzyme (Enzyme Commission number, EC 2.7.7.6/7/19/48/49) that synthesizes long chains of polymers or nucleic acids. DNA polymerase and RNA polymerase are used to assemble DNA and RNA molecules, respectively, by ...
s, which catalyse replication, are composed of proteins, and the
genetic material Nucleic acids are large biomolecules that are crucial in all cells and viruses. They are composed of nucleotides, which are the monomer components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nucleic aci ...
they interact with is composed of nucleic acids. Modeling protein–nucleic acid complexes presents some unique challenges, as described below.


History

In the 1970s, complex modelling revolved around manually identifying features on the surfaces of the interactors, and interpreting the consequences for binding, function and activity; any computer programmes were typically used at the end of the modelling process, to discriminate between the relatively few configurations which remained after all the heuristic constraints had been imposed. The first use of computers was in a study on
hemoglobin Hemoglobin (haemoglobin, Hb or Hgb) is a protein containing iron that facilitates the transportation of oxygen in red blood cells. Almost all vertebrates contain hemoglobin, with the sole exception of the fish family Channichthyidae. Hemoglobin ...
interaction in sickle-cell fibres. This was followed in 1978 by work on the
trypsin Trypsin is an enzyme in the first section of the small intestine that starts the digestion of protein molecules by cutting long chains of amino acids into smaller pieces. It is a serine protease from the PA clan superfamily, found in the dig ...
-
BPTI The drug aprotinin (Trasylol, previously Bayer and now Nordic Group pharmaceuticals), is a small protein bovine pancreatic trypsin inhibitor (BPTI), or basic trypsin inhibitor of bovine pancreas, which is an antifibrinolytic molecule that inhibi ...
complex. Computers discriminated between good and bad models using a scoring function which rewarded large interface area, and pairs of molecules in contact but not occupying the same space. The computer used a simplified representation of the interacting proteins, with one interaction centre for each residue. Favorable
electrostatic Electrostatics is a branch of physics that studies slow-moving or stationary electric charges. Since classical times, it has been known that some materials, such as amber, attract lightweight particles after rubbing. The Greek word (), mean ...
interactions, including hydrogen bonds, were identified by hand. In the early 1990s, more structures of complexes were determined, and available computational power had increased substantially. With the emergence of
bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...
, the focus moved towards developing generalized techniques which could be applied to an arbitrary set of complexes at acceptable computational cost. The new methods were envisaged to apply even in the absence of phylogenetic or experimental clues; any specific prior knowledge could still be introduced at the stage of choosing between the highest ranking output models, or be framed as input if the algorithm catered for it. 1992 saw the publication of the correlation method, an algorithm which used the
fast Fourier transform A fast Fourier transform (FFT) is an algorithm that computes the discrete Fourier transform (DFT) of a sequence, or its inverse (IDFT). A Fourier transform converts a signal from its original domain (often time or space) to a representation in ...
to give a vastly improved scalability for evaluating coarse shape complementarity on rigid-body models. This was extended in 1997 to cover coarse electrostatics. In 1996 the results of the first blind trial were published, in which six research groups attempted to predict the complexed structure of TEM-1 Beta-lactamase with Beta-lactamase inhibitor protein (BLIP). The exercise brought into focus the necessity of accommodating conformational change and the difficulty of discriminating between conformers. It also served as the prototype for the CAPRI assessment series, which debuted in 2001.


Rigid-body docking ''vs''. flexible docking

If the bond angles, bond lengths and torsion angles of the components are not modified at any stage of complex generation, it is known as ''rigid body docking''. A subject of speculation is whether or not rigid-body docking is sufficiently good for most docking. When substantial conformational change occurs within the components at the time of complex formation, rigid-body docking is inadequate. However, scoring all possible conformational changes is prohibitively expensive in computer time. Docking procedures which permit conformational change, or ''flexible docking'' procedures, must intelligently select small subset of possible conformational changes for consideration.


Methods

Successful docking requires two criteria: *Generating a set of configurations which reliably includes at least one nearly correct one. *Reliably distinguishing nearly correct configurations from the others. For many interactions, the binding site is known on one or more of the proteins to be docked. This is the case for
antibodies An antibody (Ab) or immunoglobulin (Ig) is a large, Y-shaped protein belonging to the immunoglobulin superfamily which is used by the immune system to identify and neutralize antigens such as bacteria and viruses, including those that caus ...
and for
competitive inhibitor Competitive inhibition is interruption of a chemical pathway owing to one chemical substance inhibiting the effect of another by competing with it for binding or bonding. Any metabolic or chemical messenger system can potentially be affected b ...
s. In other cases, a binding site may be strongly suggested by mutagenic or
phylogenetic In biology, phylogenetics () is the study of the evolutionary history of life using observable characteristics of organisms (or genes), which is known as phylogenetic inference. It infers the relationship among organisms based on empirical dat ...
evidence. Configurations where the proteins interpenetrate severely may also be ruled out ''a priori''. After making exclusions based on prior knowledge or stereochemical clash, the remaining space of possible complexed structures must be sampled exhaustively, evenly and with a sufficient coverage to guarantee a near hit. Each configuration must be scored with a measure that is capable of ranking a nearly correct structure above at least 100,000 alternatives. This is a computationally intensive task, and a variety of strategies have been developed.


Reciprocal space methods

Each of the proteins may be represented as a simple cubic lattice. Then, for the class of scores which are discrete
convolution In mathematics (in particular, functional analysis), convolution is a operation (mathematics), mathematical operation on two function (mathematics), functions f and g that produces a third function f*g, as the integral of the product of the two ...
s, configurations related to each other by translation of one protein by an exact lattice vector can all be scored almost simultaneously by applying the convolution theorem. It is possible to construct reasonable, if approximate, convolution-like scoring functions representing both stereochemical and electrostatic fitness. Reciprocal space methods have been used extensively for their ability to evaluate enormous numbers of configurations. They lose their speed advantage if torsional changes are introduced. Another drawback is that it is impossible to make efficient use of prior knowledge. The question also remains whether convolutions are too limited a class of scoring function to identify the best complex reliably.


Monte Carlo methods

In
Monte Carlo Monte Carlo ( ; ; or colloquially ; , ; ) is an official administrative area of Monaco, specifically the Ward (country subdivision), ward of Monte Carlo/Spélugues, where the Monte Carlo Casino is located. Informally, the name also refers to ...
, an initial configuration is refined by taking random steps which are accepted or rejected based on their induced improvement in score (see the Metropolis criterion), until a certain number of steps have been tried. The assumption is that convergence to the best structure should occur from a large class of initial configurations, only one of which needs to be considered. Initial configurations may be sampled coarsely, and much computation time can be saved. Because of the difficulty of finding a scoring function which is both highly discriminating for the correct configuration and also converges to the correct configuration from a distance, the use of two levels of refinement, with different scoring functions, has been proposed. Torsion can be introduced naturally to Monte Carlo as an additional property of each random move. Monte Carlo methods are not guaranteed to search exhaustively, so that the best configuration may be missed even using a scoring function which would in theory identify it. How severe a problem this is for docking has not been firmly established.


Evaluation


Scoring functions

To find a score which forms a consistent basis for selecting the best configuration, studies are carried out on a standard benchmark (see below) of protein–protein interaction cases. Scoring functions are assessed on the rank they assign to the best structure (ideally the best structure should be ranked 1), and on their coverage (the proportion of the benchmark cases for which they achieve an acceptable result). Types of scores studied include: *
Heuristic A heuristic or heuristic technique (''problem solving'', '' mental shortcut'', ''rule of thumb'') is any approach to problem solving that employs a pragmatic method that is not fully optimized, perfected, or rationalized, but is nevertheless ...
scores based on residue contacts. *Shape complementarity of molecular surfaces ("stereochemistry"). *Free energies, estimated using parameters from
molecular mechanics Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using Force field (chemi ...
force fields such as
CHARMM Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. The CH ...
or
AMBER Amber is fossilized tree resin. Examples of it have been appreciated for its color and natural beauty since the Neolithic times, and worked as a gemstone since antiquity."Amber" (2004). In Maxine N. Lurie and Marc Mappen (eds.) ''Encyclopedia ...
. *Phylogenetic desirability of the interacting regions. *Clustering coefficients. *Information based cues. It is usual to create hybrid scores by combining one or more categories above in a weighted sum whose weights are optimized on cases from the benchmark. To avoid bias, the benchmark cases used to optimize the weights must not overlap with the cases used to make the final test of the score. The ultimate goal in protein–protein docking is to select the ideal ranking solution according to a scoring scheme that would also give an insight into the affinity of the complex. Such a development would drive ''in silico'' protein engineering, computer-aided drug design and/or high-throughput annotation of which proteins bind or not (annotation of interactome). Several scoring functions have been proposed for binding affinity / free energy prediction. However the correlation between experimentally determined binding affinities and the predictions of nine commonly used scoring functions have been found to be nearly
orthogonal In mathematics, orthogonality (mathematics), orthogonality is the generalization of the geometric notion of ''perpendicularity''. Although many authors use the two terms ''perpendicular'' and ''orthogonal'' interchangeably, the term ''perpendic ...
(R2 ~ 0). It was also observed that some components of the scoring algorithms may display better correlation to the experimental binding energies than the full score, suggesting that a significantly better performance might be obtained by combining the appropriate contributions from different scoring algorithms. Experimental methods for the determination of binding affinities are: surface plasmon resonance (SPR),
Förster resonance energy transfer Förster resonance energy transfer (FRET), fluorescence resonance energy transfer, resonance energy transfer (RET) or electronic energy transfer (EET) is a mechanism describing energy transfer between two light-sensitive molecules (chromophores). ...
, radioligand-based techniques,
isothermal titration calorimetry In chemical thermodynamics, isothermal titration calorimetry (ITC) is a physical technique used to determine the Conjugate variables (thermodynamics), thermodynamic parameters of interactions in Solution (chemistry), solution. ITC is the only tec ...
(ITC), microscale thermophoresis (MST) or spectroscopic measurements and other fluorescence techniques. Textual information from scientific articles can provide useful cues for scoring.


Benchmarks

A benchmark of 84 protein–protein interactions with known complexed structures has been developed for testing docking methods. The set is chosen to cover a wide range of interaction types, and to avoid repeated features, such as the profile of interactors' structural families according to the
SCOP A ( or ) was a poet as represented in Old English poetry. The scop is the Old English counterpart of the Old Norse ', with the important difference that "skald" was applied to historical persons, and scop is used, for the most part, to designat ...
database. Benchmark elements are classified into three levels of difficulty (the most difficult containing the largest change in backbone conformation). The protein–protein docking benchmark contains examples of enzyme-inhibitor, antigen-antibody and homomultimeric complexes. The latest version of protein-protein docking benchmark consists of 230 complexes. A protein-DNA docking benchmark consists of 47 test cases. A protein-RNA docking benchmark was curated as a dataset of 45 non-redundant test cases with complexes solved by
X-ray crystallography X-ray crystallography is the experimental science of determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to Diffraction, diffract in specific directions. By measuring th ...
only as well as an extended dataset of 71 test cases with structures derived from homology modelling as well. The protein-RNA benchmark has been updated to include more structures solved by
X-ray crystallography X-ray crystallography is the experimental science of determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to Diffraction, diffract in specific directions. By measuring th ...
and now it consists of 126 test cases. The benchmarks have a combined dataset of 209 complexes. A binding affinity benchmark has been based on the protein–protein docking benchmark. 81 protein–protein complexes with known experimental affinities are included; these complexes span over 11 orders of magnitude in terms of affinity. Each entry of the benchmark includes several biochemical parameters associated with the experimental data, along with the method used to determine the affinity. This benchmark was used to assess the extent to which scoring functions could also predict affinities of macromolecular complexes. This Benchmark was post-peer reviewed and significantly expanded. The new set is diverse in terms of the biological functions it represents, with complexes that involve G-proteins and receptor extracellular domains, as well as antigen/antibody, enzyme/inhibitor, and enzyme/substrate complexes. It is also diverse in terms of the partners' affinity for each other, with Kd ranging between 10−5 and 10−14 M. Nine pairs of entries represent closely related complexes that have a similar structure, but a very different affinity, each pair comprising a cognate and a noncognate assembly. The unbound structures of the component proteins being available, conformation changes can be assessed. They are significant in most of the complexes, and large movements or disorder-to-order transitions are frequently observed. The set may be used to benchmark biophysical models aiming to relate affinity to structure in protein–protein interactions, taking into account the reactants and the conformation changes that accompany the association reaction, instead of just the final product.


The CAPRI assessment

The Critical Assessment of PRediction of Interactions is an ongoing series of events in which researchers throughout the community try to dock the same proteins, as provided by the assessors. Rounds take place approximately every 6 months. Each round contains between one and six target protein–protein complexes whose structures have been recently determined experimentally. The coordinates and are held privately by the assessors, with the cooperation of the structural biologists who determined them. The assessment of submissions is double blind. CAPRI attracts a high level of participation (37 groups participated worldwide in round seven) and a high level of interest from the biological community in general. Although CAPRI results are of little statistical significance owing to the small number of targets in each round, the role of CAPRI in stimulating discourse is significant. (The CASP assessment is a similar exercise in the field of protein structure prediction).


See also

* Biomolecular complex – any biological complex of protein, RNA, DNA (sometimes has lipids and carbohydrates) * Docking (molecular) – small molecule docking to proteins


References

{{Protein methods Protein structure Bioinformatics Molecular physics Molecular modelling