Proteins are generally thought to adopt unique structures determined by their amino acid sequences, as outlined by Anfinsen's dogma. However, proteins are not strictly static objects, but rather populate ensembles of (sometimes similar) conformations. Transitions between these states occur on a variety of length scales (tenths of Å to nm) and time scales (ns to s), and have been linked to functionally relevant phenomena such as allosteric signaling and enzyme catalysis.
The study of protein dynamics is most directly concerned with the transitions between these states, but can also involve the nature and equilibrium populations of the states themselves. These two perspectives—kinetics and thermodynamics, respectively—can be conceptually synthesized in an "energy landscape" paradigm: highly populated states and the kinetics of transitions between them can be described by the depths of energy wells and the heights of energy barriers, respectively.
- 1 Local flexibility: atoms and residues
- 2 Regional flexibility: intra-domain multi-residue coupling
- 3 Global flexibility: multiple domains
- 4 Implications for macromolecular evolution
- 5 References
Local flexibility: atoms and residues
Portions of protein structures often deviate from the equilibrium state. Some such excursions are harmonic, such as stochastic fluctuations of chemical bonds and bond angles. Others are anharmonic, such as sidechains that jump between separate discrete energy minima, or rotamers.
Evidence for local flexibility is often obtained from NMR spectroscopy with methods like Random Coil Index. However, it can also be derived from very high-resolution electron density maps produced by X-ray crystallography, particularly when diffraction data is collected at room temperature instead of the traditional cryogenic temperature (typically near 100 K).
Regional flexibility: intra-domain multi-residue coupling
Many residues are in close spatial proximity in protein structures. This is true for most residues that are contiguous in the primary sequence, but also for many that are distal in sequence yet are brought into contact in the final folded structure. Because of this proximity, these residues's energy landscapes become coupled based on various biophysical phenomena such as hydrogen bonds, ionic bonds, and van der Waals interactions (see figure). Transitions between states for such sets of residues therefore become correlated.
This is perhaps most obvious for surface-exposed loops, which often shift collectively to adopt different conformations in different crystal structures (see figure). However, coupled conformational heterogeneity is also sometimes evident in secondary structure. For example, consecutive residues and residues offset by 4 in the primary sequence often interact in α helices. Also, residues offset by 2 in the primary sequence point their sidechains toward the same face of β sheets and are close enough to interact sterically, as are residues on adjacent strands of the same β sheet.
When these coupled residues form pathways linking functionally important parts of a protein, they may participate in allosteric signaling. For example, when a molecule of oxygen binds to one subunit of the hemoglobin tetramer, that information is allosterically propagated to the other three subunits, thereby enhancing their affinity for oxygen. In this case, the coupled flexibility in hemoglobin allows for cooperative oxygen binding, which is physiologically useful because it allows rapid oxygen loading in lung tissue and rapid oxygen unloading in oxygen-deprived tissues (e.g. muscle).
Global flexibility: multiple domains
The presence of multiple domains in proteins gives rise to a great deal of flexibility and mobility, leading to protein domain dynamics. Domain motions can be inferred by comparing different structures of a protein (as in Database of Molecular Motions), or they can be directly observed using spectra measured by neutron spin echo spectroscopy. They can also be suggested by sampling in extensive molecular dynamics trajectories and principal component analysis. Domain motions are important for:
- catalysis
- regulatory activity
- transport of metabolites
- formation of protein assemblies
- cellular locomotion
One of the largest observed domain motions is the `swivelling' mechanism in pyruvate phosphate dikinase. The phosphoinositide domain swivels between two states in order to bring a phosphate group from the active site of the nucleotide binding domain to that of the phosphoenolpyruvate/pyruvate domain. The phosphate group is moved over a distance of 45 Å involving a domain motion of about 100 degrees around a single residue. In enzymes, the closure of one domain onto another captures a substrate by an induced fit, allowing the reaction to take place in a controlled way. A detailed analysis by Gerstein led to the classification of two basic types of domain motion; hinge and shear. Only a relatively small portion of the chain, namely the inter-domain linker and side chains undergo significant conformational changes upon domain rearrangement.
Hinges by secondary structures
A study by Hayward found that the termini of α-helices and β-sheets form hinges in a large number of cases. Many hinges were found to involve two secondary structure elements acting like hinges of a door, allowing an opening and closing motion to occur. This can arise when two neighbouring strands within a β-sheet situated in one domain, diverge apart as they join the other domain. The two resulting termini then form the bending regions between the two domains. α-helices that preserve their hydrogen bonding network when bent are found to behave as mechanical hinges, storing `elastic energy' that drives the closure of domains for rapid capture of a substrate.
Helical to extended conformation
The interconversion of helical and extended conformations at the site of a domain boundary is not uncommon. In calmodulin, torsion angles change for five residues in the middle of a domain linking α-helix. The helix is split into two, almost perpendicular, smaller helices separated by four residues of an extended strand.
Shear motions involve a small sliding movement of domain interfaces, controlled by the amino acid side chains within the interface. Proteins displaying shear motions often have a layered architecture: stacking of secondary structures. The interdomain linker has merely the role of keeping the domains in close proximity.
Domain motion and functional dynamics in enzymes
The analysis of the internal dynamics of structurally different, but functionally similar enzymes has highlighted a common relationship between the positioning of the active site and the two principal protein sub-domains. In fact, for several members of the hydrolase superfamily, the catalytic site is located close to the interface separating the two principal quasi-rigid domains. Such positioning appears instrumental for maintaining the precise geometry of the active site, while allowing for an appreciable functionally oriented modulation of the flanking regions resulting from the relative motion of the two sub-domains.
Implications for macromolecular evolution
Evidence suggests that protein dynamics are important for function, e.g. enzyme catalysis in DHFR, yet they are also posited to facilitate the acquisition of new functions by molecular evolution. This argument suggests that proteins have evolved to have stable, mostly unique folded structures, but the unavoidable residual flexibility leads to some degree of functional promiscuity, which can be amplified/harnessed/diverted by subsequent mutations.
However, there is growing awareness that intrinsically unstructured proteins are quite prevalent in eukaryotic genomes, casting further doubt on the simplest interpretation of Anfinsen's dogma: "sequence determines structure (singular)". In effect, the new paradigm is characterized by the addition of two caveats: "sequence and cellular environment determine structural ensemble".
This article incorporates text and figures from George, R. A. (2002) "Predicting Structural Domains in Proteins" Thesis, University College London, which were contributed by its author.
- Bu Z, Callaway DJ (2011). "Proteins MOVE! Protein dynamics and long-range allostery in cell signaling". Advances in Protein Chemistry and Structural Biology 83: 163–221. doi:10.1016/B978-0-12-381262-9.00005-7. PMID 21570668.
- Fraser, J. S., Clarkson, M. W., Degnan, S. C., Erion, R., Kern, D., and Alber, T. (2009). "Hidden alternative structures of proline isomerase essential for catalysis". Nature 462 (7273): 669–673. Bibcode:2009Natur.462..669F. doi:10.1038/nature08615. PMID 19956261.
- Frauenfelder, H., Sligar, S. G., and Wolynes, P. G. (1991). "The energy landscapes and motions of proteins". Science 254 (1603): 1598–1603. Bibcode:1991Sci...254.1598F. doi:10.1126/science.1749933. PMID 1749933.
- Davis, I. W., Arendall, W. B. III, Richardson, D. C., and Richardson, J. S. (2006). "The backrub motion: how protein backbone shrugs when a sidechain dances". Structure 14 (2): 265–274. doi:10.1016/j.str.2005.10.007. PMID 16472746.
- Fraser, J. S., van den Bedem, H., Samelson, A. J., Lang, P. T., Holton, J. M., Echols, N., and Alber, T. (2011). "Accessing protein conformational ensembles using room-temperature X-ray crystallography". PNAS 108 (39): 16247–16252. doi:10.1073/pnas.1111325108. PMID 21918110.
- Bu, Z., Cook, J., Callaway, D. J. E. (2001). "Dynamic regimes and correlated structural dynamics in native and denatured alpha-lactalbumin". J. Mol. Biol. 312 (4): 865–873. doi:10.1006/jmbi.2001.5006. PMID 11575938.
- Farago B, Li J, Cornilescu G, Callaway DJ, Bu Z (November 2010). "Activation of Nanoscale Allosteric Protein Domain Motion Revealed by Neutron Spin Echo Spectroscopy". Biophysical Journal 99 (10): 3473–3482. Bibcode:2010BpJ....99.3473F. doi:10.1016/j.bpj.2010.09.058. PMC 2980739. PMID 21081097.
- Bu Z, Biehl R, Monkenbusch M, Richter D, D.J.E. Callaway (2005). "Coupled protein domain motion in Taq polymerase revealed by neutron spin-echo spectroscopy.". Proc Natl Acad Sci USA 102 (49): 17646–17651. Bibcode:2005PNAS..10217646B. doi:10.1073/pnas.0503388102. PMC 1345721. PMID 16306270.
- Potestio, R., Pontiggia, F. and Micheletti, C. (2009). "Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits.". Biophysical Journal 96 (12): 4993–5002. Bibcode:2009BpJ....96.4993P. doi:10.1016/j.bpj.2009.03.051. PMC 2712024. PMID 19527659.
- Baron R and Vellore NA (2012). "LSD1/CoREST is an allosteric nanoscale clamp regulated by H3-histone-tail molecular recognition". Proc Natl Acad Sci U S A. 109 (31): 12509–14. Bibcode:2012PNAS..10912509B. doi:10.1073/pnas.1207892109. PMC 3411975. PMID 22802671.
- Gerstein M, Lesk AM, Chothia C. (1994). "Structural mechanisms for domain movements in proteins". Biochemistry 33 (22): 6739–49. doi:10.1021/bi00188a001. PMID 8204609.
- Herzberg O et al. (1996). "Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites". Proc Natl Acad Sci USA 93 (7): 2652–7. Bibcode:1996PNAS...93.2652H. doi:10.1073/pnas.93.7.2652. PMC 39685. PMID 8610096.
- Janin, J. and Wodak, S. J (1983). "Structural domains in proteins and their role in the dynamics of protein function". Prog Biophys Mol Biol 42 (1): 21–78. doi:10.1016/0079-6107(83)90003-2. PMID 6353481.
- Hayward S. (1999). "Structural principles governing domain motions in proteins". Proteins 36 (4): 425–35. doi:10.1002/(SICI)1097-0134(19990901)36:4<425::AID-PROT6>3.0.CO;2-S. PMID 10450084.
- Meador, W. E., Means, A. R., and Quiocho, F. A (1992). "Target enzyme recognition by calmodulin: 2.4A structure of a calmodulin-peptide complex". Science 257 (5074): 1251–1255. Bibcode:1992Sci...257.1251M. doi:10.1126/science.1519061. PMID 1519061.
- Ikura, M., Clore, G. M., Gronenborn, A. M., Zhu, G., Klee, C. B., and Bax, A (1992). "Solution structure of a calmodulin-target peptide complex by multidimensional NMR". Science 256 (5057): 632–638. Bibcode:1992Sci...256..632I. doi:10.1126/science.1585175. PMID 1585175.
- Tokuriki, N. and Tawfik, D. S. (2009). "Protein dynamism and evolvability". Science 324 (5924): 203–207. Bibcode:2009Sci...324..203T. doi:10.1126/science.1169375. PMID 19359577.
- Dyson, H. J. and Wright, P. E. (2005). "Intrinsically unstructured proteins and their functions". Nature Reviews Molecular Cell Biology 6 (5057): 197–208. doi:10.1038/nrm1589. PMID 15738986.