Domain Motions in Proteins

There is presently considerable interest in measuring die rates of domain flexing in multidomain proteins. Domain motions occur in signaling proteins such ascalmodulin and sugar receptors. Domain motions are thought to occur in 

Schematic representation of donor- (D) and acceptor- (A) labded domains for calmodulin. 

---

Hayward, S., Kitao, A., Berendsen, H.J.C. Model-free methods to analyze domain motions in proteins from simulation A comparison of normal mode analysis and molecular dynamics simulation of lysozyme. Proteins 27 (1997) 425-437. 

Most of the information on interdomain motions come from high-resolution crystal structures several reviews are available (Janin and Wodak 1983 Bennett andHuber 1984 Gerstein et al. 1994). Calculations ofhinge bending modes and domain motions in proteins other than lysozyme have been made. They include antibody molecules where the interdomain motions occur on a nanosecond time scale (McCammon and Karplus 1977 Oi et al. 1984), 1-arabinose-binding protein (Mao et al. 1982), liver alcohol dehydrogenase (Colona-Cesari et al. 1986) and the mouse... 

Bennett, W. S. and Huber, R. (1984) Structural and Functional Aspects of Domain Motions in Proteins, Crit. Rev. Biochem. 15, 291-384. 

The donor dec s were also used in an attempt to measure diffusion motions between the subunits. As described in Section 14 longer donor decay times are needed to measure site-to-site domain motions in proteins. Phospho-glycetate kinase has also been used as a model to study protein folding. In this case, cysteine residues were introduced throughout the protean to provide probes at different sites in order to study the vacions steps on the folding pathway. 

Interesting applications of anisotropy decays for proteins often develop not from tumbling of the protein as a whole, but from other reorientational degrees of freedom. These motions may include protein domain motions or segmental motions in proteins and peptides. The anisotropy decay in this case is non-single-exponential (see Fig. 4c) and takes the form ... 

Luo, X., Zhang, D. and Weinstein, H. (1994) Ligand-induced domain motion in the activation mechanism of a G-protein-coupled receptor, Protein Engineering 7, 1441-1448. 

Hinsen, K, A. Thomas, and M. J. Field. 1999. Analysis of domain motions in large proteins. Proteins 34 369-82. 

Bu Z, Biehl R, Monkenbusch M, Richter D, Callaway DIE Coupled protein domain motion in Taq polymerase revealed by neutron spin-echo spectroscopy. Proc. Natl. Acad. Set U. S. A. 2005,102 17646-17651. 

Protein dynamics occurs on very different time scales ([McCammon and Harvey 1987, Jardetzky 1996]). Here, we are most interested in long time scale motions such as relative motion between secondary structure elements, and inter-domain motion. 

We have previously calculated conformational free energy differences for a well-suited model system, the catalytic subunit of cAMP-dependent protein kinase (cAPK), which is the best characterized member of the protein kinase family. It has been crystallized in three different conformations and our main focus was on how ligand binding shifts the equilibrium among these ([Helms and McCammon 1997]). As an example using state-of-the-art computational techniques, we summarize the main conclusions of this study and discuss a variety of methods that may be used to extend this study into the dynamic regime of protein domain motion. 

In an early study of lysozyme ([McCammon et al. 1976]), the two domains of this protein were assumed to be rigid, and the hinge-bending motion in the presence of solvent was described by the Langevin equation for a damped harmonic oscillator. The angular displacement 0 from the equilibrium position is thus governed by... 

Conventional MS in the energy domain has contributed a lot to the understanding of the electronic ground state of iron centers in proteins and biomimetic models ([55], and references therein). However, the vibrational properties of these centers, which are thought to be related to their biological function, are much less studied. This is partly due to the fact that the vibrational states of the iron centers are masked by the vibrational states of the protein backbone and thus techniques such as Resonance Raman- or IR-spectroscopy do not provide a clear picture of the vibrational properties of these centers. A special feature of NIS is that it directly reveals the fraction of kinetic energy due to the Fe motion in a particular vibrational mode. 

Very low-frequency vibrations have been observed in proteins (e.g., Brown et al., 1972 Genzel et al., 1976), which must involve concerted motion of rather large portions of the structure. By choosing a suitable set of proteins to measure (preferably in solution), it should be possible to decide approximately what structural modes are involved. Candidates include helix torsion, coupled changes of peptide orientation in /3 strands, and perhaps relative motions of entire domains or subunits. These hypotheses should be tested, because the low-frequency vibrations probably reflect large-scale structural properties that would be very useful to know. 

The MARTINI model effectively replaces three to four heavy atoms with a bead, parameterized to reproduce condensed-phase thermodynamic data of small molecules [23]. The MARTINI model has been used to investigate many biological processes, such as lung surfactant collapse [24], nanoparticle permeation in bilayers [25], large domain motion of integral membrane proteins [26], vesicle fusion [27,28], and lateral domain formation in membranes [29]. 

---