Protein 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. 

Arnold GE, Omstein RL. Molecular dynamics study of time-correlated protein domain motions and molecular flexibility cytochrome P450BM-3. Biophys J 1997 73 1147-1159. 

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 ... 

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. 

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... 

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. 

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. 

Molecular dynamics simulations ([McCammon and Harvey 1987]) propagate an atomistic system by iteratively solving Newton s equation of motion for each atomic particle. Due to computational constraints, simulations can only be extended to a typical time scale of 1 ns currently, and conformational transitions such as protein domains movements are unlikely to be observed. 

An interesting approach has recently been chosen in the MBO(N)D program ([Moldyn 1997]). Structural elements of different size varying from individual peptide planes up to protein domains can be defined to be rigid. During an atomistic molecular dynamics simulation, all fast motion orthogonal to the lowest normal modes is removed. This allows use of ca. 20 times longer time steps than in standard simulations. 

Hinsen, K., Analysis of domain motions by approximate normal mode calculations, Proteins Struct. Funct. Genet. 1998, 33, 417-429... 

Since local motions of flexible protein domains can randomize the emission dipoles in a manner that does not reflect the overall tumbling time of the entire protein, and since there is an apparent lack of fluorophores with the appropriate properties for larger analytes, most FPIAs are useful only for determination of relatively low-molecular-weight analytes. Nevertheless, a few studies of larger-molecular-weight analytes have been reported. A competitive assay for human... 

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]. 

K. Hinsen, Proteins Struct., Genet., Fund., 33,417 (1998). Analysis of Domain Motions by... 

Neutron spectroscopy is becoming a principal tool for the study of protein dynamics (Cusack, 1986, 1989 Middendorf, 1984 Middendorf et al., 1984). Current instruments cover motions with characteristic times from 10 to 10 sec. This range embraces essentially all protein modes excited at room temperature (the soft modes), including motions of the solvent shell and also low-frequency large-scale domain motions, like the hinge-bending motion of the lysozyme domains that form the... 

In unimolecular ET, the rate can be controlled by large-scale cofactor motion, such as the quinone motion in the photosynthetic reaction centers, the Rieske subunit motion in the cytochrome bc complex (47), or the cytochrome fcs-domain in sulfite oxidase. Theoretical models for conformationally controlled ET reactions have been suggested by Hoffman and Rat-ner (48) and Bnmschwig and Sutin (49). Large-scale protein or domain motions are themselves linked to the movement of water molecules. 

Lysozyme is a key system in the development of our understanding of the structure and function of proteins. It was the first enzyme whose x-ray structure was determined at high resolution (Blake et al. 1965), one of the earliest enzymes for which a detailed reaction mechanism was proposed and one of the test systems for molecular dynamics simulations. In this section, we review some of the simulation studies of lysozyme with emphasis on the reaction mechanism and on the large scale domain motion involved in the mechanism. 

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. 

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. 

---