Backbone Relaxation Research Articles

Molecular dynamics study of calbindin D9k in the apo and singly and doubly calcium-loaded states

Molecular dynamics simulations based on detailed atomic models are used to examine the structure and dynamics of calbindin D9k, a protein possessing a pair of EF-hands able to bind two calcium ions in a cooperative fashion. Trajectories for the apo and singly (in the C-terminal binding site) and doubly loaded structures are generated and analyzed. Each system is solvated in a 27 A radius sphere of 2,285 explicit water molecules. The influence of the remaining bulk is incorporated through a stochastic boundary potential including a solvent reaction field. Long-range electrostatic interactions are treated with a special method and are not truncated. The average structural and dynamic properties upon calcium binding are studied at the atomic level to gain insight into the cooperative interactions between the two binding sites. Results from the trajectories are compared with data from nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. NMR 15N and 13C(alpha) backbone relaxation order parameters and crystallographic B-factors are calculated. Generally, there is a good qualitative agreement between calculated and observed properties. Results confirm that the doubly loaded state is closer, both structurally and dynamically, to the singly loaded state than either of these is to the apo state. It is observed that both hydrogen bonding and the packing of nonpolar side chains contribute to the coupling between the calcium binding sites. Two backbone-to-backbone hydrogen bonds linking the calcium-binding EF-hands (Leu23-0 ... HN-Val61 and Val61-O ... HN-Leu23) are sensitive to the state of occupancy. Residues Leu23 and Val61 exhibit the smallest rms fluctuations of the entire protein in the D state. In addition, the van der Waals interaction of Val61 with the rest of the protein varies with the calcium-binding state.

Molecular dynamics study of calbindin D9k in the apo and singly and doubly calcium‐loaded states

Molecular dynamics simulations based on detailed atomic models are used to examine the structure and dynamics of calbindin D9k, a protein possessing a pair of EF-hands able to bind two calcium ions in a cooperative fashion. Trajectories for the apo and singly (in the C-terminal binding site) and doubly loaded structures are generated and analyzed. Each system is solvated in a 27 Å radius sphere of 2,285 explicit water molecules. The influence of the remaining bulk is incorporated through a stochastic boundary potential including a solvent reaction field. Long-range electrostatic interactions are treated with a special method and are not truncated. The average structural and dynamic properties upon calcium binding are studied at the atomic level to gain insight into the cooperative interactions between the two binding sites. Results from the trajectories are compared with data from nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. NMR 15N and 13Cα backbone relaxation order parameters and crystallographic B-factors are calculated. Generally, there is a good qualitative agreement between calculated and observed properties. Results confirm that the doubly loaded state is closer, both structurally and dynamically, to the singly loaded state than either of these is to the apo state. It is observed that both hydrogen bonding and the packing of nonpolar side chains contribute to the coupling between the calcium binding sites. Two backbone-to-backbone hydrogen bonds linking the calcium-binding EF-hands (Leu23-O · · · HN-Val61 and Val61-O · · · HN-Leu23) are sensitive to the state of occupancy. Residues Leu23 and Val61 exhibit the smallest rms fluctuations of the entire protein in the D state. In addition, the van der Waals interaction of Val61 with the rest of the protein varies with the calcium-binding state. Proteins 33:265–284, 1998. © 1998 Wiley-Liss, Inc.

Solution studies of the SH2 domain from the fyn tyrosine kinase: secondary structure, backbone dynamics and protein association.

The SH2 domain from Fyn tyrosine kinase, corresponding to residues 155-270 of the human enzyme, was expressed as a GST-fusion protein in a pGEX-E. coli system. After thrombin cleavage and removal of GST, the protein was studied by heteronuclear NMR. Two different phosphotyrosyl-peptides were synthesized and added to the SH2 domain. One peptide corresponded to the regulatory C-terminal tail region of Fyn. Sequence-specific assignment of NMR spectra was achieved using a combination of 1H-15N-correlated 2D HSQC, 15N-edited 3D TOCSY-HMQC, and 15N-edited 3D NOESY-HMQC spectra. By analysis of the alpha-proton chemical shifts and NOE intensities, the positions of secondary structural elements were determined and found to correspond closely to that seen in the crystal structure of the, homologous, Src-SH2 domain. To investigate the internal dynamics of the protein backbone, T1 and T2 relaxation parameters were measured on the free protein, as well as on both peptide complexes. Analytical ultracentrifugation and dynamic light scattering were employed to measure the effect of concentration and peptide-binding on self-association. The results suggest that, at NMR-sample concentrations, the free protein is present in at least dimeric form. Phosphopeptide binding and lower concentration significantly, but not completely, shift the equilibrium towards monomers. The possible role of this protein association in the regulation of the Src-family tyrosine kinases is discussed.

Repacking protein cores with backbone freedom: structure prediction for coiled coils.

Progress in homology modeling and protein design has generated considerable interest in methods for predicting side-chain packing in the hydrophobic cores of proteins. Present techniques are not practically useful, however, because they are unable to model protein main-chain flexibility. Parameterization of backbone motions may represent a general and efficient method to incorporate backbone relaxation into such fixed main-chain models. To test this notion, we introduce a method for treating explicitly the backbone motions of alpha-helical bundles based on an algebraic parameterization proposed by Francis Crick in 1953 [Crick, F. H. C. (1953) Acta Crystallogr. 6, 685-689]. Given only the core amino acid sequence, a simple calculation can rapidly reproduce the crystallographic main-chain and core side-chain structures of three coiled coils (one dimer, one trimer, and one tetramer) to within 0.6-A root-mean-square deviations. The speed of the predictive method [approximately 3 min per rotamer choice on a Silicon Graphics (Mountain View, CA) 4D/35 computer] permits it to be used as a design tool.

Detailed Study of a Molecule into a Molecule: N-Acetyl-L-tryptophanamide in an Active Site Model of .alpha.-Chymotrypsin

Six complexes between a model active site of a-chymotrypsin (26 1 atoms) and N-acetyl-L-tryptophanamide (33 atoms) were optimized at the semiempirical AM1 level. In one of these complexes, a water molecule was included. A detailed study at thegeometric and energeticlevels is presented. The discussiondeals with the natureof the interaction, the effect of the environment, the ligand deformation, the backbone relaxation, the water molecule freedom, and the comparison with the molecular mechanics results.