Protein Complexes In Solution Research Articles

Accurate and rapid docking of protein-protein complexes on the basis of intermolecular nuclear overhauser enhancement data and dipolar couplings by rigid body minimization.

A simple and rapid method is presented for solving the three-dimensional structures of protein-protein complexes in solution on the basis of experimental NMR restraints that provide the requisite translational (i.e., intermolecular nuclear Overhauser enhancement, NOE, data) and orientational (i.e., backbone (1)H-(15)N dipolar couplings and intermolecular NOEs) information. Providing high-resolution structures of the proteins in the unbound state are available and no significant backbone conformational changes occur upon complexation (which can readily be assessed by analysis of dipolar couplings measured on the complex), accurate and rapid docking of the two proteins can be achieved. The method, which is demonstrated for the 40-kDa complex of enzyme I and the histidine phosphocarrier protein, involves the application of rigid body minimization using a target function comprising only three terms, namely experimental NOE-derived intermolecular interproton distance and dipolar coupling restraints, and a simple intermolecular van der Waals repulsion potential. This approach promises to dramatically reduce the amount of time and effort required to solve the structures of protein-protein complexes by NMR, and to extend the capabilities of NMR to larger protein-protein complexes, possibly up to molecular masses of 100 kDa or more.

Haem peptide–protein interactions. Part 2. — Kinetics and mechanism of the interaction of microperoxides-8 with apomyoglobin

The kinetics of the interaction between the haem octapeptide micro-peroxidase-8 (MP-8) and apomyoglobin (apoMb) have been investigated as a model for the reaction of monomeric ferriproporphyrin IX (haemin) as a model for the reactio of monomeric ferriproporphyrin IX (haemin) with apohaemoproteins. The kinetics of the reaction are consistent with a two-stage sige-intermediate interaction process. Close agreement between the association constant calculated using microscopic rate constants, and that measured by spectrophotometric titration provides powerful positiv eevidence for the correctness of the proposed mechanism. On the basis of the kinetic binidng studie sand spectrophotometric observation of the reduction of the Fe3+MP-8 ·apoMB complex we propose a novel equilibrium between a bis - and mono-axially histidyl ligated iron species for the peptide–protein complex in solution.

Structure of the fd DNA-gene 5 protein complex in solution: A neutron small-angle scattering study

Neutron small-angle scattering has been used to investigate the fd DNA-gene 5 protein complex in solution. Results are as follows. 1. (1) The mass per unit length is found to be 1380 or 1610 daltons/Å, depending upon whether one gene 5 protein molecule is assumed to bind to four or five nucleotides, respectively. These values correspond to axial subunit repeats of 7.9 or 7.0 Å and to total contour lengths in solution of 1.27 or 0.90 μm. For a helix of pitch 90 Å there are between about 11 and 13 proteins per turn. 2. (2) The cross-sectional radius of gyration at infinite contrast of the complex is 34.5 ± 1 Å. 3. (3) The structure must be quite open and solvated as indicated by the dry volume per subunit, the mass per unit length, and the radius of gyration. The volume occupied per subunit in a uniform cylinder having the measured radius of gyration and mass per unit length is about four times greater than the measured subunit dry volume in the complex. 4. (4) From the change with contrast of both the measured radius of gyration and the position of a subsidiary maximum we conclude that the DNA could not be on the outer periphery of the helical structure. This is supported by a calculation of the maximum radius of the DNA backbone. With the possible exception of the positioning of the DNA, our results for the complex in solution are in good agreement with a model proposed by McPherson et al. (1979 b) for the complex structure. 5. (5) The complex formed by reconstitution in vitro is not substantially different in its solution structure from the in vivo complex isolated from infected cells.

Chemical Cross-Linking in Biology

by chemical cross-linking tech­ nology has greatly intensified during the past 5 years. A number of excel­ lent, timely, and chemically oriented reviews of the cross-linking literature have appeared (4, 68, 87). Therefore, we have attempted to present a critical evaluation of the principles and strategies that govern the applica­ tion of cross-linking technology to the solutions of biological problems. The use of chemical cross-linking reagents as molecular rulers in the determination of quaternary structure in oligomeric protein complexes in solution and in membranes has enjoyed wide app li cation. Another as­ pect of cross-linking technology is the exploitation of heterobif unctional reagents to identif y ligand-binding components in complex biological sys­ tems. It is often difficult to determine how proteins function in multicompo­ nent, complex systems. The classical biochemical approach of isolation and characterization of protein components does not always reveal tran­ sient interactions or migratory behavior of proteins, which occur in the natural environment