B1 Domain Of Protein Research Articles

Structural consequences of an amino acid deletion in the B1 domain of protein G.

We describe the NMR structure of a deletion mutant of the B1 IgG-binding domain from Group G Streptococcus. The deletion occurs within the last beta-strand of the protein, where it may potentially have a deleterious effect on the stability of the protein if the protein were not able to conformationally adjust to the perturbation. In particular, the deletion changes the registry of the final three residues in the sheet, forcing a polar Thr to be buried in the interior of the protein and exposing a hydrophobic Val to solvent. The deletion could also potentially create a large cavity in the beta-sheet and force the alpha- and gamma-carboxylates of the C-terminal Glu residue into a partially buried region of the sheet. The structure of the mutant illustrates how the conformation of the protein adjusts to the deletion, thereby mitigating some of the potentially deleterious consequences. Although the elements of secondary structure are retained between the mutant and the wt domain, there are multiple small adjustments in the segments connecting secondary structure elements. In particular, a hydrogen bond between the Glu57 carboxylates and two main chain amides is introduced that alters the conformation in the loop connecting the helix to strand 3. In addition, to minimize hydrophobic surface exposure, the turn connecting strands 1 and 2 folds toward the core so that the molecular volume is decreased.

A kinetic model for the internal motions of proteins: Diffusion between multiple harmonic wells

The dynamics of collective protein motions derived from Molecular Dynamics simulations have been studied for two small model proteins: initiation factor I and the B1 domain of Protein G. First, we compared the structural fluctuations, obtained by local harmonic approximations in different energy minima, with the ones revealed by large scale molecular dynamics (MD) simulations. It was found that a limited set of harmonic wells can be used to approximate the configurational fluctuations of these proteins, although any single harmonic approximation cannot properly describe their dynamics. Subsequently, the kinetics of the main (essential) collective protein motions were characterized. A dual-diffusion behavior was observed in which a fast type of diffusion switches to a much slower type in a typical time of about 1–3 ps. From these results, the large backbone conformational fluctuations of a protein may be considered as “hopping” between multiple harmonic wells on a basically flat free energy surface. Proteins 1999;35:283–292. © 1999 Wiley-Liss, Inc.

A kinetic model for the internal motions of proteins: Diffusion between multiple harmonic wells

The dynamics of collective protein motions derived from Molecular Dynamics simulations have been studied for two small model proteins: initiation factor I and the B1 domain of Protein G. First, we compared the structural fluctuations, obtained by local harmonic approximations in different energy minima, with the ones revealed by large scale molecular dynamics (MD) simulations. It was found that a limited set of harmonic wells can be used to approximate the configurational fluctuations of these proteins, although any single harmonic approximation cannot properly describe their dynamics. Subsequently, the kinetics of the main (essential) collective protein motions were characterized. A dual-diffusion behavior was observed in which a fast type of diffusion switches to a much slower type in a typical time of about 1-3 ps. From these results, the large backbone conformational fluctuations of a protein may be considered as "hopping" between multiple harmonic wells on a basically flat free energy surface.

A molecular dynamics study of the 41-56 beta-hairpin from B1 domain of protein G.

The structural and dynamical behavior of the 41-56 beta-hairpin from the protein G B1 domain (GB1) has been studied at different temperatures using molecular dynamics (MD) simulations in an aqueous environment. The purpose of these simulations is to establish the stability of this hairpin in view of its possible role as a nucleation site for protein folding. The conformation of the peptide in the crystallographic structure of the protein GB1 (native conformation) was lost in all simulations. The new equilibrium conformations are stable for several nanoseconds at 300K (>10 ns), 350 K (>6.5 ns), and even at 450 K (up to 2.5 ns). The new structures have very similar hairpin-like conformations with properties in agreement with available experimental nuclear Overhauser effect (NOE) data. The stability of the structure in the hydrophobic core region during the simulations is consistent with the experimental data and provides further evidence for the role played by hydrophobic interactions in hairpin structures. Essential dynamics analysis shows that the dynamics of the peptide at different temperatures spans basically the same essential subspace. The main equilibrium motions in this subspace involve large fluctuations of the residues in the turn and ends regions. Of the six interchain hydrogen bonds, the inner four remain stable during the simulations. The space spanned by the first two eigenvectors, as sampled at 450 K, includes almost all of the 47 different hairpin structures found in the database. Finally, analysis of the hydration of the 300 K average conformations shows that the hydration sites observed in the native conformation are still well hydrated in the equilibrium MD ensemble.

Structure-based engineering of environmentally sensitive fluorophores for monitoring protein-protein interactions.

Single, extrinsic, environmentally sensitive fluorophores can be used to quantitate formation of protein-protein complexes. These can be prepared semi-synthetically by covalent coupling to single cysteine mutations introduced at positions where the fluorophore is predicted to respond to formation of the complex without adversely affecting the interaction. The three-dimensional structure of a protein-protein interface can be used to select such locations by identifying residues that are located at the edge of a buried interfacial region, and are in partial steric contact with both partners as indicated by a change in their static solvent-accessible surface area upon complex formation. Using this design approach, cysteine mutations were introduced into the B1 domain of protein G, which successfully monitor complex formation with minimal interference. Such constructs have great utility in the analysis of solution properties of interface mutants.

Backbone dynamics of a domain of protein L which binds to immunoglobulin light chains.

Protein L is a multidomain protein expressed at the surface of some strains of the anaerobic bacterial species Peptostreptococcus magnus. The molecule interacts with the variable domain of immunoglobulin (Ig) light chains through five repeated homologous domains denoted B1 to B5. The fold of the Ig-light-chain-binding B1 domain of protein L (PLB1) has been shown to comprise an alpha-helix packed against a four-stranded beta-sheet and therefore resembles the structure of the IgG-binding domains of streptococcal protein G. In the present study, amide-proton exchange and 15N-relaxation NMR measurements were performed on the B1 domain to investigate its backbone mobility. It was shown that the folded portion of PLB1 is rigid with no regions of significantly higher flexibility than average. The N-terminus, however, is highly flexible consistent with earlier studies on the solution structure of PLB1. Comparison of the amide-proton-exchange data with similar measurements performed on the IgG-binding domains of protein G indicates that the two proteins have different exchange behaviors in their second beta-strands. Both protein G and L employ this region of their structures for binding to immunoglobulins since the interaction of protein G and protein L with IgG Fab and the Ig light chain, respectively, involves residues from the second beta-strand.

Optimal protein structure alignments by multiple linkage clustering: application to distantly related proteins

A fully automatic procedure for aligning two protein structures is presented. It uses as sole structural similarity measure the root mean square (r.m.s.) deviation of superimposed backbone atoms (N, C alpha, C and O) and is designed to yield optimal solutions with respect to this measure. In a first step, the procedure identifies protein segments with similar conformations in both proteins. In a second step, a novel multiple linkage clustering algorithm is used to identify segment combinations which yield optimal global structure alignments. Several structure alignments can usually be obtained for a given pair of proteins, which are exploited here to define automatically the common structural core of a protein family. Furthermore, an automatic analysis of the clustering trees is described which enables detection of rigid-body movements between structure elements. To illustrate the performance of our procedure, we apply it to families of distantly related proteins. One groups the three alpha + beta proteins ubiquitin, ferredoxin and the B1-domain of protein G. Their common structure motif consists of four beta-strands and the only alpha-helix, with one strand and the helix being displaced as a rigid body relative to the remaining three beta-strands. The other family consists of beta-proteins from the Greek key group, in particular actinoxanthin, the immunoglobulin variable domain and plastocyanin. Their consensus motif, composed of five beta-strands and a turn, is identified, mostly intact, in all Greek key proteins except the trypsins, and interestingly also in three other beta-protein families, the lipocalins, the neuraminidases and the lectins. This result provides new insights into the evolutionary relationships in the very diverse group of all beta-proteins.