Dimitrios Morikis

A novel mechanism of PKA anchoring revealed by solution structures of anchoring complexes.

The specificity of intracellular signaling events is controlled, in part, by compartmentalization of protein kinases and phosphatases. The subcellular localization of these enzymes is often maintained by protein‐ protein interactions. A prototypic example is the compartmentalization of the cAMP‐dependent protein kinase (PKA) through its association with A‐kinase anchoring proteins (AKAPs). A docking and dimerization domain (D/D) located within the first 45 residues of each regulatory (R) subunit protomer forms a high affinity binding site for its anchoring partner. We now report the structures of two D/D‐AKAP peptide complexes obtained by solution NMR methods, one with Ht31(493–515) and the other with AKAP79(392–413). We present the first direct structural data demonstrating the helical nature of the peptides. The structures reveal conserved hydrophobic interaction surfaces on the helical AKAP peptides and the PKA R subunit, which are responsible for mediating the high affinity association in the complexes. In a departure from the dimer‐dimer interactions seen in other X‐type four‐helix bundle dimeric proteins, our structures reveal a novel hydrophobic groove that accommodates one AKAP per RIIα D/D.

The molecular basis for protein kinase A anchoring revealed by solution NMR.

Compartmentalization of signal transduction enzymes into signaling complexes is an important mechanism to ensure the specificity of intracellular events. Formation of these complexes is mediated by specialized protein motifs that participate in protein–protein interactions. The adenosine 3´,5´-cyclic monophosphate (cAMP)-dependent protein kinase (PKA) is localized through interaction of the regulatory (R) subunit dimer with A-kinase-anchoring proteins (AKAPs). We now report the solution structure of the type II PKA R-subunit fragment RIIα(1–44), which encompasses both the AKAP-binding and dimerization interfaces. This structure incorporates an X-type four-helix bundle dimerization motif with an extended hydrophobic face that is necessary for high-affinity AKAP binding. NMR data on the complex between RIIα(1–44) and an AKAP fragment reveals extensive contacts between the two proteins. Interestingly, this same dimerization motif is present in other signaling molecules, the S100 family. Therefore, the X-type four-helix bundle may represent a conserved fold for protein–protein interactions in signal transduction.

Binding Kinetics, Structure-Activity Relationship, and Biotransformation of the Complement Inhibitor Compstatin

We have previously identified a 13-residue cyclic peptide, Compstatin, that binds to complement component C3 and inhibits complement activation. Herein, we describe the binding kinetics, structure-activity relationship, and biotransformation of Compstatin. Biomolecular interaction analysis using surface-plasmon resonance showed that Compstatin bound to native C3 and its fragments C3b and C3c, but not C3d. While binding of Compstatin to native C3 was biphasic, binding to C3b and C3c followed the 1:1 Langmuir binding model; the affinities of Compstatin for C3b and C3c were 22- and 74-fold lower, respectively, than that of native C3. Analysis of Compstatin analogs synthesized for structure-function studies indicated that 1) the 11-membered ring between disulfide-linked Cys2-Cys12 constitutes a minimal structure required for optimal activity; 2) retro-inverso isomerization results in loss of inhibitory activity; and 3) some residues of the type I β-turn segment also interact with C3. In vitro studies of Compstatin in human blood indicated that a major pathway of biotransformation was the removal of Ile1, which could be blocked by N-acetylation of the peptide. These findings indicate that acetylated Compstatin is stable against enzymatic degradation and that the type I β-turn segment is not only critical for preservation of the conformational stability, but also involved in intermolecular recognition.

PREDICTING PEPTIDE STRUCTURES USING NMR DATA AND DETERMINISTIC GLOBAL OPTIMIZATION

The ability to analyze large molecular structures by NMR techniques requires efficient methods for structure calculation. Currently, there are several widely available methods for tackling these problems, which, in general, rely on the optimization of penalty‐type target functions to satisfy the conformational restraints. Typically, these methods combine simulated annealing protocols with molecular dynamics and local minimization, either in distance or torsional angle space. In this work, both a novel formulation and algorithmic procedure for the solution of the NMR structure prediction problem is outlined. First, the unconstrained, penalty‐type structure prediction problem is reformulated using nonlinear constraints, which can be individually enumerated for all, or subsets, of the distance restraints. In this way, the violation can be controlled as a constraint, in contrast to the usual penalty‐type restraints. In addition, the customary simplified objective function is replaced by a full atom force field in the torsional angle space. This guarantees a better description of atomic interactions, which dictate the native structure of the molecule along with the distance restraints. The second novel portion of this work involves the solution method. Rather than pursue the typical simulated annealing procedure, this work relies on a deterministic method, which theoretically guarantees that the global solution can be located. This branch and bound technique, based on the αBB algorithm, has already been successfully applied to the identification of global minimum energy structures of peptides modeled by full atom force fields. Finally, the approach is applied to the Compstatin structure prediction, and it is found to possess some important merits when compared to existing techniques. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1354–1370, 1999

A Gain-of-Function Mutation of Arabidopsis Lipid Transfer Protein 5 Disturbs Pollen Tube Tip Growth and Fertilization

During compatible pollination of the angiosperms, pollen tubes grow in the pistil transmitting tract (TT) and are guided to the ovule for fertilization. Lily (Lilium longiflorum) stigma/style Cys-rich adhesin (SCA), a plant lipid transfer protein (LTP), is a small, secreted peptide involved in pollen tube adhesion-mediated guidance. Here, we used a reverse genetic approach to study biological roles of Arabidopsis thaliana LTP5, a SCA-like LTP. The T-DNA insertional gain-of-function mutant plant for LTP5 (ltp5-1) exhibited ballooned pollen tubes, delayed pollen tube growth, and decreased numbers of fertilized eggs. Our reciprocal cross-pollination study revealed that ltp5-1 results in both male and female partial sterility. RT-PCR and β-glucuronidase analyses showed that LTP5 is present in pollen and the pistil TT in low levels. Pollen-targeted overexpression of either ltp5-1 or wild-type LTP5 resulted in defects in polar tip growth of pollen tubes and thereby decreased seed set, suggesting that mutant ltp5-1 acts as a dominant-active form of wild-type LTP5 in pollen tube growth. The ltp5-1 protein has additional hydrophobic C-terminal sequences, compared with LTP5. In our structural homology/molecular dynamics modeling, Tyr-91 in ltp5-1, replacing Val-91 in LTP5, was predicted to interact with Arg-45 and Tyr-81, which are known to interact with a lipid ligand in maize (Zea mays) LTP. Thus, Arabidopsis LTP5 plays a significant role in reproduction.

Compstatin, a peptide inhibitor of complement, exhibits species-specific binding to complement component C3.

Although activation of complement protein C3 is essential for the generation of normal inflammatory responses against pathogens, its unregulated activation during various pathological conditions leads to host cell damage. Previously we have identified a 13-residue cyclic peptide, Compstatin, that inhibits C3 activation. In this study, we have examined the species-specificity of Compstatin. Bimolecular interaction analysis using a real-time surface plasmon resonance-based assay showed that Compstatin exhibits exclusive specificity for primate C3s and does not bind either to C3s from lower mammalian species or to two structural homologs of C3, human C4 and C5. Furthermore, it showed that although the kinetics of binding of Compstatin to non-human primate C3s were distinctly different from those to human C3, like human C3 its mechanism of binding to non-human primate C3 was biphasic and did not follow a simple 1:1 interaction, suggesting that this binding mechanism could be important for its inhibitory activity. Analysis of Ala substitution analogs of Compstatin for their inhibitory activities against mouse and rat complement suggested that the lack of binding of Compstatin to mouse and rat C3s was not a result of sterically hindered access to the binding pocket due to individual bulky side chains or the presence of charge on the Compstatin molecule. These results suggest that Compstatins exclusive specificity for primate C3s could be exploited for the development of species-specific complement inhibitors.

Related Protein-Protein Interaction Modules Present Drastically Different Surface Topographies Despite A Conserved Helical Platform

The subcellular localization of cAMP-dependent protein kinase (PKA) occurs through interaction with A-Kinase Anchoring Proteins (AKAPs). AKAPs bind to the PKA regulatory subunit dimer of both type Ialpha and type IIalpha (RIalpha and RIIalpha). RIalpha and RIIalpha display characteristic localization within different cell types, which is maintained by interaction of AKAPs with the N-terminal dimerization and docking domain (D/D) of the respective regulatory subunit. Previously, we reported the solution structure of RIIa D/D module, both free and bound to AKAPs. We have now solved the solution structure of the dimerization and docking domain of the type Ialpha regulatory dimer subunit (RIalpha D/D). RIalpha D/D is a compact docking module, with unusual interchain disulfide bonds that help maintain the AKAP interaction surface. In contrast to the shallow hydrophobic groove for AKAP binding across the surface of the RIIalpha D/D dimeric interface, the RIalpha D/D module presents a deep cleft for proposed AKAP binding. RIalpha and RIIalpha D/D interaction modules present drastically differing dimeric topographies, despite a conserved X-type four-helix bundle structure.

Electrostatic modeling predicts the activities of orthopoxvirus complement control proteins.

Regulation of complement activation by pathogens and the host are critical for survival. Using two highly related orthopoxvirus proteins, the vaccinia and variola (smallpox) virus complement control proteins, which differ by only 11 aa, but differ 1000-fold in their ability to regulate complement activation, we investigated the role of electrostatic potential in predicting functional activity. Electrostatic modeling of the two proteins predicted that altering the vaccinia virus protein to contain the amino acids present in the second short consensus repeat domain of the smallpox protein would result in a vaccinia virus protein with increased complement regulatory activity. Mutagenesis of the vaccinia virus protein confirmed that changing the electrostatic potential of specific regions of the molecule influences its activity and identifies critical residues that result in enhanced function as measured by binding to C3b, inhibition of the alternative pathway of complement activation, and cofactor activity. In addition, we also demonstrate that despite the enhanced activity of the variola virus protein, its cofactor activity in the factor I-mediated degradation of C3b does not result in the cleavage of the α′ chain of C3b between residues 954–955. Our data have important implications in our understanding of how regulators of complement activation interact with complement, the regulation of the innate immune system, and the rational design of potent complement inhibitors that might be used as therapeutic agents.

The Electrostatic Nature of C3d-Complement Receptor 2 Association

The association of complement component C3d with B or T cell complement receptor 2 (CR2 or CD21) is a link between innate and adaptive immunity. It has been recognized in experimental studies that the C3d-CR2 association is pH- and ionic strength-dependent. This led us to perform electrostatic calculations to obtain a theoretical understanding of the mechanism of C3d-CR2 association. We used the crystallographic structures of human free C3d, free CR2 (short consensus repeat (SCR)1–2), and the C3d-CR2(SCR1–2) complex, and continuum solvent representation, to obtain a detailed atomic-level picture of the components of the two molecules that contribute to association. Based on the calculation of electrostatic potentials for the free and bound species and apparent pKa values for each ionizable residue, we show that C3d-CR2(SCR1–2) recognition is electrostatic in nature and involves not only the association interface, but also the whole molecules. Our results are in qualitative agreement with experimental data that measured the ionic strength and pH dependence of C3d-CR2 association. Also, our results for the native molecules and a number of theoretical mutants of C3d explain experimental mutagenesis studies of amino acid replacements away from the association interface that modulate binding of iC3b with full-length CR2. Finally, we discuss the packing of the two SCR domains. Overall, our data provide global and site-specific explanations of the physical causes that underlie the ionic strength dependence of C3d-CR2 association in a unified model that accounts for all experimental data, some of which were previously thought to be contradictory.

Structural Biology of the Complement System

The Building Blocks of the Complement System, D. Morikis and J. D. Lambris Complement Control Protein Modules in the Regulators of Complement Activation , D. C. Soares and P. N. Barlow The Classical Pathway C1 Complex, G. J. Arlaud, C. Gaboriaud, N. M. Thielens, L. A. Gregory, J. Juanhuix, V. Rossi, and J. C. Fontecilla-Camps Factors D and B: Substrate-Inducible Serine Proteases of the Alternative Pathway of Complement Activation, Yuanyuan Xu, Karthe Ponnuraj, Sthanam V. L. Narayana, and John E. Volanakis The Structures of Human Complement Fragments C3d and C4Ad and the Functional Insights That They Have Provided , D. E. Isenman and J. M. H. van den Elsen Complement Receptor CR2/CD21 and CR2-C3d Complexes , J. P. Hannan, G. Szakonyi, R. Asokan, X. Chen, and V. M. Holers Structure of the Anaphylatoxins C3a and C5a, D. Morikis, M. C. H. Holland, and J. D. Lambris C3b/C4b Binding Site of Complement Receptor Type 1 (CR1, CD35), M. Krych-Goldberg, P. N. Barlow, R. L. Mallin, and J. P. Atkinson From Structure to Function of a Complement Regulator: Decay-Accelerating Factor (CD55), P. Lukacik, P. Roversi, R. A. G. Smith, and S. M. Lea Complement Protein C8, L. Lebioda and J. M. Sodetz Structure-Function Relationships in CD59, B. P. Morgan and S. Tomlinson Complement-like Repeats in Proteins of the Complement System, K. Dolmer and P. G. W. Gettins Complement and Immunoglobulin Protein Structures by X-Ray and Neutron Solution Scattering and Analytical Ultracentrifugation, S. J. Perkins and B. Furtado Structure, Dynamics, Activity, and Function of Compstatin and Design of More Potent Analogues , D. Morikis and J. D. Lambris Discovery of Potent Cyclic Antagonists of Human C5a Receptors, S. M. Taylor and D. P. Fairlie