Ignace Lasters

All in one: A highly detailed rotamer library improves both accuracy and speed in the modelling of sidechains by dead-end elimination

BACKGROUND About a decade ago, the concept of rotamer libraries was introduced to model sidechains given known mainchain coordinates. Since then, several groups have developed methods to handle the challenging combinatorial problem that is faced when searching rotamer libraries. To avoid a combinatorial explosion, the dead-end elimination method detects and eliminates rotamers that cannot be members of the global minimum energy conformation (GMEC). Several groups have applied and further developed this method in the fields of homology modelling and protein design. RESULTS This work addresses at the same time increased prediction accuracy and calculation speed improvements. The proposed enhancements allow the elimination of more than one-third of the possible rotameric states before applying the dead-end elimination method. This is achieved by using a highly detailed rotamer library allowing the safe application of an energy-based rejection criterion without risking the elimination of a GMEC rotamer. As a result, we gain both in modelling accuracy and in computational speed. Being completely automated, the current implementation of the dead-end elimination prediction of protein sidechains can be applied to the modelling of sidechains of proteins of any size on the high-end computer systems currently used in molecular modelling. The improved accuracy is highlighted in a comparative study on a collection of proteins of varying size for which score results have previously been published by multiple groups. Furthermore, we propose a new validation method for the scoring of the modelled structure versus the experimental data based upon the volume overlap of the predicted and observed sidechains. This overlap criterion is discussed in relation to the classic RMSD and the frequently used +/- 40 degrees window in comparing chi 1 and chi 2 angles. CONCLUSIONS We have shown that a very detailed library allows the introduction of a safe energy threshold rejection criterion, thereby increasing both the execution speed and the accuracy of the modelling program. We speculate that the current method will allow the sidechain prediction of medium-sized proteins and complex protein interfaces involving up to 150 residues on low-end desktop computers.

The BRUGEL package: toward computer-aided design of macromolecules

The BRUGEL Package: Toward Computer-Aided Design of Macromolecules P. Delhaise, M. Bardiaux, M. De Maeyer, M. Prevost,* D. Van Belle, J. Donneux, I. Lasters, E. Van Custem,* P. Alard and S.J. Wodak* Plant Genetic Systems and *Unite de Conformation de Macromolecules Biologiques, Universite Libre de Bruxelles CP160, P2, Avenue P. Htger 1 OS&Bruxelles, Belgium Molecular modeling of large biomolecules encompasses today a number of different highly complementary aspects. These include graphic display of complex mole- cular models, computer simulations such as molecular dynamics and molecular mechanics, and comparison and analysis of different structures, as well as efficient access to databases. The advent of faster computers and more modular hardware architecture where networking is an important requirement, the proliferation of software standards and, most important, the increased demand and popularity of molecular modeling with molecular biologists, protein designers and drug designers, are calling for swift changes in many of the basic concepts of molecular modeling software. Our efforts in responding to these recent developments within the BRUGEL package are described. BRUGEL is a fully integrated molecular modeling package espe- cially suited for macromolecules. One of its most remark- able features is the manipulation of molecular objects (one-dimensional Boolean arrays that contain the value TRUE or FALSE for each atom). These objects can be created by a variety of user-defined criteria and by combination of existing objects using SET theory, and be subsequently used for all numerical or display manip- ulations requiring atom selection. A similar concept is also applied to tables containing numerical values (scalars, vectors). In addition, BRUGEL features pro- gramming tools for user-written functions and offers working solutions in a network environment. Its applica- tions to the analysis of protein structure and function and to problems of protein design will be illustrated. The use of up-to-date software engineering techniques will also be discussed in view of the adaptability capaci- ties of the product to future needs, to new algorithms and hardware solutions. Finally, we will discuss the different types of shading options we have developed on the Evans & Sutherland PS390 screen. A Quantum Molecular Dynamic Free Energy Perturha- tion Method Applied to Chemical Reactions in the Condensed Phase Paul A. Bash, Martin J. Field and Martin Karplus Department of Chemistry, Harvard University, Cambridge, MA 02138, USA A semiempirical quantum mechanical method is com- bined with molecular mechanics to obtain a potential function for studying chemical reactions in condensed phase systems. Molecular dynamics simulations based on this potential function are implemented to perform thermodynamic perturbation calculations. The method is utilized to calculate the free energy activation barrier for an SN2 reaction in solution. The results compare well with our experiments and those from other theoreti- cal treatments. This technique is also used to study the isomerization of dihydroxyacetone phosphate (DHAP) to glyceraldehyde phosphate (GAP) catalyzed by the enzyme triose phosphate isomerase (TIM). Plausible pathways for the reaction are determined starting from the 1.9 A resolution X-ray crystal structure for TIM complexed with the inhibitor phosphoglycolo- hydroxamic acid (PGH) (Davinport et al.). Energy pro- files are calculated from these pathways and compared with experimental values (Knowles et al.). Calculations using a model with His-95 both singly and doubly protonated are carried out to investigate alternative mechanisms that result from the protonation state of this residue. A 16mm film that accompanies this work shows the different aspects of quantum molecular dynamics. A Fast Algorithm for Rendering Space-Filling Molecule Pictures David Bacon and Wayne F. Anderson MRC Group on Protein Structure and Function, Department of Biochemistry, University of Alberta, Alberta, Canada Pictures that display the “surface” of a molecule are becoming increasingly important as X-ray crystallo- graphy and related techniques reveal larger structures. This need is becoming particularly acute with the widespread current interest in drug design, where a very accurate impression of active sites is required for predicting complementary substrates. To make a good “space-filling” molecule picture by computer, it is necessary both to determine which parts of the surface are visible from some viewpoint (hidden- surface elimination) and to shade this make it look as if the model exists physically in space. Depth seems to be most strongly perceived if shadows are cast by the appropriate parts of model on other when the model is lit by a simulated light source from somewhere behind and over a shoulder of the viewer. Speed is a central concern, especially when a long series of images is to be computed, as in a movie. The new algorithm is designed to take special advantage of the relatively uniform spatial distribution of atoms in average molecules, and it happens that this algorithm is well suited to the shadow calculation, because the latter is nothing more than a hidden-surface elimination from the viewpoint of a light source. The basic idea behind the new hidden-surface algorithm is to divide the “screen” up into a set of rectangular tiles, so that the data associated with each J. Mol. Graphics, 1988, Vol. 6, December 219

Computation of the binding of fully flexible peptides to proteins with flexible side chains.

Docking algorithms play an important role in the process of rational drug design and in understanding the mechanism of molecular recognition. An important determinant for successful docking is the extent to which the configurational space (including conformational changes) of the li‐gand/receptor system is searched. Here we describe a new, combinatorial method for flexible docking of peptides to proteins that allows full rotation around all single bonds of the peptide ligand and around those of a large set of receptor side chains. We have simulated the binding of several viral peptides to murine major histocompatibility complex class I H‐2Kb. In addition, we have explored the limits of our method by simulating a complex between calmodulin and an 18‐residue long helical peptide from calmodulin‐dependent protein kinase IIα. The calculated peptide conformations generally matched well with the X‐ray structures. Essential information about local flexibility and about residues that are responsible for strong binding was obtained. We have frequently observed considerable side‐chain flexibility during the simulations, showing the need for a flexible treatment of the receptor. Our method may also be useful whenever the receptor side‐chain conformation is not available or uncertain, as illustrated by the docking of an H‐2Kb binding nonapeptide to the receptor structure taken from an octapeptide/H‐2Kb complex.—Desmet, J., Wilson, I. A., Joniau, M., De Maeyer, M., Lasters, I. Computation of the binding of fully flexible peptides to proteins with flexible side chains. FASEB J 11, 164‐172 (1997)

Trematode Myoglobins, Functional Molecules with a Distal Tyrosine

The myoglobins of two trematodes, Paramphistomum epiclitum and Isoparorchis hypselobagri, were isolated to homogeneity. The native molecules are monomeric with Mr 16,000-17,000 and pI 6.5-7.5. In each species, at least four different globin isoforms occur. Primary structure was determined at the protein level. The globin chains contain 147 amino acid residues. Although major determinants of the globin fold are conserved, characteristic substitutions are present. A Tyr residue occurs at the helical positions B10 and E7 (distal position). This is confirmed by NMR measurements (Zhang, W., Rashid, K. A., Haque, M., Siddiqi, A. H., Vinogradov, S. N., Moens, L. & La Mar, G. N. (1997) J. Biol. Chem. 272, 3000-3006). A distal Tyr normally provokes oxidation of the iron atom and the inability to bind oxygen, whereas a Tyr-B10 is indicative for a high oxygen affinity. In contrast, trematode myoglobins are functional molecules with a high oxygen affinity. Molecular modeling predicts two possible positions for the aromatic ring of Tyr-E7: one being outside the heme pocket making it freely accessible to the ligand and one within the heme pocket potentially able to form a second hydrogen bond with the iron-bound oxygen. A hydrogen bond between Tyr-B10 and the bound oxygen as in the Ascaris hemoglobin is predicted as well. The predicted structure may explain the high oxygen affinity of the trematode myoglobins.

Structural basis of IL-23 antagonism by an Alphabody protein scaffold

Protein scaffolds can provide a promising alternative to antibodies for various biomedical and biotechnological applications, including therapeutics. Here we describe the design and development of the Alphabody, a protein scaffold featuring a single-chain antiparallel triple-helix coiled-coil fold. We report affinity-matured Alphabodies with favourable physicochemical properties that can specifically neutralize human interleukin (IL)-23, a pivotal therapeutic target in autoimmune inflammatory diseases such as psoriasis and multiple sclerosis. The crystal structure of human IL-23 in complex with an affinity-matured Alphabody reveals how the variable interhelical groove of the scaffold uniquely targets a large epitope on the p19 subunit of IL-23 to harness fully the hydrophobic and hydrogen-bonding potential of tryptophan and tyrosine residues contributed by p19 and the Alphabody, respectively. Thus, Alphabodies are suitable for targeting protein–protein interfaces of therapeutic importance and can be tailored to interrogate desired design and binding-mode principles via efficient selection and affinity-maturation strategies.

The “Dead-End Elimination” Theorem: A New Approach to the Side-Chain Packing Problem

The prediction of a protein’s tertiary structure is still computationally infeasible, mainly because of the huge number of a priori possible global conformations. The prediction of side-chain conformations that are attached to a given, fixed main-chain structure is considered as a less complex but still important subproblem with applications to, for instance, homology modeling (Lee and Subbiah, 1991). Nevertheless, the determination of the global minimum energy conformation (GMEC) of a set of protein side chains was up to now still limited to small, densely packed units (Ponder and Richards, 1987; Lee and Levitt, 1991).

Dead-end based modeling tools to explore the sequence space that is compatible with a given scaffold.

The dead-end elimination algorithm has proven to be a powerful tool in protein homology modeling since it allows one to determine rapidly the global minimum-energy conformation (GMEC) of an arbitrarily large collection of side chains, given fixed backbone coordinates. After introducing briefly the necessary background, we focus on logic arguments that increase the efficacy of the dead-end elimination process. Second, we present new theoretical considerations on the use of the dead-end elimination method as a tool to identify sequences that are compatible with a given scaffold structure. Third, we initiate a search for properties derived from the computed GMEC structure to predict whether a given sequence can be well packed in the core of a protein. Three properties will be considered: the nonbonded energy, the accessible surface area, and the extent by which the GMEC side-chain conformations deviate from a locally optimal conformation.