Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes: structural analysis of the peptide complexes with SH2 domains.

Computer simulations using the simplified energy function and simulated tempering dynamics have accurately determined the native structure of the pYVPML, SVLpYTAVQPNE, and SPGEpYVNIEF peptides in the complexes with SH2 domains. Structural and equilibrium aspects of the peptide binding with SH2 domains have been studied by generating temperature-dependent binding free energy landscapes. Once some native peptide-SH2 domain contacts are constrained, the underlying binding free energy profile has the funnel-like shape that leads to a rapid and consistent acquisition of the native structure. The dominant native topology of the peptide-SH2 domain complexes represents an extended peptide conformation with strong specific interactions in the phosphotyrosine pocket and hydrophobic interactions of the peptide residues C-terminal to the pTyr group. The topological features of the peptide-protein interface are primarily determined by the thermodynamically stable phosphotyrosyl group. A diversity of structurally different binding orientations has been observed for the amino-terminal residues to the phosphotyrosine. The dominant native topology for the peptide residues carboxy-terminal to the phosphotyrosine is tolerant to flexibility in this region of the peptide-SH2 domain interface observed in equilibrium simulations. The energy landscape analysis has revealed a broad, entropically favorable topology of the native binding mode for the bound peptides, which is robust to structural perturbations. This could provide an additional positive mechanism underlying tolerance of the SH2 domains to hydrophobic conservative substitutions in the peptide specificity region.

Deciphering common failures in molecular docking of ligand-protein complexes.

Common failures in predicting crystal structures of ligand-protein complexes are investigated for three ligand-protein systems by a combined thermodynamic and kinetic analysis of the binding energy landscapes. Misdocked predictions in ligand-protein docking are classified as 'soft' and 'hard' failures. While a soft failure arises when the search algorithm is unable to find the global energy minimum corresponding to the crystal structure, a hard failure results from a flaw of the energy function to qualify the crystal structure as the predicted lowest energy conformation in docking simulations. We find that neither the determination of a single structure with the lowest energy nor finding the most common binding mode is sufficient to predict crystal structures of the complexes, which belong to the category of hard failures. In a proposed hierarchical approach, structural similarity clustering of the conformations, generated from equilibrium simulations with the simplified energy function, is followed by energy refinement with the AMBER force field. This protocol, that involves a hierarchy of energy functions, resolves some common failures in ligand-protein docking and detects crystallographic binding modes that were not found during docking simulations.

Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions.

The thermodynamic and kinetic aspects of molecular recognition for the methotrexate (MTX)-dihydrofolate reductase (DHFR) ligand-protein system are investigated by the binding energy landscape approach. The impact of 'hot' and 'cold' errors in ligand mutations on the thermodynamic stability of the native MTX-DHFR complex is analyzed, and relationships between the molecular recognition mechanism and the degree of ligand optimization are discussed. The nature and relative stability of intermediates and thermodynamic phases on the ligand-protein association pathway are studied, providing new insights into connections between protein folding and molecular recognition mechanisms, and cooperativity of ligand-protein binding. The results of kinetic docking simulations are rationalized based on the thermodynamic properties determined from equilibrium simulations and the shape of the underlying binding energy landscape. We show how evolutionary ligand selection for a receptor active site can produce well-optimized ligand-protein systems such as MTX-DHFR complex with the thermodynamically stable native structure and a direct transition mechanism of binding from unbound conformations to the unique native structure.

Thermodynamics and kinetics of ligand-protein binding studied with the weighted histogram analysis method and simulated annealing.

The thermodynamics of ligand-protein molecular recognition is investigated by the energy landscape approach for two systems: methotrexate(MTX)--dihydrofolate reductase(DHFR) and biotin-streptavidin. The temperature-dependent binding free energy profile is determined using the weighted histogram analysis method. Two different force fields are employed in this study: a simplified model of ligand-protein interactions and the AMBER force field with a soft core smoothing component, used to soften the repulsive part of the potential. The results of multiple docking simulations are rationalized from the shape of the binding free energy profile that characterizes the thermodynamics of the binding process.

An Amerindian derivation for Latin American creole illnesses and their treatment.

We present an extended argument which we consider to be sufficient demonstration that a humoral tradition, notably a hot and cold classification, underlies medical etiologies and treatments used by certain groups of South American Indians, and that this is indigenous. We argue that several major, widespread categories of illness and treatments also have a mainly indigenous, Amerindian derivation: that they have not been derived, as often assumed, from unique importations from Spain or other Old World countries, so dating only from the Conquest and surviving in Latin American folk systems up to the present. Our ethnographic data derive from the Akawaio and northern Pemon (Arekuna, Taurepan and Kamarakoto), Carib-speaking Indians in the Guiana Highlands of the border areas of Venezuela, Brazil and Guyana. We stress the following points: The existence amongst these Amerindians, as amongst many Latin American creole and peasant groups, of certain specific and distinctive forms and interpretations of illness, their causations and cures. These include the binary oppositions of hot and cold and the notion of imbalance accompanying the concept of the mediate and harmonious state: sould loss through shock and fright: the capture of soul: whirlwind or cold air sickness: illness from contagious and powerful forces. Similarities between practitioners and remedies also exist. An interdependent relationship between indigenous concepts and language relating to the medical system Is demonstrated. Close associations between the medical system and the physical environment and the depiction of these in metaphors and symbols are detailed. Historical evidence in 17th century literature on Carib peoples is taken into account as well as evidence from remote, mostly unacculturated Amerindian societies of the recent past and of today. In the case of the Akawaio and Pemon, only the beginnings of syncretism in the medical system have been discovered. If our ethnographic data and the conclusions we draw are accepted, then question arises as to whether the hot/cold opposition and other medical concepts and practices relating to a humoral tradition in other Latin American groups, Amerindian and creole, are not wholley or in the main indigenous--as some scholars have already begun to suggest. If they are indigenous then they should be studied as such. We consider that there is a case for studying syncretism in medicine. We see this as a process whereby adoptions and adaptations are made selectively from incoming systems; where essential, indigenous elements may be reinforced and modified by the incoming, but where basic structures, objectives and characteristics of the indigenous remain identifiable and a continuity is achieved.