David Perahia

Success of the PCILO method and failure of the CNDO/2 method for predicting conformations in some conjugated systems

Abstract Contrary to the CNDO/2 method, the PCILO method accounts correctly for the preferred conformation of glyoxal, butadiene, benzaldehyde, benzoic acid, biphenyl and 2,2′-difluorobiphenyl.

Computation of low-frequency normal modes in macromolecules: Improvements to the method of diagonalization in a mixed basis and application to hemoglobin

The method of diagonalization in a mixed basis (DIMB) that was published previously (Mouawad.), L. and Perahia D., Biopolymers 33, 599, 1993), allows the computation of the low-frequency vibrational modes for large macromolecules. Improvements to this method are presented here, namely the single and double truncation window techniques. The best convergence rate is obtained with the double truncation windows, which couple most efficiently the parts of the macromolecule which are far in sequence but close in space. Both methods were applied to the T-state of hemoglobin, to compare their efficiency. The resulting modes are analyzed in order to study the pathways between T- and R-states of this protein. They show that the quaternary conformational are mainly due to one mode at 2 cm-1.

Hydration scheme of uracil and cytosine

The comparison of a pure electrostatic approximation and complete supermolecule SCF ab initio computations on the hydration scheme of uracil and cytosine shows that the electrostatic procedure is capable to reproduce the general aspects of the results of the supermolecule treatment provided that different distances of shortest approach be adopted for the distances between the oxygen of water and the nitrogen of NH2 or NH groups or the oxygen of C-O groups on the one hand and the oxygen of water and pyridine-type nitrogens on the other hand.

Molecular orbital calculations on the conformation of polypeptides and proteins. IV. The conformation of the prolyl and hydroxyprolyl residues.

Abstract Quantum-mechanical calculations by the all-valence electrons PCILO method carried out previously for the glycyl, alanyl, phenylalanyl, tyrosyl, histidyl and tryptophanyl residues are now extended to the particular case (because of the limitations imposed by the rigidity of the pyrrolidine ring upon the rotational angle Φ) of the prolyl and hydroxyprolyl residues. Both the cis and trans forms have been explicitly considered. The calculations carried out with Φ = 122° predict the existence of two energy minima for the individual residue, centred around ψ = 140 to 150° and ψ = 330 to 340°. The results are in good agreement with empirical computations (probably because in this particular case the stable conformations are largely determined by the minimum in the repulsion energy) which they complete and extend and with the available data on the conformation of these residues in lysozyme and myoglobin. The calculations predict the energy difference between the most stable cis and trans conformers of proline to be of the order of 0·5 kcal/mole in favor of the latter. The search for the most advantageous pathway for the cis-trans interconversion indicates that it should occur for the rotation of ω between 180 and 0° for ψ around 150°, the calculated energy barrier being 16·2 kcal/mole. Calculations carried out for a model of the prolyl residue in its homopolymers indicate that in these compounds the stable conformations are limited, both for the cis and trans polymers, only to ψ centred around 330°. The trans form should be about 1·4 kcal/mole more stable than the cis one. The barrier for the cis-trans isomerisation is, in this case, of the order of 15 kcal/mole and the easiest path runs through ω = 180° → 90° → 0°.

How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis.

Better treatment of protein flexibility is essential in structure-based drug design projects such as virtual screening and protein-ligand docking. Diversity in ligand-binding mechanisms and receptor conformational changes makes it difficult to treat dynamic features of the receptor during the docking simulation. Thus, the use of pregenerated multiple receptor conformations is applied today in virtual screening studies. However, generation of a small relevant set of receptor conformations remains challenging. To address this problem, we propose a new protocol for the generation of multiple receptor conformations via normal mode analysis and for the selection of several receptor conformations suitable for docking/virtual screening. We validated this protocol on cyclin-dependent kinase 2, which possesses a binding site located at the interface between two subdomains and is known to undergo significant conformational changes in the active site region upon ligand binding. We believe that the suggested rules for the choice of suitable receptor conformations can be applied to other targets when dealing with in silico screening on flexible receptors.

Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study

Aspartate transcarbamylase (ATCase) initiates the pyrimidine biosynthetic pathway in Escherichia coli. Binding of aspartate to this allosteric enzyme induces a cooperative transition between the tensed (T) and relaxed (R) states of the enzyme which involves large quaternary and tertiary rearrangements. The mechanisms of the transmission of the regulatory signal to the active site (60 Å away) and that of the cooperative transition are not known in detail, although a large number of single, double, and triple site‐specific mutants and chimeric forms of ATCase have been obtained and kinetically characterized. A previous analysis of the very low‐frequency normal modes of both the T and R state structures of ATCase identified some of the large‐amplitude motions mediating the intertrimer elongation and rotation that occur during the cooperative transition (Thomas et al., J. Mol. Biol. 257:1070–1087, 1996; Thomas et al., J. Mol. Biol. 261:490–506, 1996). As a complement to that study, the deformation of the quaternary and tertiary structure of ATCase by normal modes below 5 cm−1 is investigated in this article. The ability of the modes to reproduce the domain motions occurring during the transition is analyzed, with special attention to the interdomain closure in the catalytic chain, which has been shown to be critical for homotropic cooperativity. The calculations show a coupling between the quaternary motions and more localized motions involving specific residues. The particular dynamic behavior of these residues is examined in the light of biochemical results to obtain insights into their role in the transmission of the allosteric signal. Proteins 1999;34:96–112.

Conformational dynamics and enzyme activity

Conformational flexibility and structural fluctuations play an important role in enzyme activity. A great variety of internal motions ranging over different time scales and of different amplitudes are involved in the catalytic cycle. These different types of motions and their functional consequences are considered in the light of experimental data and theoretical analyses. The conformational changes upon substrate binding, and particularly the hinge-bending motion which occurs in enzymes made of two domains, are analyzed from several well documented examples. The conformational events accompanying the different steps of the catalytic cycle are discussed. The last section concerns the motions involved in the allosteric transition which regulates the enzyme activity.

Molecular orbital calculations on the conformation of nucleic acids and their constituents: III. Backbone structure of di- and polynucleotides

Abstract Molecular orbital calculations, using the all-valence electrons method PCILO (Perturbative Configuration Interaction using Localized Orbitals), carried out previously for the glycosyl torsion angle χ cn have now been extended to the principal torsion angles of the backbone structure of polynucleotides, Ψ, Ф, ω, ω′ and Ф′ (in the notations of Sundaralingam). Conformational energy maps have been constructed for the four combinations of two consecutive angles: (ω′-ω), (Ф′-ω′), (ω-Ф) and (Ф-Ψ) with appropriate values adopted for the torsion of the angles not involved in the particular map under construction. The results of the PCILO computations are compared with data available from X-ray crystallography of related compounds and with similar calculations carried out by the empirical methods and by a simple quantum mechanical procedure (Extended Huckel Theory).

Molecular orbital calculations on the conformation of nucleic acids and their constituents. IV. Conformations about the exocyclic C(4′)-C(5′) bond

Abstract Quantum-mechanical computations carried out by the PCILO (perturbative configuration interaction using localized orbitals) method predict that the gg conformation of the exocyclic C(4′)-C(5′) bond should be the most stable one in purine and pyrimidine nucleosides and nucleotides, irrespective of the puckering of the sugar, at least as long as these puckerings belong to the most frequent C(3′)-endo, C(2′)-endo and C(3′)-exo categories. This prediction is in agreement with recent results of NMR studies in solution and with a large body of X-ray crystallographic results, to the extent that the cases in which the compounds exist in the crystal in the gt or tg forms may reasonably be attributed to the effect of environmental forces. The results also provide evidence for a number of fine details of the situation. A particularly significant result concerns the demonstration of an analogy between the behavior of the C(3′)-endo pyrimidine nucleosides and C(2′)-endo purine nucleosides on the one hand (strong preference for the gg conformers in both types) and between the C(2′)-endo pyrimidine nucleosides and C(3′)-endo purine nucleosides on the other (weak preference for the gg conformers in both types). The precision of the PCILO results is much greater than that of empirical or EHT (Extended Huckel theory) computations.

Targeting STAT1 by myricetin and delphinidin provides efficient protection of the heart from ischemia/reperfusion-induced injury.

Flavonoids exhibit a variety of beneficial effects in cardiovascular diseases. Although their therapeutic properties have been attributed mainly to their antioxidant action, they have additional protective mechanisms such as inhibition of signal transducer and activator of transcription 1 (STAT1) activation. Here, we have investigated the cardioprotective mechanisms of strong antioxidant flavonoids such as quercetin, myricetin and delphinidin. Although all of them protect the heart from ischemia/reperfusion‐injury, myricetin and delphinidin exert a more pronounced protective action than quercetin by their capacity to inhibit STAT1 activation. Biochemical and computer modeling analysis indicated the direct interaction between STAT1 and flavonoids with anti‐STAT1 activity.