Configuration interaction tenichque is applied to the valence bond theory. Virtual VB orbitals are built, which are localized and orthogonal to their corresponding occupied orbitals and the excited VB structures are d...Configuration interaction tenichque is applied to the valence bond theory. Virtual VB orbitals are built, which are localized and orthogonal to their corresponding occupied orbitals and the excited VB structures are defined, which come from their corresponding fundamental VB structures. The testing calculations of H 2, LiH, HF show that the VB results using CI method match those of the molecular orbital based on the coupled cluster CCSD method, and the CI technique may become a useful tool in VB method.展开更多
Specific and dynamic biological interactions pave the blueprint of signal networks in cell. For example, a great variety of specific protein-ligand interactions define how intracellular signals flow. Taking advantage ...Specific and dynamic biological interactions pave the blueprint of signal networks in cell. For example, a great variety of specific protein-ligand interactions define how intracellular signals flow. Taking advantage of the specificity of these interactions, we postulate an "affinity-guided covalent conjugation" strategy to lock binding ligands through covalent reactions between the ligand and the receptor protein. The presence of a nucleophile close to the ligand binding site of a protein is sine qua none of this reaction. Specific noncovalent interaction of a ligand derivative(which contains an electrophile at a designed position) to the ligand binding site of the protein brings the electrophile to the close proximity of the nucleophile. Subsequently, a conjugation reaction spontaneously takes place between the nucleophile and the electrophile, and leads to an intermolecular covalent linkage. This strategy was first showcased in coiled coil peptides which include a cysteine mutation at a selected position. The short peptide sequence was used for covalent labeling of cell surface receptors. The same strategy was then used to guide the design of a set of protein Lego bricks for covalent assembly of protein complexes of unnatural geometry. We finally made "reactive peptides" for natural adaptor proteins that play significant roles in signal transduction. The peptides were designed to react with a single domain of the multidomain adaptor protein, delivered into the cytosol of neurons, and re-directed the intracellular signal of neuronal migration. The trilogy of protein labeling, assembly, and inhibition of intracellular signals, all through a specific covalent bond, fully demonstrated the generality and versatility of "affinity-guided covalent conjugation" in various applications.展开更多
The binding energies of thirty-six hydrogen-bonded peptide-base complexes, including the peptide backbone-ase complexes and amino acid side chain-base complexes, are evaluated using the analytic potential energy funct...The binding energies of thirty-six hydrogen-bonded peptide-base complexes, including the peptide backbone-ase complexes and amino acid side chain-base complexes, are evaluated using the analytic potential energy function established in our lab recently and compared with those obtained from MP2, AMBER99, OPLSAA/L, and CHARMM27 calculations. The comparison indicates that the analytic potential energy function yields the binding energies for these complexes as reasonable as MP2 does, much better than the force fields do. The individual N H…O=C, N H…N, C H…O=C, and C H…N attractive interaction energies and C=O…O=C, N H…H N, C H…H N, and C H…H C repulsive interaction energies, which cannot be easily obtained from ab initio calculations, are calculated using the dipole-dipole interaction term of the analytic potential energy function. The individual N H…O=C, C H…O=C, C H…N attractive interactions are about 5.3±1.8, 1.2±0.4, and 0.8 kcal/mol, respectively, the individual N H … N could be as strong as about 8.1 kcal/mol or as weak as 1.0 kcal/mol, while the individual C=O…O=C, N H…H N, C H…H N, and C H…H C repulsive interactions are about 1.8±1.1, 1.7±0.6, 0.6±0.3, and 0.35±0.15 kcal/mol. These data are helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies.展开更多
文摘Configuration interaction tenichque is applied to the valence bond theory. Virtual VB orbitals are built, which are localized and orthogonal to their corresponding occupied orbitals and the excited VB structures are defined, which come from their corresponding fundamental VB structures. The testing calculations of H 2, LiH, HF show that the VB results using CI method match those of the molecular orbital based on the coupled cluster CCSD method, and the CI technique may become a useful tool in VB method.
基金supported by the University Grants Committee of Hong Kong (ECS grant CUHK 404812, GRF grants 403711 and 404413, and Ao E/M-09/12)
文摘Specific and dynamic biological interactions pave the blueprint of signal networks in cell. For example, a great variety of specific protein-ligand interactions define how intracellular signals flow. Taking advantage of the specificity of these interactions, we postulate an "affinity-guided covalent conjugation" strategy to lock binding ligands through covalent reactions between the ligand and the receptor protein. The presence of a nucleophile close to the ligand binding site of a protein is sine qua none of this reaction. Specific noncovalent interaction of a ligand derivative(which contains an electrophile at a designed position) to the ligand binding site of the protein brings the electrophile to the close proximity of the nucleophile. Subsequently, a conjugation reaction spontaneously takes place between the nucleophile and the electrophile, and leads to an intermolecular covalent linkage. This strategy was first showcased in coiled coil peptides which include a cysteine mutation at a selected position. The short peptide sequence was used for covalent labeling of cell surface receptors. The same strategy was then used to guide the design of a set of protein Lego bricks for covalent assembly of protein complexes of unnatural geometry. We finally made "reactive peptides" for natural adaptor proteins that play significant roles in signal transduction. The peptides were designed to react with a single domain of the multidomain adaptor protein, delivered into the cytosol of neurons, and re-directed the intracellular signal of neuronal migration. The trilogy of protein labeling, assembly, and inhibition of intracellular signals, all through a specific covalent bond, fully demonstrated the generality and versatility of "affinity-guided covalent conjugation" in various applications.
基金supported by the National Natural Science Foundation of China(20973088,21173109,21133005)the Specialized Research Fund for the Doctoral Program of Higher Education(20102136110001)
文摘The binding energies of thirty-six hydrogen-bonded peptide-base complexes, including the peptide backbone-ase complexes and amino acid side chain-base complexes, are evaluated using the analytic potential energy function established in our lab recently and compared with those obtained from MP2, AMBER99, OPLSAA/L, and CHARMM27 calculations. The comparison indicates that the analytic potential energy function yields the binding energies for these complexes as reasonable as MP2 does, much better than the force fields do. The individual N H…O=C, N H…N, C H…O=C, and C H…N attractive interaction energies and C=O…O=C, N H…H N, C H…H N, and C H…H C repulsive interaction energies, which cannot be easily obtained from ab initio calculations, are calculated using the dipole-dipole interaction term of the analytic potential energy function. The individual N H…O=C, C H…O=C, C H…N attractive interactions are about 5.3±1.8, 1.2±0.4, and 0.8 kcal/mol, respectively, the individual N H … N could be as strong as about 8.1 kcal/mol or as weak as 1.0 kcal/mol, while the individual C=O…O=C, N H…H N, C H…H N, and C H…H C repulsive interactions are about 1.8±1.1, 1.7±0.6, 0.6±0.3, and 0.35±0.15 kcal/mol. These data are helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies.
