6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

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Quantum mechanical continuum solvation models.

F. Vinyl Sulfones and Other Michael Acceptors 4683 G. Azodicarboxamides 4695 IV. Acylating Agents 4695 A. Aza-peptides 4695 B. Carbamates 4699 C. Peptidyl Acyl Hydroxamates 4700 D. â-Lactams and Related Inhibitors 4704 E. Heterocyclic Inhibitors 4714 1. Isocoumarins 4715 2. Benzoxazinones 4722 3. Saccharins 4725 4. Miscellaneous Heterocyclic Inhibitors 4728 V. Phosphonylation Agents 4728 A. Peptide Phosphonates 4728 B. Phosphonyl Fluorides 4734 VI. Sulfonylating Agents 4735 A. Sulfonyl Fluorides 4735 VII. Miscellaneous Inhibitors 4736 VIII. Summary and Perspectives 4737 IX. Acknowledgments 4740 X. Note Added in Proof 4740 XI. References 4740

Irreversible inhibitors of serine, cysteine, and threonine proteases.

Structure-based mutational analysis of serine protease specificity has produced a large database of information useful in addressing biological function and in establishing a basis for targeted design efforts. Critical issues examined include the function of water molecules in providing strength and specificity of binding, the extent to which binding subsites are interdependent, and the roles of polypeptide chain flexibility and distal structural elements in contributing to specificity profiles. The studies also provide a foundation for exploring why specificity modification can be either straightforward or complex, depending on the particular system.

Structural basis of substrate specificity in the serine proteases

No wonder you activities are, reading will be always needed. It is not only to fulfil the duties that you need to finish in deadline time. Reading will encourage your mind and thoughts. Of course, reading will greatly develop your experiences about everything. Reading molecular biology of the gene is also a way as one of the collective books that gives many advantages. The advantages are not only for you, but for the other peoples with those meaningful benefits.

Molecular Biology of the Gene.

A conceptually novel pyrrole synthesis is reported, efficiently merging enamines and (unactivated) alkynes under oxidative conditions. In an intermolecular Rh catalyzed process, the challenging allylic sp3 C−H activation of the enamine substrates is followed by the cyclization with the alkyne (R3 = CO2R). Alternatively, in some cases (R3 = CN), the enamine can be utilized for a vinylic sp2 C−H activation. A total of 17 examples with yields above 60% is presented, together with the results of an initial mechanistic investigation.

Pyrrole Synthesis via Allylic sp3 C−H Activation of Enamines Followed by Intermolecular Coupling with Unactivated Alkynes

We have created a simple algorithm for automatically predicting the explicit solvent atom distribution of biomolecules. The explicit distribution is coerced from the three-dimensional (3D) continuous distribution resulting from a 3D reference interaction site model (3D-RISM) calculation. This procedure predicts optimal location of solvent molecules and ions given a rigid biomolecular structure and the solvent composition. We show examples of predicting water molecules near the KNI-272 bound form of HIV-1 protease and predicting both sodium ions and water molecules near the rotor ring of F-adenosine triphosphate (ATP) synthase. Our results give excellent agreement with experimental structure with an average prediction error of 0.39-0.65 A. Further, unlike experimental methods, this method does not suffer from the partial occupancy limit. Our method can be performed directly on 3D-RISM output within minutes. It is extremely useful for examining multiple specific solvent-solute interactions, as a convenient method for generating initial solvent structures for molecular dynamics calculations, and may assist in refinement of experimental structures. © 2012 Wiley Periodicals, Inc.

Placevent: an algorithm for prediction of explicit solvent atom distribution-application to HIV-1 protease and F-ATP synthase.

Recent progress in the theory of molecular recognition in biomolecules is reviewed, which has been made based on the statistical mechanics of liquids or the RISM/3D-RISM theory during the last five years in the authors’ group. The method requires just the structure of protein and the potential energy parameters for the biomolecules and solutions as inputs. The calculation is carried out in two steps. The first step is to obtain the pair correlation functions for solutions consisting of water and ligands based on the RISM theory. Then, given the pair correlation functions prepared in the first step, we calculate the 3D-distribution functions of water and ligands around and inside protein based on the 3D-RISM theory. The molecular recognition of a ligand by the protein is realized by the 3D-distribution functions: if one finds some conspicuous peaks in the distribution of a ligand inside protein, then the ligand is regarded as “recognized” by the protein. Some biochemical processes are investigated, which a...

Molecular recognition in biomolecules studied by statistical-mechanical integral-equation theory of liquids.

Cations (Ca2+, Na+, K+) selectively bound by human lysozyme and its mutants are probed by the 3D-RISM theory, a statistical mechanics theory of liquids.

Norio Yoshida

Papers

Placevent: an algorithm for prediction of explicit solvent atom distribution-application to HIV-1 protease and F-ATP synthase.

Molecular recognition in biomolecules studied by statistical-mechanical integral-equation theory of liquids.

Selective ion-binding by protein probed with the 3D-RISM theory.

Di-.pi.-cyclooctatetraenethorium

Substrate specificity of two chymotrypsin-like proteases from rat mast cells. Studies with peptide 4-nitroanilides and comparison with cathepsin G.