Biomedical subjects

Yihan Shao

Publications and source records attributed to Yihan Shao.

8 recordsLinked to original sources

PubMed2026

Active-site arginines differentially control Cas12a DNA cleavage and specificity.

Cas12a is a CRISPR-Cas nuclease with biochemical features that make it useful for genome editing and nucleic acid diagnostics. However, its off-target and non-specific trans and CRISPR RNA-independent DNA cleavages can reduce the accuracy and limit applications requiring high fidelity. Here, we analyzed the role of two conserved arginine residues, R918 and R921, found in the RuvC active site pocket of Francisella novicida Cas12a. Through amino acid substitutions, biochemical assays, kinetic analysis, and computational study, we establish that a positive charge at 921 is required for CRISPR RNA-dependent DNA cleavage (cis cleavage), whereas R918 primarily enhances cleavage efficiency. Replacing R918 with lysine or alanine eliminates trans activity while retaining cis cleavage, whereas replacing R921 with lysine eliminates trans activity and replacing with alanine abolishes cis and trans cleavages. Furthermore, these changes significantly decrease RNA-independent cleavage and improve mismatch discrimination during cis cleavage, especially at PAM-distal sites. Structural analysis shows that R918 assists in the conversion of the lid covering the RuvC active site to an alpha helical form, while R921 stabilizes the DNA in the active site. Molecular dynamics simulations reveal that while R921 is critical in supporting the positioning of scissile phosphate, R918 is essential in maintaining catalytic-site organization through lid's conformational change as well as in positioning DNA through its role in stabilizing the active site framework. Together, our results highlight the importance of R918 and R921 in Cas12a's activity and the potential of modifying active pocket residues to reduce unwanted DNA cleavage while increasing on-target specificity.

CRISPR-Cas↗

PubMed2007

An improved algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Møller-Plesset perturbation theory: application to alanine tetrapeptide conformational analysis.

We present a new algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Møller-Plesset perturbation theory (RI-MP2) and thoroughly assess its computational performance and chemical accuracy. This algorithm addresses the potential I/O bottlenecks associated with disk-based storage and access of the RI-MP2 t-amplitudes by utilizing a semi-direct batching approach and yields computational speed-ups of approximately 2-3 over the best conventional MP2 analytical gradient algorithms. In addition, we attempt to provide a straightforward guide to performing reliable and cost-efficient geometry optimizations at the RI-MP2 level of theory. By computing relative atomization energies for the G3/99 set and optimizing a test set of 136 equilibrium molecular structures, we demonstrate that satisfactory relative accuracy and significant computational savings can be obtained using Pople-style atomic orbital basis sets with the existing auxiliary basis expansions for RI-MP2 computations. We also show that RI-MP2 geometry optimizations reproduce molecular equilibrium structures with no significant deviations (>0.1 pm) from the predictions of conventional MP2 theory. As a chemical application, we computed the extended-globular conformational energy gap in alanine tetrapeptide at the extrapolated RI-MP2/cc-pV(TQ)Z level as 2.884, 4.414, and 4.994 kcal/mol for structures optimized using the HF, DFT (B3LYP), and RI-MP2 methodologies and the cc-pVTZ basis set, respectively. These marked energetic discrepancies originate from differential intramolecular hydrogen bonding present in the globular conformation optimized at these levels of theory and clearly demonstrate the importance of long-range correlation effects in polypeptide conformational analysis.

Alanine↗

PubMed2006

Dual-basis analytic gradients. 1. Self-consistent field theory.

Analytic gradients of dual-basis Hartree-Fock and density functional theory energies have been derived and implemented, which provide the opportunity for capturing large basis-set gradient effects at reduced cost. Suggested pairings for gradient calculations are 6-31G/6-31G**, dual[-f,-d]/cc-pVTZ, and 6-311G*/6-311 + +G(3df,3pd). Equilibrium geometries are produced within 0.0005 A of large-basis results for the latter two pairings. Though a single, iterative SCF response equation must be solved (unlike standard SCF gradients), it may be obtained in the smaller basis set, and integral screening further reduces the cost for well-chosen subsets. Total nuclear force calculations exhibit up to 75% savings, relative to large-basis calculations.

Journal Article↗

PubMed2006

Dual-basis second-order Moller-Plesset perturbation theory: A reduced-cost reference for correlation calculations.

The resolution-of-the-identity (RI) approximation has placed the onus of the cost of a second-order Moller-Plesset (MP2) calculation on the underlying self-consistent field (SCF) calculation for many moderately sized molecules. A dual-basis approach to the SCF calculation, based on previous methods demonstrated for density functional theory, is combined with RI-MP2 calculations, and small basis subsets for cc-pVTZ, cc-pVQZ, and 6-311++G(3df,3pd) are presented. These subsets provide time savings of greater than 90%, with negligible errors in absolute and relative energies, compared to the associated full-basis counterpart. The method is tested with a series of rotational barriers, relative conformational energies of alanine tetrapeptides, as well as the full G3/99 molecular set. RI-MP2 calculations on alanine octapeptides (40 heavy atoms, 3460 basis functions), using cc-pVQZ, are presented. Results improve upon previous methods that diagonalize the virtual space separately.

Journal Article↗

PubMed2006

Advances in methods and algorithms in a modern quantum chemistry program package.

Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.

Algorithms↗

PubMed2005

Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential.

A combined DFT quantum mechanical and AMBER molecular mechanical potential (QM/MM) is presented for use in molecular modeling and molecular simulations of large biological systems. In our approach we evaluate Lennard-Jones parameters describing the interaction between the quantum mechanical (QM) part of a system, which is described at the B3LYP/6-31+G* level of theory, and the molecular mechanical (MM) part of the system, described by the AMBER force field. The Lennard-Jones parameters for this potential are obtained by calculating hydrogen bond energies and hydrogen bond geometries for a large set of bimolecular systems, in which one hydrogen bond monomer is described quantum mechanically and the other is treated molecular mechanically. We have investigated more than 100 different bimolecular systems, finding very good agreement between hydrogen bond energies and geometries obtained from the combined QM/MM calculations and results obtained at the QM level of theory, especially with respect to geometry. Therefore, based on the Lennard-Jones parameters obtained in our study, we anticipate that the B3LYP/6-31+G*/AMBER potential will be a precise tool to explore intermolecular interactions inside a protein environment.

Acetamides↗

PubMed2004

An efficient method for calculating maxima of homogeneous functions of orthogonal matrices: applications to localized occupied orbitals.

We present here three new algorithms (one purely iterative and two DIIS-like [Direct Inversion in the Iteractive Subspace]) to compute maxima of homogeneous functions of orthogonal matrices. These algorithms revolve around the mathematical lemma that, given an invertible matrix A, the function f(U)=Tr(AU) has exactly one local (and global) maximum for U special orthogonal [i.e., UU(T)=1 and det(U)=1]. This is proved in the Appendix. One application of these algorithms is the computation of localized orbitals, including, for example, Boys and Edmiston-Ruedenberg (ER) orbitals. The Boys orbitals are defined as the set of orthonormal orbitals which, for a given vector space of orbitals, maximize the sum of the distances between orbital centers. The ER orbitals maximize total self-interaction energy. The algorithm presented here computes Boys orbitals roughly as fast as the traditional method (Jacobi sweeps), while, for large systems, it finds ER orbitals potentially much more quickly than traditional Jacobi sweeps. In fact, the required time for convergence of our algorithm scales quadratically in the region of a few hundred basis functions (though cubicly asymptotically), while Jacobi sweeps for the ER orbitals traditionally scale as the number of occupied orbitals to the fifth power. As an example of the utility of the method, we provide below the ER orbitals of nitrated and nitrosated benzene, and we discuss the chemical implications.

Journal Article↗

PubMed2003

Sparse matrix multiplications for linear scaling electronic structure calculations in an atom-centered basis set using multiatom blocks.

A sparse matrix multiplication scheme with multiatom blocks is reported, a tool that can be very useful for developing linear-scaling methods with atom-centered basis functions. Compared to conventional element-by-element sparse matrix multiplication schemes, efficiency is gained by the use of the highly optimized basic linear algebra subroutines (BLAS). However, some sparsity is lost in the multiatom blocking scheme because these matrix blocks will in general contain negligible elements. As a result, an optimal block size that minimizes the CPU time by balancing these two effects is recovered. In calculations on linear alkanes, polyglycines, estane polymers, and water clusters the optimal block size is found to be between 40 and 100 basis functions, where about 55-75% of the machine peak performance was achieved on an IBM RS6000 workstation. In these calculations, the blocked sparse matrix multiplications can be 10 times faster than a standard element-by-element sparse matrix package.

Journal Article↗