The accurate prediction of enzyme kinetics from first principles is one of the central goals of theoretical biochemistry. Currently there is considerable debate [1][2][3] about the applicability of transition state theory (TST) to compute rate constants of enzyme-catalyzed reactions. Classical TST is known to be insufficient in some cases, but corrections for dynamical recrossing and quantum mechanical tunneling can be included. [1,2,4] Many effects that go beyond the framework of TST have been proposed, particularly focusing on the possible role of protein dynamics and conformational effects on the enzyme activity. Unfortunately, the overall importance of these effects for the effective reaction rate is difficult (if not impossible) to determine experimentally. However, if one could compute the quasi-thermodynamical free energy of activation with chemical accuracy (i.e. 1 kcal mol À1 ), comparison with the effective measured free energy of activation would directly show the importance of other effects.Combined quantum mechanical/molecular mechanical (QM/MM) methods have become an important tool for computational modeling of enzyme-catalyzed reactions. Only the substrate(s) and relevant residues in the active site are treated quantum mechanically, the rest of the protein is described at the empirical MM level. This lowers the computational expense, making it possible to treat large enzyme systems and the surrounding solvent, and to sample phase space. Nevertheless, the number of QM atoms is still relatively large, and until now only low levels of QM theory, such as semiempirical methods or density functional theory (DFT), have been feasible. Semiempirical methods, though applicable to large systems, are generally not accurate enough because computed free energies of activation may have an error of ten or more kcal mol À1 . DFT (especially with the B3LYP functional [5] ) offers improved accuracy but still lacks key physical interactions (e.g., dispersion). Often, DFT underestimates barrier heights by several kcal mol À1 , which cannot be systematically improved. Thus, when theoretical barriers do not agree with those from experiment, it is not clear whether the discrepancy arises from deficiencies in the electronic structure theory and the sampling, in the experimental observations, or in the underlying theoretical framework of QM/MM and TST.Consequently, there is a need for high-level electronic structure calculations for reliable predictions of enzyme reactivity. The ab initio electron correlation methods MP2 (Møller-Plesset second-order perturbation theory), CCSD (coupled-cluster theory with single and double excitations), and CCSD(T) (CCSD with a perturbative treatment of triple excitations) provide a well-established hierarchy that converge reliably to give high accuracy, and rate constants of gasphase reactions involving only a few atoms can be predicted with error bars comparable to those found experimentally. [6,7] However, the computational expense of these methods increases very rapidly with the number o...

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid hostguest binding energies. Link to publication Citation for published version (APA): Mikulskis, P., Cioloboc, D., Andrejić, M., Khare, S., Brorsson, J., Genheden, S., ... Ryde, U. (2014). Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies. Journal of Computer-Aided Molecular Design, 28(4), 375-400. DOI: 10.1007/s10822-014-9739-x General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights.• Users may download and print one copy of any publication from the public portal for the purpose of private study or research.• You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal AbstractWe have estimated free energies for the binding of nine cyclic carboxylate guest molecules to the octa-acid host in the SAMPL4 blind-test challenge with four different approaches. First, we used standard free-energy perturbation calculations of relative binding affinities, performed at the molecular-mechanics (MM) level with TIP3P waters, the GAFF force field, and two different sets of charges for the host and the guest, obtained either with the restrained electrostatic potential or AM1-BCC methods. Both charge sets give good and nearly identical results, with a mean absolute deviation (MAD) of 4 kJ/mol and a correlation coefficient (R 2 ) of 0.8 compared to experimental results. Second, we tried to improve these predictions with 28 800 density-functional theory (DFT) calculations for selected snapshots and the non-Boltzmann Bennett acceptance-ratio method, but this led to much worse results, probably because of a too large difference between the MM and DFT potential-energy functions. Third, we tried to calculate absolute affinities using minimised DFT structures. This gave intermediate-quality results with MADs of 5-9 kJ/mol and R 2 = 0.6-0.8, depending on how the structures were obtained. Finally, we tried to improve these results using local coupled-cluster calculations with single and double excitations, and non-iterative perturbative treatment of triple excitations (LCCSD(T0)), employing the polarisable multipole interactions with supermolecular pairs approach. Unfortunately, this only degraded the predictions, probably because a mismatch between the solvation energies obtained at the DFT and LCCSD(T0) levels.Key Words: binding affinities, host-guest, free-energies perturbation, density-functional calculations, CCSD(T), polarisable multipole interactions. 2 IntroductionOne of the largest challenges of computational chemistry is to predict the binding affinity of a small ligand to a larger receptor molecule, e.g. a drug candidate to its receptor prot...

The proteasome is a validated target for anticancer therapy, and proteasome inhibition is employed in the clinic for the treatment of tumors and hematological malignancies. Here, we describe crystal structures of the native human 20S proteasome and its complexes with inhibitors, which either are drugs approved for cancer treatment or are in clinical trials. The structure of the native human 20S proteasome was determined at an unprecedented resolution of 1.8 angstroms. Additionally, six inhibitor-proteasome complex structures were elucidated at resolutions between 1.9 and 2.1 angstroms. Collectively, the high-resolution structures provide new insights into the catalytic mechanisms of inhibition and necessitate a revised description of the proteasome active site. Knowledge about inhibition mechanisms provides insights into peptide hydrolysis and can guide strategies for the development of next-generation proteasome-based cancer therapeutics.

Theoreticians and experimentalists should work together more closely to establish reliable rankings and benchmarks for quantum chemical methods. Comparison to carefully designed experimental benchmark data should be a priority. Guidelines to improve the situation for experiments and calculations are proposed.

Mother of all folding: cold isolated linear alkanes C(n)H(2n+2) prefer an extended all-trans conformation before cohesive forces between the chain ends induce a folded hairpin structure for longer chains. It is shown by Raman spectroscopy at 100-150 K that the folded structure becomes more stable beyond n(C) = 17 or 18 carbon atoms. High-level quantum-chemical calculations yield n(C) = 17 ± 1 as the critical chain length.

In a large variety of studies, the coupled-cluster method with singles, doubles and perturbative triples (CCSD(T)) is used as a reference for benchmarking the performance of density functional theory (DFT) functionals. In the case of open-shell species this theory can be applied in different forms depending on the restricted or unrestricted treatment of spin. In this study, we show that these different approaches can produce results which deviate by ∼5 kcal/mol for different species on the potential energy surfaces. This was demonstrated for a simple model of the C-H activation carried out by non-heme iron enzymes. Assessing the limits of CCSD(T) prior to its use as a general benchmark tool is warranted. This was done using higher-order coupled cluster calculations as well as multiconfigurational second-order perturbation theory (CASPT2), since iron-oxo species present some multireference character. Furthermore, we tested two different implementations of the local coupled cluster method and compared them to the CCSD(T) results, showing that even though these novel approaches are promising, without further developments they appear not to be suitable for describing two-state reactivity of the system investigated in the current study. Additionally, we implemented and assessed the performance of the hotspot approach for local unrestricted CCSD(T) scheme which aims at reducing the pair error for systems containing transition metals.

The hydroxylation reaction catalyzed by p-hydroxybenzoate hydroxylase has been investigated by quantum mechanical/molecular mechanical (QM/MM) calculations at different levels of QM theory. The solvated enzyme was modeled (approximately 23,000 atoms in total, 49 QM atoms). The geometries of reactant and transition state were optimized for ten representative pathways using semiempirical (AM1) and density functional (B3LYP) methods as QM components. Single-point calculations at B3LYP/MM optimized geometries were performed with local correlation methods [LMP2, LCCSD(T0)] and augmented triple-zeta basis sets. A careful validation of the latter approach with regard to all computational parameters indicates convergence of the QM contribution to the computed barriers to within approximately 1 kcal mol(-1). Comparison with the available experimental data supports this assessment.

The accurate prediction of enzyme kinetics from first principles is one of the central goals of theoretical biochemistry. Currently there is considerable debate [1][2][3] about the applicability of transition state theory (TST) to compute rate constants of enzyme-catalyzed reactions. Classical TST is known to be insufficient in some cases, but corrections for dynamical recrossing and quantum mechanical tunneling can be included. [1,2,4] Many effects that go beyond the framework of TST have been proposed, particularly focusing on the possible role of protein dynamics and conformational effects on the enzyme activity. Unfortunately, the overall importance of these effects for the effective reaction rate is difficult (if not impossible) to determine experimentally. However, if one could compute the quasi-thermodynamical free energy of activation with chemical accuracy (i.e. 1 kcal mol À1 ), comparison with the effective measured free energy of activation would directly show the importance of other effects.Combined quantum mechanical/molecular mechanical (QM/MM) methods have become an important tool for computational modeling of enzyme-catalyzed reactions. Only the substrate(s) and relevant residues in the active site are treated quantum mechanically, the rest of the protein is described at the empirical MM level. This lowers the computational expense, making it possible to treat large enzyme systems and the surrounding solvent, and to sample phase space. Nevertheless, the number of QM atoms is still relatively large, and until now only low levels of QM theory, such as semiempirical methods or density functional theory (DFT), have been feasible. Semiempirical methods, though applicable to large systems, are generally not accurate enough because computed free energies of activation may have an error of ten or more kcal mol À1 . DFT (especially with the B3LYP functional [5] ) offers improved accuracy but still lacks key physical interactions (e.g., dispersion). Often, DFT underestimates barrier heights by several kcal mol À1 , which cannot be systematically improved. Thus, when theoretical barriers do not agree with those from experiment, it is not clear whether the discrepancy arises from deficiencies in the electronic structure theory and the sampling, in the experimental observations, or in the underlying theoretical framework of QM/MM and TST.Consequently, there is a need for high-level electronic structure calculations for reliable predictions of enzyme reactivity. The ab initio electron correlation methods MP2 (Møller-Plesset second-order perturbation theory), CCSD (coupled-cluster theory with single and double excitations), and CCSD(T) (CCSD with a perturbative treatment of triple excitations) provide a well-established hierarchy that converge reliably to give high accuracy, and rate constants of gasphase reactions involving only a few atoms can be predicted with error bars comparable to those found experimentally. [6,7] However, the computational expense of these methods increases very rapidly with the number o...