BuRNN: Buffer Region Neural Network Approach for Polarizable-Embedding Neural Network/Molecular Mechanics Simulations

Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have advanced the field of computational chemistry tremendously. However, they require the partitioning of a system into two different regions that are treated at different levels of theory, which can cause artifacts at the interface. Furthermore, they are still limited by high computational costs of quantum chemical calculations. In this work, we develop the buffer region neural network (BuRNN), an alternative approach to existing QM/MM schemes, which introduces a buffer region that experiences full electronic polarization by the inner QM region to minimize artifacts. The interactions between the QM and the buffer region are described by deep neural networks (NNs), which leads to the high computational efficiency of this hybrid NN/MM scheme while retaining quantum chemical accuracy. We demonstrate the BuRNN approach by performing NN/MM simulations of the hexa-aqua iron complex.

PROFICS: A bacterial selection system for directed evolution of proteases

Proteases serve as important tools in biotechnology and as valuable drugs or drug targets. Efficient protein engineering methods to study and modulate protease properties are thus of great interest for a plethora of applications. We established PROFICS (PRotease Optimization via Fusion-Inhibited Carbamoyltransferase-based Selection), a bacterial selection system, which enables the optimization of proteases for biotechnology, therapeutics or diagnosis in a simple overnight process. During the PROFICS process, proteases are selected for their ability to specifically cut a tag from a reporter enzyme and leave a native N-terminus. Precise and efficient cleavage after the recognition sequence reverses the phenotype of an Escherichia coli knockout strain deficient in an essential enzyme of pyrimidine synthesis. A toolbox was generated to select for proteases with different preferences for P1' residues (the residue immediately following the cleavage site). The functionality of PROFICS is demonstrated with viral proteases and human caspase-2. PROFICS improved caspase-2 activity up to 25-fold after only one round of mutation and selection. Additionally, we found a significantly improved tolerance for all P1' residues caused by a mutation in a substrate interaction site. We showed that this improved activity enables cells containing the new variant to outgrow cells containing all other mutants, facilitating its straightforward selection. Apart from optimizing enzymatic activity and P1' tolerance, PROFICS can be used to reprogram specificities, erase off-target activity, optimize expression via tags/codon usage, or even to screen for potential drug-resistance-conferring mutations in therapeutic targets such as viral proteases in an unbiased manner.

Reaction intermediate rotation during the decarboxylation of coproheme to heme b in C. diphtheriae

Monoderm bacteria utilize coproheme decarboxylases (ChdCs) to generate heme b by a stepwise decarboxylation of two propionate groups of iron coproporphyrin III (coproheme), forming two vinyl groups. This work focuses on actinobacterial ChdC from Corynebacterium diphtheriae (CdChdC) to elucidate the hydrogen peroxide-mediated decarboxylation of coproheme via monovinyl monopropionyl deuteroheme (MMD) to heme b, with the principal aim being to understand the reorientation mechanism of MMD during turnover. Wild-type CdChdC and variants, namely H118A, H118F, and A207E, were studied by resonance Raman and ultraviolet-visible spectroscopy, mass spectrometry, and molecular dynamics simulations. As actinobacterial ChdCs use a histidine (H118) as a distal base, we studied the H118A and H118F variants to elucidate the effect of 1) the elimination of the proton acceptor and 2) steric constraints within the active site. The A207E variant mimics the proximal H-bonding network found in chlorite dismutases. This mutation potentially increases the rigidity of the proximal site and might impair the rotation of the reaction intermediate MMD. We found that both wild-type CdChdC and the variant H118A convert coproheme mainly to heme b upon titration with H2O2. Interestingly, the variant A207E mostly accumulates MMD along with small amounts of heme b, whereas H118F is unable to produce heme b and accumulates only MMD. Together with molecular dynamics simulations, the spectroscopic data provide insight into the reaction mechanism and the mode of reorientation of MMD, i.e., a rotation in the active site versus a release and rebinding.

Charge-Changing Perturbations and Path Sampling via Classical Molecular Dynamic Simulations of Simple Guest-Host Systems

Currently, two different methods dominate the field of biomolecular free-energy calculations for the prediction of binding affinities. Pathway methods are frequently used for large ligands that bind on the surface of a host, such as protein-protein complexes. Alchemical methods, on the other hand, are preferably applied for small ligands that bind to deeply buried binding sites. The latter methods are also widely known to be heavily artifacted by the representation of electrostatic energies in periodic simulation boxes, in particular, when net-charge changes are involved. Different methods have been described to deal with these artifacts, including postsimulation correction schemes and instantaneous correction schemes (e.g., co-alchemical perturbation of ions). Here, we use very simple test systems to show that instantaneous correction schemes with no change in the system net charge lower the artifacts but do not eliminate them. Furthermore, we show that free energies from pathway methods suffer from the same artifacts.

Actinobacterial Coproheme Decarboxylases Use Histidine as a Distal Base to Promote Compound I Formation

Coproheme decarboxylases (ChdCs) catalyze the final step in heme b biosynthesis of monoderm and some diderm bacteria. In this reaction, coproheme is converted to heme b via monovinyl monopropionate deuteroheme (MMD) in two consecutive decarboxylation steps. In Firmicutes decarboxylation of propionates 2 and 4 of coproheme depend on hydrogen peroxide and the presence of a catalytic tyrosine. Here we demonstrate that ChdCs from Actinobacteria are unique in using a histidine (H118 in ChdC from Corynebacterium diphtheriae, CdChdC) as a distal base in addition to the redox-active tyrosine (Y135). We present the X-ray crystal structures of coproheme-CdChdC and MMD-CdChdC, which clearly show (i) differences in the active site architecture between Firmicutes and Actinobacteria and (ii) rotation of the redox-active reaction intermediate (MMD) after formation of the vinyl group at position 2. Distal H118 is shown to catalyze the heterolytic cleavage of hydrogen peroxide (k_app = (4.90 ± 1.25) × 10⁴ M^–1 s^–1). The resulting Compound I is rapidly converted to a catalytically active Compound I* (oxoiron(IV) Y135^•) that initiates the radical decarboxylation reactions. As a consequence of the more efficient Compound I formation, actinobacterial ChdCs exhibit a higher catalytic efficiency in comparison to representatives from Firmicutes. On the basis of the kinetic data of wild-type CdChdC and the variants H118A, Y135A, and H118A/Y135A together with high-resolution crystal structures and molecular dynamics simulations, we present a molecular mechanism for the hydrogen peroxide dependent conversion of coproheme via MMD to heme b and discuss differences between ChdCs from Actinobacteria and Firmicutes.

Correcting electrostatic artifacts due to net-charge changes in the calculation of ligand binding free energies

Alchemically derived free energies are artifacted when the perturbed moiety has a nonzero net charge. The source of the artifacts lies in the effective treatment of the electrostatic interactions within and between the perturbed atoms and remaining (partial) charges in the simulated system. To treat the electrostatic interactions effectively, lattice-summation (LS) methods or cutoff schemes in combination with a reaction-field contribution are usually employed. Both methods render the charging component of the calculated free energies sensitive to essential parameters of the system like the cutoff radius or the box side lengths. Here, we discuss the results of three previously published studies of ligand binding. These studies presented estimates of binding free energies that were artifacted due to the charged nature of the ligands. We show that the size of the artifacts can be efficiently calculated and raw simulation data can be corrected. We compare the corrected results with experimental estimates and nonartifacted estimates from path-sampling methods. Although the employed correction scheme involves computationally demanding continuum-electrostatics calculations, we show that the correction estimate can be deduced from a small sample of configurations rather than from the entire ensemble. This observation makes the calculations of correction terms feasible for complex biological systems. To show the general applicability of the proposed procedure, we also present results where the correction scheme was used to correct independent free energies obtained from simulations employing a cutoff scheme or LS electrostatics. In this work, we give practical guidelines on how to apply the appropriate corrections easily.

The effects of elevated intraabdominal pressure, hypercarbia, and positioning on the hemodynamic responses to laparoscopic colectomy in pigs

BACKGROUND

This study investigated three factors postulated to be sources of physiological stress in laparoscopic surgery: hypercarbia, elevated intraabdominal pressure, and the steep Trendelenburg position. Our research was designed to define the effects of each of these potential stressors on hemodynamic responses observed during laparoscopic colectomy in pigs.

METHODS

Twenty-four pigs were randomized into the following four groups, based on the method for obtaining surgical exposure while a colectomy or laparoscopic-assisted colectomy was performed: Open surgery (n = 6), CO2 pneumoperitoneum (n = 6), Helium pneumoperitoneum (n = 6), and abdominal wall Lifter (n = 6). The animals were paralyzed with minute ventilation adjusted. All animals underwent extensive pulmonary and hemodynamic monitoring with measurements of the following parameters: RR, Vt, minute ventilation, O2, sat, ETCO2, PVR, HR, MAP, CO, PAP, CVP, PCWP, SV, LVSWI, DO2, and VO2. The laparoscopic pigs were placed in the steep Trendelenburg position during surgery.

RESULTS

The effect of a CO pneumoperitoneum was to increase PaCO2 PVR and cause an acidemia that could not be prevented by an increase in minute ventilation. Elevated intraabdominal pressure decreased UO. Both pneumoperitoneum groups had a fourfold increase in IVCP, a measure of intraabdominal pressure. Some of this increase was due to placement into the Trendelenburg position; IVCP increased to a lesser degree in the Lifter group. The steep Trendelenburg position caused significant increases in PAP, CVP, and PCWP; however, a contributory effect of elevated intraabdominal pressure cannot be ruled out. None of these procedures had any significant effect on the HR or MAP. There was a significant increase in CO in the CO2 and Lifter groups; however, when CO was controlled for HR effects, there was no significant effect on SV from any of these different procedures. LVSWI, DO2, and VO2 were not affected by any of the different exposure methods.

CONCLUSIONS

The effects of laparoscopic surgery and open surgery on hemodynamic responses are minimal, and no one method is superior to another when performed in pigs that are healthy, hydrated, and hyperventilated to keep ETCO2 < 40. However, since elderly and sick patients have a lower threshold for physiologic decompensation, we can infer that the small hemodynamic changes noted in this study might become significant factors when surgery is performed on compromised patients. The finding that an abdominal wall lifting device causes the fewest metabolic and hemodynamic effects makes its use an important consideration when performing laparoscopic surgery in patients with cardiopulmonary compromise, hemodynamic instability, or any preexisting renal insufficiency.

A prospective comparison of laparoscopic exposure techniques for rectal mobilization and sigmoid resection

BACKGROUND

We determined the efficacy of a pneumoperitoneum and a gasless abdominal wall lifting device in providing exposure for low rectal mobilization and sigmoid resection in a swine model. The results of these laparoscopic techniques were compared with those obtained using standard open surgical methods.

STUDY DESIGN

We conducted a prospective randomized nonblinded trial. Twenty-four adult female pigs were randomized into three groups depending on exposure technique: group 1, open (n = 6); group 2, carbon dioxide (n = 6) or helium (n = 6) pneumoperitoneum; and group 3, a mechanical abdominal wall lifting device (n = 6). A low rectal mobilization and sigmoid resection with a double-stapled, circular, end-to-end anastomosis was performed in all pigs. In group 2, a laparoscopic-assisted approach was used. Parameters assessed included length of operation, length of the colonic specimen, number of lymph nodes per specimen, and extent of anterior and posterior rectal mobilization (centimeters from the anal verge).

RESULTS

Operative times were significantly shorter for group 1 than for group 2; no significant differences were found between the two laparoscopic subgroups. No significant difference was found in length of the colonic specimen or in number of lymph nodes harvested for each group. Extent of anterior and posterior rectal mobilization was also not significantly different for the three groups. Although mean mobilization lengths for each group were not significantly different, the range of values was broader in the laparoscopic groups.

CONCLUSIONS

A comparable mobilization and bowel resection can be performed laparoscopically, regardless of the exposure technique used. Gasless laparoscopy may prove useful in patients in whom pneumoperitoneum is contraindicated; it will not replace pneumoperitoneum as the only method for obtaining laparoscopic exposure because of the ease of use and frank superiority of the pneumoperitoneum in most circumstances. Abdominal wall lifting devices seem to be a reasonable alternative to pneumoperitoneum for sigmoid resection and rectal mobilization.