Observing many researchers using the same data and hypothesis reveals a hidden universe of uncertainty.

This study explores how researchers' analytical choices affect the reliability of scientific findings. Most discussions of reliability problems in science focus on systematic biases. We broaden the lens to emphasize the idiosyncrasy of conscious and unconscious decisions that researchers make during data analysis. We coordinated 161 researchers in 73 research teams and observed their research decisions as they used the same data to independently test the same prominent social science hypothesis: that greater immigration reduces support for social policies among the public. In this typical case of social science research, research teams reported both widely diverging numerical findings and substantive conclusions despite identical start conditions. Researchers' expertise, prior beliefs, and expectations barely predict the wide variation in research outcomes. More than 95% of the total variance in numerical results remains unexplained even after qualitative coding of all identifiable decisions in each team's workflow. This reveals a universe of uncertainty that remains hidden when considering a single study in isolation. The idiosyncratic nature of how researchers' results and conclusions varied is a previously underappreciated explanation for why many scientific hypotheses remain contested. These results call for greater epistemic humility and clarity in reporting scientific findings.

Reliability and validity of the medial standing overhead arm reach (SOAR) test as a measure of functional hip adduction motion.

OBJECTIVE: The Posterior Standing Overhead Arm Reach (SOAR) test has been previously reported as a reliable clinical measure of closed chain hip extension motion. The proposed Medial SOAR test expands on that testing approach to provide a similar measure of functional hip adduction motion. This was a preliminary intrarater and interrater reliability and validity study of the Medial SOAR test as a measure of functional hip adduction. DESIGN: Cross-sectional. SETTING: University motion analysis laboratory. PARTICIPANTS: Fifty hips were assessed in 25 (22 female) asymptomatic participants (mean age = 23.4 years, SD = 0.8). MAIN MEASURES: Maximum hip adduction during the Medial SOAR test was measured with a standard goniometer independently by two examiners. The test was also performed using three-dimensional motion capture. The intrarater and interrater reliability of the goniometric measure was determined using intraclass correlation coefficients, and the relationship between measures obtained via goniometry and three-dimensional motion capture was assessed with Pearson correlations and Bland-Altman analysis. RESULTS: Intrarater reliability (ICC2,3) was 0.88 (95% CI = 0.80-0.92) for Examiner 1 and 0.87 (95% CI = 0.79-0.92) for Examiner 2. The standard error of measurement and minimal detectable change were less than 3.0°. Interrater reliability demonstrated an intraclass correlation coefficient = 0.62 (95% CI = 0.28-0.79). Pearson correlations were significant with low-to-moderate associations (r = 0.49, P < 0.001; r = 0.24, P = 0.045). CONCLUSIONS: Similar to the previously reported Posterior SOAR test, the Medial SOAR test demonstrated acceptable intrarater and interrater reliability, along with low-to-moderate associations with three-dimensional motion capture. The Medial SOAR test has the potential to provide a reliable and accurate assessment of closed chain hip adduction.

Admission Pa o2 and Mortality Among PICU Patients and Select Diagnostic Subgroups.

OBJECTIVES: Evaluate the relationship between admission Pa o2 and mortality in a large multicenter dataset and among diagnostic subgroups. DESIGN: Retrospective cohort study. SETTING: North American PICUs participating in Virtual Pediatric Systems, LLC (VPS), 2015-2019. PATIENTS: Noncardiac patients 18 years or younger admitted to a VPS PICU with admission Pa o2 . INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Thirteen thousand seventy-one patient encounters were included with an overall mortality of 13.52%. Age categories were equally distributed among survivors and nonsurvivors with the exception of small differences among neonates and adolescents. Importantly, there was a tightly fitting quadratic relationship between admission Pa o2 and mortality, with the highest mortality rates seen among hypoxemic and hyperoxemic patients (likelihood-ratio test p < 0.001). This relationship persisted after adjustment for illness severity using modified Pediatric Index of Mortality 3 scores. A similar U-shaped relationship was demonstrated among patients with diagnoses of trauma, head trauma, sepsis, renal failure, hemorrhagic shock, and drowning. However, among the 1,500 patients admitted following cardiac arrest, there was no clear relationship between admission Pa o2 and mortality. CONCLUSIONS: In a large multicenter pediatric cohort, admission Pa o2 demonstrates a tightly fitting quadratic relationship with mortality. The persistence of this relationship among some but not all diagnostic subgroups suggests the pathophysiology of certain disease states may modify the hyperoxemia association.

Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS.

The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these benefits, it has been necessary to reformulate some of the most fundamental algorithms, including the Verlet list, pair searching, and cutoffs. Here, we present the heterogeneous parallelization and acceleration design of molecular dynamics implemented in the GROMACS codebase over the last decade. The setup involves a general cluster-based approach to pair lists and non-bonded pair interactions that utilizes both GPU and central processing unit (CPU) single instruction, multiple data acceleration efficiently, including the ability to load-balance tasks between CPUs and GPUs. The algorithm work efficiency is tuned for each type of hardware, and to use accelerators more efficiently, we introduce dual pair lists with rolling pruning updates. Combined with new direct GPU-GPU communication and GPU integration, this enables excellent performance from single GPU simulations through strong scaling across multiple GPUs and efficient multi-node parallelization.

Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies.

Human liver glycerol 3-phosphate dehydrogenase ( hlGPDH) catalyzes the reduction of dihydroxyacetone phosphate (DHAP) to form glycerol 3-phosphate, using the binding energy associated with the nonreacting phosphodianion of the substrate to properly orient the enzyme-substrate complex within the active site. Herein, we report the crystal structures for unliganded, binary E·NAD, and ternary E·NAD·DHAP complexes of wild type hlGPDH, illustrating a new position of DHAP, and probe the kinetics of multiple mutant enzymes with natural and truncated substrates. Mutation of Lys120, which is positioned to donate a proton to the carbonyl of DHAP, results in similar increases in the activation barrier to hlGPDH-catlyzed reduction of DHAP and to phosphite dianion-activated reduction of glycolaldehyde, illustrating that these transition states show similar interactions with the cationic K120 side chain. The K120A mutation results in a 5.3 kcal/mol transition state destabilization, and 3.0 kcal/mol of the lost transition state stabilization is rescued by 1.0 M ethylammonium cation. The 6.5 kcal/mol increase in the activation barrier observed for the D260G mutant hlGPDH-catalyzed reaction represents a 3.5 kcal/mol weakening of transition state stabilization by the K120A side chain and a 3.0 kcal/mol weakening of the interactions with other residues. The interactions, at the enzyme active site, between the K120 side chain and the Q295 and R269 side chains were likewise examined by double-mutant analyses. These results provide strong evidence that the enzyme rate acceleration is due mainly or exclusively to transition state stabilization by electrostatic interactions with polar amino acid side chains.

Sharing Data from Molecular Simulations.

Given the need for modern researchers to produce open, reproducible scientific output, the lack of standards and best practices for sharing data and workflows used to produce and analyze molecular dynamics (MD) simulations has become an important issue in the field. There are now multiple well-established packages to perform molecular dynamics simulations, often highly tuned for exploiting specific classes of hardware, each with strong communities surrounding them, but with very limited interoperability/transferability options. Thus, the choice of the software package often dictates the workflow for both simulation production and analysis. The level of detail in documenting the workflows and analysis code varies greatly in published work, hindering reproducibility of the reported results and the ability for other researchers to build on these studies. An increasing number of researchers are motivated to make their data available, but many challenges remain in order to effectively share and reuse simulation data. To discuss these and other issues related to best practices in the field in general, we organized a workshop in November 2018 ( https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/ ). Here, we present a brief overview of this workshop and topics discussed. We hope this effort will spark further conversation in the MD community to pave the way toward more open, interoperable, and reproducible outputs coming from research studies using MD simulations.

A cytoplasmic pathway for gapmer antisense oligonucleotide-mediated gene silencing in mammalian cells.

Antisense oligonucleotides (ASOs) are known to trigger mRNA degradation in the nucleus via an RNase H-dependent mechanism. We have now identified a putative cytoplasmic mechanism through which ASO gapmers silence their targets when transfected or delivered gymnotically (i.e. in the absence of any transfection reagent). We have shown that the ASO gapmers can interact with the Ago-2 PAZ domain and can localize into GW-182 mRNA-degradation bodies (GW-bodies). The degradation products of the targeted mRNA, however, are not generated by Ago-2-directed cleavage. The apparent identification of a cytoplasmic pathway complements the previously known nuclear activity of ASOs and concurrently suggests that nuclear localization is not an absolute requirement for gene silencing.

Involvement of phosphorylated Apis mellifera CREB in gating a honeybee's behavioral response to an external stimulus.

The transcription factor cAMP-response element-binding protein (CREB) is involved in neuronal plasticity. Phosphorylation activates CREB and an increased level of phosphorylated CREB is regarded as an indicator of CREB-dependent transcriptional activation. In honeybees(Apis mellifera)we recently demonstrated a particular high abundance of the phosphorylated honeybee CREB homolog (pAmCREB) in the central brain and in a subpopulation of mushroom body neurons. We hypothesize that these high pAmCREB levels are related to learning and memory formation. Here, we tested this hypothesis by analyzing brain pAmCREB levels in classically conditioned bees and bees experiencing unpaired presentations of conditioned stimulus (CS) and unconditioned stimulus (US). We demonstrate that both behavioral protocols display differences in memory formation but do not alter the level of pAmCREB in bee brains directly after training. Nevertheless, we report that bees responding to the CS during unpaired stimulus presentations exhibit higher levels of pAmCREB than nonresponding bees. In addition, Trichostatin A, a histone deacetylase inhibitor that is thought to enhance histone acetylation by CREB-binding protein, increases the bees' CS responsiveness. We conclude that pAmCREB is involved in gating a bee's behavioral response driven by an external stimulus.

Laboratory-Evolved Enzymes Provide Snapshots of the Development of Enantioconvergence in Enzyme-Catalyzed Epoxide Hydrolysis.

Engineered enzyme variants of potato epoxide hydrolase (StEH1) display varying degrees of enrichment of (2R)-3-phenylpropane-1,2-diol from racemic benzyloxirane. Curiously, the observed increase in the enantiomeric excess of the (R)-diol is not only a consequence of changes in enantioselectivity for the preferred epoxide enantiomer, but also to changes in the regioselectivity of the epoxide ring opening of (S)-benzyloxirane. In order to probe the structural origin of these differences in substrate selectivity and catalytic regiopreference, we solved the crystal structures for the evolved StEH1 variants. We used these structures as a starting point for molecular docking studies of the epoxide enantiomers into the respective active sites. Interestingly, despite the simplicity of our docking analysis, the apparent preferred binding modes appear to rationalize the experimentally determined regioselectivities. The analysis also identifies an active site residue (F33) as a potentially important interaction partner, a role that could explain the high conservation of this residue during evolution. Overall, our experimental, structural, and computational studies provide snapshots into the evolution of enantioconvergence in StEH1-catalyzed epoxide hydrolysis.

Cooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily.

It is becoming widely accepted that catalytic promiscuity, i.e., the ability of a single enzyme to catalyze the turnover of multiple, chemically distinct substrates, plays a key role in the evolution of new enzyme functions. In this context, the members of the alkaline phosphatase superfamily have been extensively studied as model systems in order to understand the phenomenon of enzyme multifunctionality. In the present work, we model the selectivity of two multiply promiscuous members of this superfamily, namely the phosphonate monoester hydrolases from Burkholderia caryophylli and Rhizobium leguminosarum. We have performed extensive simulations of the enzymatic reaction of both wild-type enzymes and several experimentally characterized mutants. Our computational models are in agreement with key experimental observables, such as the observed activities of the wild-type enzymes, qualitative interpretations of experimental pH-rate profiles, and activity trends among several active site mutants. In all cases the substrates of interest bind to the enzyme in similar conformations, with largely unperturbed transition states from their corresponding analogues in aqueous solution. Examination of transition-state geometries and the contribution of individual residues to the calculated activation barriers suggest that the broad promiscuity of these enzymes arises from cooperative electrostatic interactions in the active site, allowing each enzyme to adapt to the electrostatic needs of different substrates. By comparing the structural and electrostatic features of several alkaline phosphatases, we suggest that this phenomenon is a generalized feature driving selectivity and promiscuity within this superfamily and can be in turn used for artificial enzyme design.

Empirical valence bond simulations of the hydride transfer step in the monoamine oxidase B catalyzed metabolism of dopamine.

Monoamine oxidases (MAOs) A and B are flavoenzymes responsible for the metabolism of biogenic amines such as dopamine, serotonin and noradrenaline. In this work, we present a comprehensive study of the rate-limiting step of dopamine degradation by MAO B, which consists in the hydride transfer from the methylene group of the substrate to the flavin moiety of the FAD prosthetic group. This article builds on our previous quantum chemical study of the same reaction using a cluster model (Vianello et al., Eur J Org Chem 2012; 7057), but now considering the full dimensionality of the hydrated enzyme with extensive configurational sampling. We show that MAO B is specifically tuned to catalyze the hydride transfer step from the substrate to the flavin moiety of the FAD prosthetic group and that it lowers the activation barrier by 12.3 kcal mol⁻¹ compared to the same reaction in aqueous solution, a rate enhancement of more than nine orders of magnitude. Taking into account the deprotonation of the substrate prior to the hydride transfer reaction, the activation barrier in the enzyme is calculated to be 16.1 kcal mol⁻¹, in excellent agreement with the experimental value of 16.5 kcal mol⁻¹. Additionally, we demonstrate that the protonation state of the active site residue Lys296 does not have an influence on the hydride transfer reaction.

Energetic tuning by tRNA modifications ensures correct decoding of isoleucine and methionine on the ribosome.

Chemical modifications of tRNAs are critical for accurate translation of the genetic code on the ribosome. The discrimination between isoleucine (AUA) and methionine (AUG) codons depends on such modifications of the wobble position in isoleucine tRNA anticodon loops, in all kingdoms of life. Bacteria and archaea employ functionally similar lysine- and agmatine-conjugated cytidine derivatives to ensure decoding fidelity, but the thermodynamics underlying codon discrimination remains unknown. Here, we report structure-based computer simulations that quantitatively reveal the energetics of this decoding strategy in archaea. The results further show that the agmatidine modification confers tRNA specificity primarily by desolvation of the incorrect codon in the non-cognate complex. Tautomerism is found to play no significant role in this decoding system as the usual amino form of the modified tRNA is by far the most stable.

Emerging Applications and Regulatory Strategies for Advanced Medicines Manufacturing - Towards the Development of a Platform Approach.

The last decade has seen Advanced Medicines Manufacturing (AMM) progress from isolated product developments to the creation of industry-academic centres of excellence, regulatory innovation progressing leading to new standards, and product commercialisation across multiple product formats. This paper examines these developments focusing on successful applications and strategies presented at the 2023 Symposium of the International Consortium for Advanced Medicines Manufacturing (ICAMM). Despite these exemplar applications, there remain significant challenges to the sector-wide adoption of AMM technologies. Drawing on Symposium delegate expert responses to open-ended questions, our coding-based thematic analysis suggest three primary enablers drive successful adoption of AMM technologies at scale, namely: the ability to leverage pre-competitive collaborations to challenge-based problem solving; information and knowledge sharing through centres of excellence; and the development of AMM specific regulatory standards. Further analysis of expert responses identified the emergence of a 'Platform creation' approach to AMM innovation; characterised by: i) New collaboration modes; ii) Exploration of common product-process platforms for new dosage forms and therapy areas; iii) Development of modular equipment assets that enable scale-out, and offer more decentralized or distributed manufacturing models; iv) Standards based on product-process platform archetypes; v) Implementation strategies where platform-thinking and AMM technologies can significantly reduce timelines between discovery, approval and GMP readiness. We provide a definition of the Platform creation concept for AMM and discuss the requirements for its systematic development.

Discovery of potent and efficacious urea-containing nicotinamide phosphoribosyltransferase (NAMPT) inhibitors with reduced CYP2C9 inhibition properties.

Potent, reversible inhibition of the cytochrome P450 CYP2C9 isoform was observed in a series of urea-containing nicotinamide phosphoribosyltransferase (NAMPT) inhibitors. This unwanted property was successfully removed from the described inhibitors through a combination of structure-based design and medicinal chemistry activities. An optimized compound which did not inhibit CYP2C9 exhibited potent anti-NAMPT activity (17; BC NAMPT IC50=3 nM; A2780 antiproliferative IC50=70 nM), good mouse PK properties, and was efficacious in an A2780 mouse xenograft model. The crystal structure of this compound in complex with the NAMPT protein is also described.

Identification of amides derived from 1H-pyrazolo[3,4-b]pyridine-5-carboxylic acid as potent inhibitors of human nicotinamide phosphoribosyltransferase (NAMPT).

Potent, 1H-pyrazolo[3,4-b]pyridine-containing inhibitors of the human nicotinamide phosphoribosyltransferase (NAMPT) enzyme were identified using structure-based design techniques. Many of these compounds exhibited nanomolar antiproliferation activities against human tumor lines in in vitro cell culture experiments, and a representative example (compound 26) demonstrated encouraging in vivo efficacy in a mouse xenograft tumor model derived from the A2780 cell line. This molecule also exhibited reduced rat retinal exposures relative to a previously studied imidazo-pyridine-containing NAMPT inhibitor. Somewhat surprisingly, compound 26 was only weakly active in vitro against mouse and monkey tumor cell lines even though it was a potent inhibitor of NAMPT enzymes derived from these species. The compound also exhibited only minimal effects on in vivo NAD levels in mice, and these changes were considerably less profound than those produced by an imidazo-pyridine-containing NAMPT inhibitor. The crystal structures of compound 26 and the corresponding PRPP-derived ribose adduct in complex with NAMPT were also obtained.

Communicating With Unconscious Patients: An Overview.

BACKGROUND: Nurses are told to speak to their unconscious patients because hearing is said to be the last sense to depart. There was little reliable evidence before the 1990s that patients in an unconscious state could hear and understand what was being said. That led to reluctance on the part of health professionals to communicate with these unresponsive patients. OBJECTIVE: This historical overview aims to present researched evidence from the 1990s to the present detailing awareness that occurs in unconscious patients, when that awareness increases, and how to detect that awareness. It also includes research about the benefits of communicating with unconscious patients and descriptions of how registered nurses and other health care professionals, from a postsurvey after a continuing education course on experiences of unconscious patients, plan to communicate with unconscious patients. METHODS: A literature search was conducted, which included more than 150 articles and books about experiences of unconscious patients in several electronic databases, including PubMed, CINAHL, and the British Nursing Index. In addition, an analysis of 105 postcourse responses by registered nurses (89%) and other health professionals (11%), licensed practical nurses, emergency medical technicians, and cardiac technicians after taking a continuing education course on experiences of previously unconscious patients were analyzed. RESULTS: The Glasgow Coma Scale and the Full Outline of Unresponsiveness scale are helpful behavioral tools to identify levels of coma but miss detecting awareness in patients who can hear and understand but cannot move. The estimates are that 25% to 40% (J Trauma. 1975;15:94-98; J Neurosci Nurs. 1988;20:223-228; J Neurosci Nurs. 1990;22(1):52-53; Am J Crit Care. 1995;3:227-232) of patients diagnosed with a disorder of consciousness can hear and understand what is being said in their environment. Substantial evidence supports that isolation and loneliness, such as experienced by some patients perceived to be unaware, can be physically and psychologically harmful. CONCLUSIONS: Strong evidence shows that some patients diagnosed as being in a vegetative state can hear and understand what is being said in their environment. Interviews with previously unconscious patients and electrophysiological methods show that awareness can be detected in patients perceived to be unconscious. There is documented evidence that patients experience awareness when going into unconsciousness, even when they appear unaware and when moved. To our knowledge, these times have not been researched using electrophysiological devices but established from interviews.

Obtaining optical purity for product diols in enzyme-catalyzed epoxide hydrolysis: contributions from changes in both enantio- and regioselectivity.

Enzyme variants of the plant epoxide hydrolase StEH1 displaying improved stereoselectivities in the catalyzed hydrolysis of (2,3-epoxypropyl)benzene were generated by directed evolution. The evolution was driven by iterative saturation mutagenesis in combination with enzyme activity screenings where product chirality was the decisive selection criterion. Analysis of the underlying causes of the increased diol product ratios revealed two major contributing factors: increased enantioselectivity for the corresponding epoxide enantiomer(s) and, in some cases, a concomitant change in regioselectivity in the catalyzed epoxide ring-opening half-reaction. Thus, variant enzymes that catalyzed the hydrolysis of racemic (2,3-epoxypropyl)benzene into the R-diol product in an enantioconvergent manner were isolated.

A preliminary study of the reliability and validity of the Posterior Standing Overhead Arm Reach (SOAR) test as a measure of functional hip extension motion.

BACKGROUND: Current clinical tests do not provide a method to reliably measure closed chain hip extension. We developed the Posterior Standing Overhead Arm Reach (SOAR) test for this purpose. OBJECTIVES: This was a preliminary intrarater and interrater reliability and validity study of the Posterior SOAR test as a measure of functional hip extension. DESIGN: Cross-sectional. METHOD: Hip extension on the Posterior SOAR test was measured with a standard goniometer independently by two examiners. The test was then repeated using three-dimensional (3D) motion capture. Intraclass correlation coefficients (ICC) were used to determine the intrarater and interrater reliability of the goniometric measure and Pearson correlations were used to assess the relationship between measures obtained via goniometry and 3D motion capture. RESULTS: Fifty hips were assessed in 25 (14 female, 11 male) asymptomatic participants (mean age = 24.0 years, SD = 1.1). Intrarater reliability (ICC2,3) was 0.80 (95% CI = 0.68-0.88) for Examiner 1 and 0.77 (95% CI = 0.64-0.86) for Examiner 2, indicating excellent reliability. The standard error of the measure (SEM90) ranged from 2.5° to 3.0° with a minimal detectable change (MDC90) of 3.5° to 4.2°. Interrater reliability was good with ICC = 0.65 (95% CI = 0.36-0.80). Pearson correlations were significant with low to moderate associations (r = 0.36, P = 0.009; r = 0.51, P < 0.001). CONCLUSIONS: The Posterior SOAR test demonstrated excellent intrarater reliability, good interrater reliability, and low to moderate associations with 3D motion capture. The Posterior SOAR test has the potential to provide a reliable and accurate assessment of closed chain hip extension.

Best Practices in Constant pH MD Simulations: Accuracy and Sampling.

Various approaches have been proposed to include the effect of pH in molecular dynamics (MD) simulations. Among these, the λ-dynamics approach proposed by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys. 1996, 105, 2414-2423] can be performed with little computational overhead and hfor each typeence be used to routinely perform MD simulations at microsecond time scales, as shown in the accompanying paper [Aho, N. et al. J. Chem. Theory Comput. 2022, DOI: 10.1021/acs.jctc.2c00516]. At such time scales, however, the accuracy of the molecular mechanics force field and the parametrization becomes critical. Here, we address these issues and provide the community with guidelines on how to set up and perform long time scale constant pH MD simulations. We found that barriers associated with the torsions of side chains in the CHARMM36m force field are too high for reaching convergence in constant pH MD simulations on microsecond time scales. To avoid the high computational cost of extending the sampling, we propose small modifications to the force field to selectively reduce the torsional barriers. We demonstrate that with such modifications we obtain converged distributions of both protonation and torsional degrees of freedom and hence consistent pKa estimates, while the sampling of the overall configurational space accessible to proteins is unaffected as compared to normal MD simulations. We also show that the results of constant pH MD depend on the accuracy of the correction potentials. While these potentials are typically obtained by fitting a low-order polynomial to calculated free energy profiles, we find that higher order fits are essential to provide accurate and consistent results. By resolving problems in accuracy and sampling, the work described in this and the accompanying paper paves the way to the widespread application of constant pH MD beyond pKa prediction.

Scalable Constant pH Molecular Dynamics in GROMACS.

Molecular dynamics (MD) computer simulations are used routinely to compute atomistic trajectories of complex systems. Systems are simulated in various ensembles, depending on the experimental conditions one aims to mimic. While constant energy, temperature, volume, and pressure are rather straightforward to model, pH, which is an equally important parameter in experiments, is more difficult to account for in simulations. Although a constant pH algorithm based on the λ-dynamics approach by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414-2423] was implemented in a fork of the GROMACS molecular dynamics program, uptake has been rather limited, presumably due to the poor scaling of that code with respect to the number of titratable sites. To overcome this limitation, we implemented an alternative scheme for interpolating the Hamiltonians of the protonation states that makes the constant pH molecular dynamics simulations almost as fast as a normal MD simulation with GROMACS. In addition, we implemented a simpler scheme, called multisite representation, for modeling side chains with multiple titratable sites, such as imidazole rings. This scheme, which is based on constraining the sum of the λ-coordinates, not only reduces the complexity associated with parametrizing the intramolecular interactions between the sites but also is easily extendable to other molecules with multiple titratable sites. With the combination of a more efficient interpolation scheme and multisite representation of titratable groups, we anticipate a rapid uptake of constant pH molecular dynamics simulations within the GROMACS user community.