Substrate-independent activation pathways of the CRISPR-Cas9 HNH nuclease.

A hallmark of tightly regulated high-fidelity enzymes is that they become activated only after encountering cognate substrates, often by an induced-fit mechanism rather than conformational selection. Upon analysis of molecular dynamics trajectories, we recently discovered that the Cas9 HNH domain exists in three conformations: 1) Y836 (which is two residues away from the catalytic D839 and H840 residues) is hydrogen bonded to the D829 backbone amide, 2) Y836 is hydrogen bonded to the backbone amide of D861 (which is one residue away from the third catalytic residue N863), and 3) Y836 is not hydrogen bonded to either residue. Each of the three conformers differs from the active state of HNH. The conversion between the inactive and active states involves a local unfolding-refolding process that displaces the Cα and side chain of the catalytic N863 residue by ∼5 Å and ∼10 Å, respectively. In this study, we report the two largest principal components of coordinate variance of the HNH domain throughout molecular dynamics trajectories to establish the interconversion pathways of these conformations. We show that conformation 2 is an obligate step between conformations 1 and 3, which are not directly interconvertible without conformation 2. The loss of hydrogen bonding of the Y836 side chain in conformation 3 likely plays an essential role in activation during local unfolding-refolding of an α-helix containing the catalytic N863. Three single Lys-to-Ala mutants appear to eliminate this substrate-independent activation pathway of the wild-type HNH nuclease, thereby enhancing the fidelity of HNH cleavage.

MDiGest: A Python package for describing allostery from molecular dynamics simulations.

Many biological processes are regulated by allosteric mechanisms that communicate with distant sites in the protein responsible for functionality. The binding of a small molecule at an allosteric site typically induces conformational changes that propagate through the protein along allosteric pathways regulating enzymatic activity. Elucidating those communication pathways from allosteric sites to orthosteric sites is, therefore, essential to gain insights into biochemical processes. Targeting the allosteric pathways by mutagenesis can allow the engineering of proteins with desired functions. Furthermore, binding small molecule modulators along the allosteric pathways is a viable approach to target reactions using allosteric inhibitors/activators with temporal and spatial selectivity. Methods based on network theory can elucidate protein communication networks through the analysis of pairwise correlations observed in molecular dynamics (MD) simulations using molecular descriptors that serve as proxies for allosteric information. Typically, single atomic descriptors such as α-carbon displacements are used as proxies for allosteric information. Therefore, allosteric networks are based on correlations revealed by that descriptor. Here, we introduce a Python software package that provides a comprehensive toolkit for studying allostery from MD simulations of biochemical systems. MDiGest offers the ability to describe protein dynamics by combining different approaches, such as correlations of atomic displacements or dihedral angles, as well as a novel approach based on the correlation of Kabsch-Sander electrostatic couplings. MDiGest allows for comparisons of networks and community structures that capture physical information relevant to allostery. Multiple complementary tools for studying essential dynamics include principal component analysis, root mean square fluctuation, as well as secondary structure-based analyses.

Distinct allosteric pathways in imidazole glycerol phosphate synthase from yeast and bacteria.

Understanding the relationship between protein structures and their function is still an open question that becomes very challenging when allostery plays an important functional role. Allosteric proteins, in fact, exploit different ranges of motions (from sidechain local fluctuations to long-range collective motions) to effectively couple distant binding sites, and of particular interest is whether allosteric proteins of the same families with similar functions and structures also necessarily share the same allosteric mechanisms. Here, we compared the early dynamics initiating the allosteric communication of a prototypical allosteric enzyme from two different organisms, i.e., the imidazole glycerol phosphate synthase (IGPS) enzymes from the thermophilic bacteria and the yeast, working at high and room temperatures, respectively. By combining molecular dynamics simulations and network models derived from graph theory, we found rather distinct early allosteric dynamics in the IGPS from the two organisms, involving significatively different allosteric pathways in terms of both local and collective motions. Given the successful prediction of key allosteric residues in the bacterial IGPS, whose mutation disrupts its allosteric communication, the outcome of this study paves the way for future experimental studies on the yeast IGPS that could foster therapeutic applications by exploiting the control of IGPS enzyme allostery.

Insights into Binding of Single-Stranded Viral RNA Template to the Replication-Transcription Complex of SARS-CoV-2 for the Priming Reaction from Molecular Dynamics Simulations.

A minimal replication-transcription complex (RTC) of SARS-CoV-2 for synthesis of viral RNAs includes the nsp12 RNA-dependent RNA polymerase and two nsp8 RNA primase subunits for de novo primer synthesis, one nsp8 in complex with its accessory nsp7 subunit and the other without it. The RTC is responsible for faithfully copying the entire (+) sense viral genome from its first 5'-end to the last 3'-end nucleotides through a replication-intermediate (RI) template. The single-stranded (ss) RNA template for the RI is its 33-nucleotide 3'-poly(A) tail adjacent to a well-characterized secondary structure. The ssRNA template for viral transcription is a 5'-UUUAU-3' next to stem-loop (SL) 1'. We analyze the electrostatic potential distribution of the nsp8 subunit within the RTC around the template strand of the primer/template (P/T) RNA duplex in recently published cryo-EM structures to address the priming reaction using the viral poly(A) template. We carried out molecular dynamics (MD) simulations with a P/T RNA duplex, the viral poly(A) template, or a generic ssRNA template. We find evidence that the viral poly(A) template binds similarly to the template strand of the P/T RNA duplex within the RTC, mainly through electrostatic interactions, providing new insights into the priming reaction by the nsp8 subunit within the RTC, which differs significantly from the existing proposal of the nsp7/nsp8 oligomer formed outside the RTC. High-order oligomerization of nsp8 and nsp7 for SARS-CoV observed outside the RTC of SARS-CoV-2 is not found in the RTC and not likely to be relevant to the priming reaction.

Structural Basis for Reduced Dynamics of Three Engineered HNH Endonuclease Lys-to-Ala Mutants for the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Associated 9 (CRISPR/Cas9) Enzyme.

Many bacteria possess type-II immunity against invading phages or plasmids known as the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) system to detect and degrade the foreign DNA sequences. The Cas9 protein has two endonucleases responsible for double-strand breaks (the HNH domain for cleaving the target strand of DNA duplexes and RuvC domain for the nontarget strand, respectively) and a single-guide RNA-binding domain where the RNA and target DNA strands are base-paired. Three engineered single Lys-to-Ala HNH mutants (K810A, K848A, and K855A) exhibit an enhanced substrate specificity for cleavage of the target DNA strand. We report in this study that in the wild-type (wt) enzyme, D835, Y836, and D837 within the Y836-containing loop (comprising E827-D837) adjacent to the catalytic site have uncharacterizable broadened 1H15N nuclear magnetic resonance (NMR) features, whereas remaining residues in the loop have different extents of broadened NMR spectra. We find that this loop in the wt enzyme exhibits three distinct conformations over the duration of the molecular dynamics simulations, whereas the three Lys-to-Ala mutants retain only one conformation. The versatility of multiple alternate conformations of this loop in the wt enzyme could help to recruit noncognate DNA substrates into the HNH active site for cleavage, thereby reducing its substrate specificity relative to the three mutants. Our study provides further experimental and computational evidence that Lys-to-Ala substitutions reduce dynamics of proteins and thus increase their stability.

Structural Insights into Binding of Remdesivir Triphosphate within the Replication-Transcription Complex of SARS-CoV-2.

Remdesivir is an adenosine analogue that has a cyano substitution in the C1' position of the ribosyl moiety and a modified base structure to stabilize the linkage of the base to the C1' atom with its strong electron-withdrawing cyano group. Within the replication-transcription complex (RTC) of SARS-CoV-2, the RNA-dependent RNA polymerase nsp12 selects remdesivir monophosphate (RMP) over adenosine monophosphate (AMP) for nucleotide incorporation but noticeably slows primer extension after the added RMP of the RNA duplex product is translocated by three base pairs. Cryo-EM structures have been determined for the RTC with RMP at the nucleotide-insertion (i) site or at the i + 1, i + 2, or i + 3 sites after product translocation to provide a structural basis for a delayed-inhibition mechanism by remdesivir. In this study, we applied molecular dynamics (MD) simulations to extend the resolution of structures to the measurable maximum that is intrinsically limited by MD properties of these complexes. Our MD simulations provide (i) a structural basis for nucleotide selectivity of the incoming substrates of remdesivir triphosphate over adenosine triphosphate and of ribonucleotide over deoxyribonucleotide, (ii) new detailed information on hydrogen atoms involved in H-bonding interactions between the enzyme and remdesivir, and (iii) direct information on the catalytically active complex that is not easily captured by experimental methods. Our improved resolution of interatomic interactions at the nucleotide-binding pocket between remedesivir and the polymerase could help to design a new class of anti-SARS-CoV-2 inhibitors.

How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM.

The atomic coordinates derived from cryo-electron microscopy (cryo-EM) maps can be inaccurate when the voxel scaling factors are not properly calibrated. Here, we describe a method for correcting relative voxel scaling factors between pairs of cryo-EM maps for the same or similar structures that are expanded or contracted relative to each other. We find that the correction of scaling factors reduces the amplitude differences of Fourier-inverted structure factors from voxel-rescaled maps by up to 20-30%, as shown by two cryo-EM maps of the SARS-CoV-2 spike protein measured at pH 4.0 and pH 8.0. This allows for the calculation of the difference map after properly scaling, revealing differences between the two structures for individual amino acid residues. Unexpectedly, the analysis uncovers two previously overlooked differences of amino acid residues in structures and their local structural changes. Furthermore, we demonstrate the method as applied to two cryo-EM maps of monomeric apo-photosystem II from the cyanobacteria Synechocystis sp. PCC 6803 and Thermosynechococcus elongatus. The resulting difference maps reveal many changes in the peripheral transmembrane PsbX subunit between the two species.

Chasing unphysical TD-DFT excited states in transition metal complexes with a simple diagnostic tool.

Transition Metal Complexes (TMCs) are known for the rich variety of their excited states showing different nature and degrees of locality. Describing the energies of these excited states with the same degree of accuracy is still problematic when using time-dependent density functional theory in conjunction with the most current density functional approximations. In particular, the presence of unphysically low lying excited states possessing a relevant Charge Transfer (CT) character may significantly affect the spectra computed at such a level of theory and, more relevantly, the interpretation of their photophysical behavior. In this work, we propose an improved version of the MAC index, recently proposed by the authors and collaborators, as a simple and computationally inexpensive diagnostic tool that can be used for the detection and correction of the unphysically predicted low lying excited states. The analysis, performed on five prototype TMCs, shows that spurious and ghost states can appear in a wide spectral range and that it is difficult to detect them only on the basis of their CT extent. Indeed, both delocalization of the excited state and CT extent are criteria that must be combined, as in the MAC index, to detect unphysical states.

Increasing the Cytotoxicity of Ru(II) Polypyridyl Complexes by Tuning the Electronic Structure of Dioxo Ligands.

Due to the great potential expressed by an anticancer drug candidate previously reported by our group, namely, Ru-sq ([Ru(DIP)2(sq)](PF6) (DIP, 4,7-diphenyl-1,10-phenanthroline; sq, semiquinonate ligand), we describe in this work a structure-activity relationship (SAR) study that involves a broader range of derivatives resulting from the coordination of different catecholate-type dioxo ligands to the same Ru(DIP)2 core. In more detail, we chose catechols carrying either an electron-donating group (EDG) or an electron-withdrawing group (EWG) and investigated the physicochemical and biological properties of their complexes. Several pieces of experimental evidences demonstrated that the coordination of catechols bearing EDGs led to deep-red positively charged complexes 1-4 in which the preferred oxidation state of the dioxo ligand is the uninegatively charged semiquinonate. Complexes 5 and 6, on the other hand, are blue/violet neutral complexes, which carry an EWG-substituted dinegatively charged catecholate ligand. The biological investigation of complexes 1-6 led to the conclusion that the difference in their physicochemical properties has a strong impact on their biological activity. Thus, complexes 1-4 expressed much higher cytotoxicities than complexes 5 and 6. Complex 1 constitutes the most promising compound in the series and was selected for a more in depth biological investigation. Apart from its remarkably high cytotoxicity (IC50 = 0.07-0.7 µM in different cancerous cell lines), complex 1 was taken up by HeLa cells very efficiently by a passive transportation mechanism. Moreover, its moderate accumulation in several cellular compartments (i.e., nucleus, lysosomes, mitochondria, and cytoplasm) is extremely advantageous in the search for a potential drug with multiple modes of action. Further DNA metalation and metabolic studies pointed to the direct interaction of complex 1 with DNA and to the severe impairment of the mitochondrial function. Multiple targets, together with its outstanding cytotoxicity, make complex 1 a valuable candidate in the field of chemotherapy research. It is noteworthy that a preliminary biodistribution study on healthy mice demonstrated the suitability of complex 1 for further in vivo studies.

Rationally Designed Long-Wavelength Absorbing Ru(II) Polypyridyl Complexes as Photosensitizers for Photodynamic Therapy.

The utilization of photodynamic therapy (PDT) for the treatment of various types of cancer has gained increasing attention over the last decades. Despite the clinical success of approved photosensitizers (PSs), their application is sometimes limited due to poor water solubility, aggregation, photodegradation, and slow clearance from the body. To overcome these drawbacks, research efforts are devoted toward the development of metal complexes and especially Ru(II) polypyridine complexes based on their attractive photophysical and biological properties. Despite the recent research developments, the vast majority of complexes utilize blue or UV-A light to obtain a PDT effect, limiting the penetration depth inside tissues and, therefore, the possibility to treat deep-seated or large tumors. To circumvent these drawbacks, we present the first example of a DFT guided search for efficient PDT PSs with a substantial spectral red shift toward the biological spectral window. Thanks to this design, we have unveiled a Ru(II) polypyridine complex that causes phototoxicity in the very low micromolar to nanomolar range at clinically relevant 595 nm, in monolayer cells as well as in 3D multicellular tumor spheroids.

Using density based indexes to characterize excited states evolution.

With the aim of offering new computational tools helping in the description of photochemical reactions and phenomena occurring at the excited state, we present in this work the capability of a density based index (Π) in locating decay channels from higher to lower excited states. The Π index, previously applied to disclose non-radiative decay channels from the first excited state to the ground state, is very simple in its formulation and can be evaluated, practically with no extra computational cost, and coupled to any quantum method able to provide excited states densities. Indeed, this index relies only on the knowledge of energetics and electron densities of the different electronic states involved in the decay. In the present work, we show the proficiency of the Π index in the general case of decay between excited states by applying it to two model systems well characterized both theoretically and experimentally. In both cases, this descriptor was successful in spotting the regions where excited states are more likely to decay, thus suggesting its potential interest for further application in the design of new compounds. © 2018 Wiley Periodicals, Inc.

A Ru(II) polypyridyl complex bearing aldehyde functions as a versatile synthetic precursor for long-wavelength absorbing photodynamic therapy photosensitizers.

The use of Photodynamic Therapy (PDT) for the treatment of several kinds of cancer as well as bacterial, fungal or viral infections has received increasing attention during the last decade. However, the currently clinically approved photosensitizers (PSs) have several drawbacks, including photobleaching, slow clearance from the organism and poor water solubility. To overcome these shortcomings, many efforts have been made in the development of new types of PSs, such as Ru(II) polypyridyl complexes. Nevertheless, most studied Ru(II) polypyridyl complexes have a low absorbance in the spectral therapeutic window. In this work, we show that, by carefully selecting substituents on the polypyridyl complex, it is possible to prepare a complex absorbing at a much higher wavelength. Specifically, we report on the synthesis as well as in-depth experimental and theoretical characterisation of a Ru(II) polypyridyl complex (complex 3) combining a shift in absorbance towards the spectral therapeutic window with a high 1O2 production. To overcome the absence or poor selectivity of most approved PSs into targeted cells/bacteria, they can be linked to targeting moieties. In this line, compound 3 was designed with reactive aldehyde groups, which can be used as a highly versatile synthetic precursor for further conjugation. As a proof of concept, 3 was reacted with benzylamine and the stability of the resulting conjugate 4 was investigated in DMSO, PBS and cell media. 4 showed an impressive ability to act as a PDT PS with no measurable dark cytotoxicity and photocytotoxicity in the low micromolar range against cancerous HeLa cells from 450 nm up to 540 nm.

How are the charge transfer descriptors affected by the quality of the underpinning electronic density?

With the aim of investigating qualitatively and quantitatively the impact of using excited state relaxed or unrelaxed density for the estimation of nature and characteristic of electronic excited states, we analyzed the behavior of 52 exchange correlation functionals for the prediction of density-based indexes such as those recently introduced in literature to evaluate the charge transfer distance (DCT ) (Le Bahers et al. J. Chem. Theory Comput. 2011, 7, 2498) in the case of a prototype family of push-pull dyes. Our results show that while a qualitatively consistent assessment of the nature of the excited states is obtained using either the unrelaxed or the relaxed density, from a quantitative standpoint we observe large discrepancies in the charge transfer distance for electronic transitions having substantial CT character. This behavior is independent of nature of the exchange-correlation functional used. © 2018 Wiley Periodicals, Inc.

Using Density Based Indexes and Wave Function Methods for the Description of Excited States: Excited State Proton Transfer Reactions as a Test Case.

To provide tools to interpret photochemical reactions, in this paper we demonstrate how a recently developed density-based index (DCT), up to now used in conjunction with time dependent density functional theory methods, can be extended to multiconfigurational methods. This index can guide chemists in the interpretation of photochemical reactions providing a measure of the spatial extent of a photoinduced charge transfer and, more generally, of charge transfer phenomena. This qualitative and quantitative description can be particularly relevant in the case of multiconfigurational calculations providing a simple tool for the interpretation of their complex outputs. To prove the potentiality of this approach we have considered a simple intramolecular excited state proton transfer reaction as study case and applied both wave function (CASSCF-CASPT2) and density-based methods in conjunction with a DCT analysis. Our results confirm that, also in the case of multiconfigurational methods, the DCT provides very useful information about the structural reorganization of a molecule at the excited state.

Charge transfer excitations in TDDFT: A ghost-hunter index.

This work presents a new index, MAC , enabling the on-the-fly detection of ghost charge transfer (CT) states, a major problem in time-dependent density-functional theory calculations. This computationally inexpensive index, derived as a modification of the Mulliken estimation of transition energy for CT excitations, relies on two basic ingredients: an effective CT distance, computed using our density-based index (DCT ), and an orbital weighted estimation of the Ionization Potential and Electron Affinity. Some model systems, representative of both intermolecular and intramolecular CT excitations, were chosen as test cases. The robustness of our approach was verified by analyzing the behavior of functionals belonging to different classes (GGA, global hybrids and range separated hybrids). The results obtained show that ghost states are correctly spotted, also in the delicate case of intramolecular excitations displaying substantial donor-bridge-acceptor delocalization, in a regime for which the standard Mulliken formulation attends its limits. © 2017 Wiley Periodicals, Inc.

Kernel-elastic autoencoder for molecular design.

We introduce the kernel-elastic autoencoder (KAE), a self-supervised generative model based on the transformer architecture with enhanced performance for molecular design. KAE employs two innovative loss functions: modified maximum mean discrepancy (m-MMD) and weighted reconstruction (LWCEL). The m-MMD loss has significantly improved the generative performance of KAE when compared to using the traditional Kullback-Leibler loss of VAE, or standard maximum mean discrepancy. Including the weighted reconstruction loss LWCEL, KAE achieves valid generation and accurate reconstruction at the same time, allowing for generative behavior that is intermediate between VAE and autoencoder not available in existing generative approaches. Further advancements in KAE include its integration with conditional generation, setting a new state-of-the-art benchmark in constrained optimizations. Moreover, KAE has demonstrated its capability to generate molecules with favorable binding affinities in docking applications, as evidenced by AutoDock Vina and Glide scores, outperforming all existing candidates from the training dataset. Beyond molecular design, KAE holds promise to solve problems by generation across a broad spectrum of applications.

A salt bridge of the C-terminal carboxyl group regulates PHPT1 substrate affinity and catalytic activity.

PHPT1 is a histidine phosphatase that modulates signaling in eukaryotes through its catalytic activity. Here, we present an analysis of the structure and dynamics of PHPT1 through a combination of solution NMR, molecular dynamics, and biochemical experiments. We identify a salt bridge formed between the R78 guanidinium moiety and the C-terminal carboxyl group on Y125 that is critical for ligand binding. Disruption of the salt bridge by appending a glycine residue at the C-terminus (G126) leads to a decrease in catalytic activity and binding affinity for the pseudo substrate, para-nitrophenylphosphate (pNPP), as well as the active site inhibitor, phenylphosphonic acid (PPA). We show through NMR chemical shift, 15N relaxation measurements, and analysis of molecular dynamics trajectories, that removal of this salt bridge results in an active site that is altered both structurally and dynamically thereby significantly impacting enzymatic function and confirming the importance of this electrostatic interaction.

Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism.

The receptor-binding domains (RBDs) of the SARS-CoV-2 spike trimer exhibit "up" and "down" conformations often targeted by neutralizing antibodies. Only in the "up" configuration can RBDs bind to the ACE2 receptor of the host cell and initiate the process of viral multiplication. Here, we identify a lead compound (3-oxo-valproate-coenzyme A conjugate or Val-CoA) that stabilizes the spike trimer with RBDs in the down conformation. Val-CoA interacts with three R408 residues, one from each RBD, which significantly reduces the inter-subunit R408-R408 distance by ∼ 13 Å and closes the central pore formed by the three RBDs. Experimental evidence is presented that R408 is part of a triggering mechanism that controls the prefusion to postfusion state transition of the spike trimer. By stabilizing the RBDs in the down configuration, this and other related compounds can likely attenuate viral transmission. The reported findings for binding of Val-CoA to the spike trimer suggest a new approach for the design of allosteric antiviral drugs that do not have to compete for specific virus-receptor interactions but instead hinder the conformational motion of viral membrane proteins essential for interaction with the host cell. Here, we introduce an approach to target the spike protein by identifying lead compounds that stabilize the RBDs in the trimeric "down" configuration. When these compounds trimerize monomeric RBD immunogens as co-immunogens, they could also induce new types of non-ACE2 blocking antibodies that prevent local cell-to-cell transmission of the virus, providing a novel approach for inhibition of SARS-CoV-2.

Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase.

Allosteric drugs have the potential to revolutionize biomedicine due to their enhanced selectivity and protection against overdosage. However, we need to better understand allosteric mechanisms in order to fully harness their potential in drug discovery. In this study, molecular dynamics simulations and nuclear magnetic resonance spectroscopy are used to investigate how increases in temperature affect allostery in imidazole glycerol phosphate synthase. Results demonstrate that temperature increase triggers a cascade of local amino acid-to-amino acid dynamics that remarkably resembles the allosteric activation that takes place upon effector binding. The differences in the allosteric response elicited by temperature increase as opposed to effector binding are conditional to the alterations of collective motions induced by either mode of activation. This work provides an atomistic picture of temperature-dependent allostery, which could be harnessed to more precisely control enzyme function.

MptpA Kinetics Enhanced by Allosteric Control of an Active Conformation.

Understanding allostery in the Mycobacterium tuberculosis low molecular weight protein tyrosine phosphatase (MptpA) is a subject of great interest since MptpA is one of two protein tyrosine phosphatases (PTPs) from the pathogenic organism Mycobacterium tuberculosis expressed during host cell infection. Here, we combine computational modeling with solution NMR spectroscopy and we find that Q75 is an allosteric site. Removal of the polar side chain of Q75 by mutation to leucine results in a cascade of events that reposition the acid loop over the active site and relocates the catalytic aspartic acid (D126) at an optimal position for proton donation to the leaving aryl group of the substrate and for subsequent hydrolysis of the thiophosphoryl intermediate. The computational analysis is consistent with kinetic data, and NMR spectroscopy, showing that the Q75L mutant exhibits enhanced reaction kinetics with similar substrate binding affinity. We anticipate that our findings will motivate further studies on the possibility that MptpA remains passivated during the chronic state of infection and increases its activity as part of the pathogenic life cycle of M. tuberculosis possibly via allosteric means.