The role of water in protein-DNA recognition

Molecular Origin of Distinct Hydration Dynamics in Double Helical DNA and RNA Sequences

Water molecules are essential to determine the structure of nucleic acids and mediate their interactions with other biomolecules. Here, we characterize the hydration dynamics of analogous DNA and RNA double helices with unprecedented resolution and elucidate the molecular origin of their differences: first, the localization of the slowest hydration water molecules─in the minor groove in DNA, next to phosphates in RNA─and second, the markedly distinct hydration dynamics of the two phosphate oxygen atoms OR and OS in RNA. Using our Extended Jump Model for water reorientation, we assess the relative importance of previously proposed factors, including the local topography, water bridges, and the presence of ions. We show that the slow hydration dynamics at RNA OR sites is not due to bridging water molecules but is caused by both the larger excluded volume and the stronger initial H-bond next to OR, due to the different phosphate orientations in A-form double helical RNA.

Entropy Tug-of-War Determines Solvent Effects in the Liquid-Liquid Phase Separation of a Globular Protein

Liquid-liquid phase separation (LLPS) plays a key role in the compartmentalization of cells via the formation of biomolecular condensates. Here, we combined atomistic molecular dynamics (MD) simulations and terahertz (THz) spectroscopy to determine the solvent entropy contribution to the formation of condensates of the human eye lens protein γD-Crystallin. The MD simulations reveal an entropy tug-of-war between water molecules that are released from the protein droplets and those that are retained within the condensates, two categories of water molecules that were also assigned spectroscopically. A recently developed THz-calorimetry method enables quantitative comparison of the experimental and computational entropy changes of the released water molecules. The strong correlation mutually validates the two approaches and opens the way to a detailed atomic-level understanding of the different driving forces underlying the LLPS.

On Water Arrangements in Right- and Left-Handed DNA Structures

DNA requires hydration to maintain its structural integrity. Crystallographic analyses have enabled patterns of water arrangements to be visualized. We survey these water motifs in this review, focusing on left- and right-handed duplex and quadruplex DNAs, together with the i-motif. Common patterns of linear spines of water organization in grooves have been identified and are widely prevalent in right-handed duplexes and quadruplexes. By contrast, a left-handed quadruplex has a distinctive wheel of hydration populating the almost completely circular single groove in this structure.

De novo prediction of explicit water molecule positions by a novel algorithm within the protein design software MUMBO

By mediating interatomic interactions, water molecules play a major role in protein-protein, protein-DNA and protein-ligand interfaces, significantly affecting affinity and specificity. This notwithstanding, explicit water molecules are usually not considered in protein design software because of high computational costs. To challenge this situation, we analyzed the binding characteristics of 60,000 waters from high resolution crystal structures and used the observed parameters to implement the prediction of water molecules in the protein design and side chain-packing software MUMBO. To reduce the complexity of the problem, we incorporated water molecules through the solvation of rotamer pairs instead of relying on solvated rotamer libraries. Our validation demonstrates the potential of our algorithm by achieving recovery rates of 67% for bridging water molecules and up to 86% for fully coordinated waters. The efficacy of our algorithm is highlighted further by the prediction of 3 different proteinligand complexes. Here, 91% of water-mediated interactions between protein and ligand are correctly predicted. These results suggest that the new algorithm could prove highly beneficial for structure-based protein design, particularly for the optimization of ligand-binding pockets or protein-protein interfaces.

Functional regulation of an intrinsically disordered protein via a conformationally excited state

A longstanding goal in the field of intrinsically disordered proteins (IDPs) is to characterize their structural heterogeneity and pinpoint the role of this heterogeneity in IDP function. Here, we use multinuclear chemical exchange saturation (CEST) nuclear magnetic resonance to determine the structure of a thermally accessible globally folded excited state in equilibrium with the intrinsically disordered native ensemble of a bacterial transcriptional regulator CytR. We further provide evidence from double resonance CEST experiments that the excited state, which structurally resembles the DNA-bound form of cytidine repressor (CytR), recognizes DNA by means of a "folding-before-binding" conformational selection pathway. The disorder-to-order regulatory switch in DNA recognition by natively disordered CytR therefore operates through a dynamical variant of the lock-and-key mechanism where the structurally complementary conformation is transiently accessed via thermal fluctuations.

Insights into DNA solvation found in protein-DNA structures

The proteins that bind double-helical DNA present various microenvironments that sense and/or induce signals in the genetic material. The high-resolution structures of protein-DNA complexes reveal the nature of both the microenvironments and the conformational responses in DNA and protein. Complex networks of interactions within the structures somehow tie the protein and DNA together and induce the observed spatial forms. Here we show how the cumulative buildup of amino acid atoms around the sugars, phosphates, and bases in different protein-DNA complexes produces a binding cloud around the double helix and how different types of atoms fill that cloud. Rather than focusing on the principles of molecular binding and recognition suggested by the arrangements of amino acids and nucleotides in the macromolecular complexes, we consider the proteins in contact with DNA as organized solvents. We describe differences in the mix of atoms that come in closest contact with DNA, subtle sequence-dependent features in the microenvironment of the sugar-phosphate backbone, a direct link between the localized buildup of ionic species and the electrostatic potential surfaces of the DNA bases, and sites of atomic buildup above and below the basepair planes that transmit the unique features of the base environments along the chain backbone. The inferences about solvation that can be drawn from the survey provide new stimuli for improvement of nucleic acid force fields and fresh ideas for exploration of the properties of DNA in solution.

Alignment of major-groove hydrogen bond arrays uncovers shared information between different DNA sequences that bind the same protein

Protein-DNA binding is of a great interest due to its importance in many biological processes. Previous studies have presented many factors responsible for the recognition and specificity, but understanding the minimal informational requirements for proteins that bind to multiple DNA-sites is still an understudied area of bioinformatics. Here we focus on the hydrogen bonds displayed by the target DNA in the major groove that take part in protein-binding. We show that analyses focused on the base pair identity may overlook key hydrogen bonds. We have developed an algorithm that converts a nucleotide sequence into an array of hydrogen bond donors and acceptors and methyl groups. It then aligns these non-covalent interaction arrays to identify what information is being maintained among multiple DNA sequences. For three different DNA-binding proteins, Lactose repressor, controller protein and λ-CI repressor, we uncovered the minimal pattern of hydrogen bonds that are common amongst all the binding sequences. Notably in the three proteins, key interacting hydrogen bonds are maintained despite nucleobase mutations in the corresponding binding sites. We believe this work will be useful for developing new DNA binding proteins and shed new light on evolutionary relationships.

From structure and dynamics to biomolecular functions: The ubiquitous role of solvent in biology

Biological activity requires a solvent that can provide a suitable environment, which satisfies the twin need for stability and the ability to change. Among all the solvents water plays the most important role. We review, analyze, and comment on recent works on the structure and dynamics of water around biomolecules and their role in specific biological functions. While studies in the past have focused on understanding the biomolecule-water interactions through a hydration layer; recently the attention has shifted towards understanding functions at a molecular level. Such a microscopic understanding clearly requires elucidation of detailed dynamical processes where solvent molecules play an important role. Finally, we comment on the advances made in understanding the role of water inside a biological cell.

Host-pathogen protein-nucleic acid interactions: A comprehensive review

Recognition of pathogen-derived nucleic acids by host cells is an effective host strategy to detect pathogenic invasion and trigger immune responses. In the context of pathogen-specific pharmacology, there is a growing interest in mapping the interactions between pathogen-derived nucleic acids and host proteins. Insight into the principles of the structural and immunological mechanisms underlying such interactions and their roles in host defense is necessary to guide therapeutic intervention. Here, we discuss the newest advances in studies of molecular interactions involving pathogen nucleic acids and host factors, including their drug design, molecular structure and specific patterns. We observed that two groups of nucleic acid recognizing molecules, Toll-like receptors (TLRs) and the cytoplasmic retinoic acid-inducible gene (RIG)-I-like receptors (RLRs) form the backbone of host responses to pathogen nucleic acids, with additional support provided by absent in melanoma 2 (AIM2) and DNA-dependent activator of Interferons (IFNs)-regulatory factors (DAI) like cytosolic activity. We review the structural, immunological, and other biological aspects of these representative groups of molecules, especially in terms of their target specificity and affinity and challenges in leveraging host-pathogen protein-nucleic acid interactions (HP-PNI) in drug discovery.

Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks

Database-derived water probability densities around structurally and sequentially distinct DNA dinucleotide fragments reproduce the known hydration motifs, which thus can be used as building blocks to predict DNA hydration.

Water plays an important role in stabilizing the structure of DNA and mediating its interactions. Here, the hydration of DNA was analyzed in terms of dinucleotide fragments from an ensemble of 2727 nonredundant DNA chains containing 41 853 dinucleotides and 316 265 associated first-shell water molecules. The dinucleotides were classified into categories based on their 16 sequences and the previously determined structural classes known as nucleotide conformers (NtCs). The construction of hydrated dinucleotide building blocks allowed dinucleotide hydration to be calculated as the probability of water density distributions. Peaks in the water densities, known as hydration sites (HSs), uncovered the interplay between base and sugar-phosphate hydration in the context of sequence and structure. To demonstrate the predictive power of hydrated DNA building blocks, they were then used to predict hydration in an independent set of crystal and NMR structures. In ten tested crystal structures, the positions of predicted HSs and experimental waters were in good agreement (more than 40% were within 0.5 Å) and correctly reproduced the known features of DNA hydration, for example the ‘spine of hydration’ in B-DNA. Therefore, it is proposed that hydrated building blocks can be used to predict DNA hydration in structures solved by NMR and cryo-EM, thus providing a guide to the interpretation of experimental data and computer models. The data for the hydrated building blocks and the predictions are available for browsing and visualization at the website https://watlas.datmos.org/watna/.

Solvent effects on the NMR shieldings of stacked DNA base pairs

Stacking effects are among the most important effects in DNA. We have recently studied their influence in fragments of DNA through the analysis of NMR magnetic shieldings, firstly in vacuo. As a continuation of this line of research we show here the influence of solvent effects on the shieldings through the application of both explicit and implicit models. We found that the explicit solvent model is more appropriate for consideration due to the results matching better in general with experiments, as well as providing clear knowledge of the electronic origin of the value of the shieldings. Our study is grounded on a recently developed theoretical model of our own, by which we are able to learn about the magnetic effects of given fragments of DNA molecules on selected base pairs. We use the shieldings of the atoms of a central base pair (guanine-cytosine) of a selected fragment of DNA molecules as descriptors of physical effects, like π-stacking and solvent effects. They can be taken separately and altogether. The effect of π-stacking is introduced through the addition of some pairs above and below of the central base pair, and now, the solvent effect is considered including a network of water molecules that consist of two solvation layers, which were fixed in the calculations performed in all fragments. We show that the solvent effects enhance the stacking effects on the magnetic shieldings of atoms that belong to the external N-H bonds. The net effect is of deshielding on both atoms. There is also a deshielding effect on the carbon atoms that belong to CO bonds, for which the oxygen atom has an explicit hydrogen bond (HB) with a solvent water molecule. Solvent effects are found to be no higher than a few percent of the total value of the shieldings (between 1% and 5%) for most atoms, although there are few for which such an effect can be higher. There is one nitrogen atom, the acceptor of the HB between guanine and cytosine, that is more highly shielded (around 15 ppm or 10%) when the explicit solvent is considered. In a similar manner, the most external nitrogen atom of cytosine and the hydrogen atom that is bonded to it are highly deshielded (around 10 ppm for nitrogen and around 3 ppm for hydrogen).

Tenuous transcriptional threshold of human sex determination. II. SRY exploits water-mediated clamp at the edge of ambiguity

Y-encoded transcription factor SRY initiates male differentiation in therian mammals. This factor contains a high-mobility-group (HMG) box, which mediates sequence-specific DNA binding with sharp DNA bending. A companion article in this issue described sex-reversal mutations at box position 72 (residue 127 in human SRY), invariant as Tyr among mammalian orthologs. Although not contacting DNA, the aromatic ring seals the domain's minor wing at a solvent-exposed junction with a basic tail. A seeming paradox was posed by the native-like biochemical properties of inherited Swyer variant Y72F: its near-native gene-regulatory activity is consistent with the father's male development, but at odds with the daughter's XY female somatic phenotype. Surprisingly, aromatic rings (Y72, F72 or W72) confer higher transcriptional activity than do basic or polar side chains generally observed at solvated DNA interfaces (Arg, Lys, His or Gln). Whereas biophysical studies (time-resolved fluorescence resonance energy transfer and heteronuclear NMR spectroscopy) uncovered only subtle perturbations, dissociation of the Y72F complex was markedly accelerated relative to wild-type. Studies of protein-DNA solvation by molecular-dynamics (MD) simulations of an homologous high-resolution crystal structure (SOX18) suggest that Y72 para-OH anchors a network of water molecules at the tail-DNA interface, perturbed in the variant in association with nonlocal conformational fluctuations. Loss of the Y72 anchor among SRY variants presumably "unclamps" its basic tail, leading to (a) rapid DNA dissociation despite native affinity and (b) attenuated transcriptional activity at the edge of sexual ambiguity. Conservation of Y72 suggests that this water-mediated clamp operates generally among SRY and metazoan SOX domains.

Low-frequency vibrations of water molecules in DNA minor groove

Water molecules around the DNA form the hydration shell having different structural and dynamical features in different regions of the double helix. In the DNA minor groove, water molecules are highly ordered and in the case of AT nucleotide sequence, the formation of a hydration spine is observed. In the present research, the vibrations of the hydration spine have been studied to establish the mode of translational vibrations of water molecules in the DNA low-frequency spectra (water-spine vibrations). Using the developed phenomenological model with the parameters determined for different nucleotides of the DNA fragment CGCGAATTCGCG, the frequencies of vibrations of the hydration spine have been obtained within 185 ± 20 cm[Formula: see text] depending on type of nucleotide. The obtained frequencies are in the same region as the translational vibrations of water molecules in the bulk. To select the mode of water-spine vibrations from those modes that are present in the bulk water, the dynamics of DNA with different nucleotide contents has been analyzed, and the possible influence of heavy water has been estimated. The determined features of the mode of water vibrations in the hydration spine of DNA minor groove indicate that this mode may be observed in the experimental spectra.

Symmetric Nucleosides as Potent Purine Nucleoside Phosphorylase Inhibitors

Nucleic acids are one of the most enigmatic biomolecules crucial to several biological processes. Nucleic acid-protein interactions are vital for the coordinated and controlled functioning of a cell, leading to the design of several nucleoside/nucleotide analogues capable of mimicking these interactions and hold paramount importance in the field of drug discovery. Purine nucleoside phosphorylase is a well-established drug target due to its association with numerous immunodeficiency diseases. Here, we study the binding of human purine nucleoside phosphorylase (PNP) to some bidirectional symmetric nucleosides, a class of nucleoside analogues that are more flexible due to the absence of sugar pucker restraints. We compared the binding energies of PNP-symmetric nucleosides to the binding energies of PNP-inosine/Imm-H (a transition-state analogue), by means of 200 ns long all-atom explicit-solvent Gaussian accelerated molecular dynamics simulations followed by energetics estimation using the MM-PBSA methodology. Quite interestingly, we observed that a few symmetric nucleosides, namely, ν3 and ν4, showed strong binding with PNP (-14.1 and -12.6 kcal/mol, respectively), higher than inosine (-6.3 kcal/mol) and Imm-H (-9.6 kcal/mol). This is rationalized by an enhanced hydrogen-bond network for symmetric nucleosides compared to inosine and Imm-H while maintaining similar van der Waals contacts. We note that the chemical structures of both ν3 and ν4, due to an additional unsaturation in them, resemble enzymatic transition states and fall in the category of transition-state analogues (TSAs), which are quite popular.

Highlighting the potential utility of MBP crystallization chaperone for Arabidopsis BIL1/BZR1 transcription factor-DNA complex

The maltose-binding protein (MBP) fusion tag is one of the most commonly utilized crystallization chaperones for proteins of interest. Recently, this MBP-mediated crystallization technique was adapted to Arabidopsis thaliana (At) BRZ-INSENSITIVE-LONG (BIL1)/BRASSINAZOLE-RESISTANT (BZR1), a member of the plant-specific BZR TFs, and revealed the first structure of AtBIL1/BZR1 in complex with target DNA. However, it is unclear how the fused MBP affects the structural features of the AtBIL1/BZR1-DNA complex. In the present study, we highlight the potential utility of the MBP crystallization chaperone by comparing it with the crystallization of unfused AtBIL1/BZR1 in complex with DNA. Furthermore, we assessed the validity of the MBP-fused AtBIL1/BZR1-DNA structure by performing detailed dissection of crystal packings and molecular dynamics (MD) simulations with the removal of the MBP chaperone. Our MD simulations define the structural basis underlying the AtBIL1/BZR1-DNA assembly and DNA binding specificity by AtBIL1/BZR1. The methodology employed in this study, the combination of MBP-mediated crystallization and MD simulation, demonstrates promising capabilities in deciphering the protein-DNA recognition code.

Water spines and networks in G-quadruplex structures

Quadruplex DNAs can fold into a variety of distinct topologies, depending in part on loop types and orientations of individual strands, as shown by high-resolution crystal and NMR structures. Crystal structures also show associated water molecules. We report here on an analysis of the hydration arrangements around selected folded quadruplex DNAs, which has revealed several prominent features that re-occur in related structures. Many of the primary-sphere water molecules are found in the grooves and loop regions of these structures. At least one groove in anti-parallel and hybrid quadruplex structures is long and narrow and contains an extensive spine of linked primary-sphere water molecules. This spine is analogous to but fundamentally distinct from the well-characterized spine observed in the minor groove of A/T-rich duplex DNA, in that every water molecule in the continuous quadruplex spines makes a direct hydrogen bond contact with groove atoms, principally phosphate oxygen atoms lining groove walls and guanine base nitrogen atoms on the groove floor. By contrast, parallel quadruplexes do not have extended grooves, but primary-sphere water molecules still cluster in them and are especially associated with the loops, helping to stabilize loop conformations.

Decoupling between the translation and rotation of water in the proximity of a protein molecule

The interaction between water and biomacromolecules is of fundamental interest in biophysics, biochemistry and physical chemistry. By combining neutron scattering and molecular dynamics simulations on a perdeuterated protein at a series of hydration levels, we demonstrated that the translational motion of water is slowed down more significantly than its rotation, when water molecules approach the protein molecule. Further analysis of the simulation trajectories reveals that the observed decoupling results from the fact that the translational motion of water is more correlated over space and more retarded by the charged/polar residues and spatial confinement on the protein surface, than the rotation. Moreover, around the stable protein residues (with smaller atomic fluctuations), water exhibits more decoupled dynamics, indicating a connection between the observed translation-rotation decoupling in hydration water and the local stability of the protein molecule.

Marshall's nucleic acid: From double-helical structure to a potent intercalator

Deoxyribonucleic acid (DNA) not only stores genetic information but also emerged as a popular drug target. Modified nucleotides/nucleosides have been extensively studied in recent years wherein the sugar/nucleobase/phosphate-backbone has been altered. Several such molecules are FDA approved, capable of targeting nucleic acids and proteins. In this article, we modified negatively charged phosphate backbone to marshall's acid-based neutral backbone and analyzed the resultant structures by utilizing Gaussian accelerated molecular dynamics simulations (1 μs) in aqueous media at 150 mM salt concentration. We noted that the double-helical marshall's nucleic acid structure was partially denatured during the course of simulations, however, after using conformationally locked sugar, the marshall's nucleic acid (hereby called MNA) maintained the double-helical structure throughout the simulations. Despite the fact that MNA has a more extended backbone than the regular DNA, surprisingly, both showed similar helical rise (~3.4 Å) along with a comparable Watson-Crick hydrogen bond profile. The backbone difference was majorly compensated in terms of helical twist (~56° (MNA) and ~ 35° (control DNA)). Further, we examined a few MNA based ss-dinucleotides as intercalating ligands for a regular B-DNA. Quite strikingly, the ligands unwinded the DNA and showed intercalating properties with high DNA binding affinities. Hence, the use of small fragments of MNA based molecules in DNA targeted drug discovery is foreseen.

Anomalous sub-diffusion of water in biosystems: From hydrated protein powders to concentrated protein solution to living cells

Water is essential to life and its translational motion in living systems mediates various biological processes, including transportation of function-required ingredients and facilitating the interaction between biomacromolecules. By combining neutron scattering and isotopic labeling, the present work characterizes translational motion of water on a biomolecular surface, in a range of systems: a hydrated protein powder, a concentrated protein solution, and in living Escherichia coli (E. coli) cells. Anomalous sub-diffusion of water is observed in all samples, which is alleviated upon increasing the water content. Complementary molecular dynamics simulations and coarse-grained numerical modeling demonstrated that the sub-diffusive behavior results from the heterogeneous distribution of microscopic translational mobility of interfacial water. Moreover, by comparing the experimental results measured on E. coli cells with those from a concentrated protein solution with the same amount of water, we show that water in the two samples has a similar average mobility, however the underlying distribution of motion is more heterogeneous in the living cell.

Interaction of ASOs with PC4 Is Highly Influenced by the Cellular Environment and ASO Chemistry

The activity of PS-ASOs is strongly influenced by association with both inter- and intracellular proteins. The sequence, chemical nature, and structure of the ASO can have profound influences on the interaction of PS-ASOs with specific proteins. A more thorough understanding of how these pharmacological agents interact with various proteins and how chemical modifications, sequence, and structure influence interactions with proteins is needed to inform future ASO design efforts. To better understand the chemistry of PS-ASO interactions, we have focused on human positive cofactor 4 (PC4). Although several studies have investigated the in vitro binding properties of PC4 with endogenous nucleic acids, little is known about the chemistry of interaction of PS-ASOs with this protein. Here we examine in detail the impact of ASO backbone chemistry, 2'-modifications, and buffer environment on the binding affinity of PC4. In addition, using site-directed mutagenesis, we identify those amino acids that are specifically required for ASO binding interactions, and by substitution of abasic nucleotides we identify the positions on the ASO that most strongly influence affinity for PC4. Finally, to confirm that the interactions observed in vitro are biologically relevant, we use a recently developed complementation reporter system to evaluate the kinetics and subcellular localization of the interaction of ASO and PC4 in live cells.

Kinetic and subcellular analysis of PS-ASO/protein interactions with P54nrb and RNase H1

The rapid RNase H1-dependent mislocalization of heterodimer proteins P54nrb and PSF to nucleoli is an early event in the pathway that explains the effects of most toxic phosphorothioate ASOs (PS-ASOs). Using a recently developed NanoLuciferace (NLuc)-based structural complementation reporter system which allows us to observe ASO/protein interactions in real time in live cells, we have determined that safe and toxic PS-ASOs associate with these proteins with kinetics and impact on subcellular localization that differ. Toxic PS-ASOs interact in a complex that includes RNase H1, P54nrb and PSF; but RNase H1/P54nrb complexes were observed in only the cells treated with toxic, but not safe PS-ASOs. In addition, experiments performed in vitro suggest that RNA is also a required component of the complex. The protein–protein interaction between P54nrb and RNase H1 requires the spacer region of RNAse H1, while the P54nrb core domains are required for association with RNase H1. In addition, we have determined that PS-ASOs bind P54nrb via RRM1 and RRM2, while they bind RNase H1 primarily via the hybrid binding domain, however catalytic domain interactions also contribute to overall affinity. These ASO–protein interactions are highly influenced by the chemistry of the PS-ASO binding environment, however little correlation between affinity for specific proteins and PS-ASO toxicity was observed.

Hydrogen-Bond Free Energy of Local Biological Water

Here, we propose an experimental methodology based on femtosecond-resolved fluorescence spectroscopy to measure the hydrogen (H)-bond free energy of water at protein surfaces under isothermal conditions. A demonstration was conducted by installing a non-canonical isostere of tryptophan (7-azatryptophan) at the surface of a coiled-coil protein to exploit the photoinduced proton transfer of its chromophoric moiety, 7-azaindole. The H-bond free energy of this biological water was evaluated by comparing the rates of proton transfer, sensitive to the hydration environment, at the protein surface and in bulk water, and it was found to be higher than that of bulk water by 0.4 kcal mol^-1 . The free-energy difference is dominated by the entropic cost in the H-bond network among water molecules at the hydrophilic and charged protein surface. Our study opens a door to accessing the energetics and dynamics of local biological water to give insight into its roles in protein structure and function.

Distinctive behavior and two-dimensional vibrational dynamics of water molecules inside glycine solvation shell

We present a first principles molecular dynamics study of a deuterated aqueous solution of a single glycine moiety to explore the structure, dynamics, and two-dimensional infrared spectra of water molecules found in the solvation shell of glycine.

A structure-based model for the prediction of protein-RNA binding affinity

Protein-RNA recognition is highly affinity-driven and regulates a wide array of cellular functions. In this study, we have curated a binding affinity data set of 40 protein-RNA complexes, for which at least one unbound partner is available in the docking benchmark. The data set covers a wide affinity range of eight orders of magnitude as well as four different structural classes. On average, we find the complexes with single-stranded RNA have the highest affinity, whereas the complexes with the duplex RNA have the lowest. Nevertheless, free energy gain upon binding is the highest for the complexes with ribosomal proteins and the lowest for the complexes with tRNA with an average of -5.7 cal/mol/Å2 in the entire data set. We train regression models to predict the binding affinity from the structural and physicochemical parameters of protein-RNA interfaces. The best fit model with the lowest maximum error is provided with three interface parameters: relative hydrophobicity, conformational change upon binding and relative hydration pattern. This model has been used for predicting the binding affinity on a test data set, generated using mutated structures of yeast aspartyl-tRNA synthetase, for which experimentally determined ΔG values of 40 mutations are available. The predicted ΔGempirical values highly correlate with the experimental observations. The data set provided in this study should be useful for further development of the binding affinity prediction methods. Moreover, the model developed in this study enhances our understanding on the structural basis of protein-RNA binding affinity and provides a platform to engineer protein-RNA interfaces with desired affinity.

Polyelectrolytes induce water-water correlations that result in dramatic viscosity changes and nuclear quantum effects

Ions interact with water via short-ranged ion-dipole interactions. Recently, an additional unexpected long-ranged interaction was found: The total electric field of ions influences water-water correlations over tens of hydration shells, leading to the Jones Ray effect, a 0.3% surface tension depression. Here, we report such long-range interactions contributing substantially to both molecular and macroscopic properties. Femtosecond elastic second harmonic scattering (fs-ESHS) shows that long-range electrostatic interactions are remarkably strong in aqueous polyelectrolyte solutions, leading to an increase in water-water correlations. This increase plays a role in the reduced viscosity, which changes more than two orders of magnitude with polyelectrolyte concentration. Using D₂O instead of H₂O shifts both the fs-ESHS and the viscosity curve by a factor of ~10 and reduces the maximum viscosity value by 20 to 300%, depending on the polyelectrolyte. These phenomena cannot be explained using a mean-field approximation of the solvent and point to nuclear quantum effects.

Enzymatic degradation of extracellular DNA exposed to chlorpyrifos and chlorpyrifos-methyl in an aqueous system

The persistence of extracellular DNA (eDNA) is crucial for ensuring species diversity and ecological function in aquatic systems. However, scarce information exists about the impact of pesticides on eDNA, although they often co-exist in the aquatic environment. Using a variety of spectroscopic analyses, eDNA degradation and the associated alterations in DNA secondary structure was investigated by exposing DNase I to tested DNA in the presence of chlorpyrifos, a commonly used organophosphate pesticide. Molecular dynamics simulation was used to explore the weak interactions between the tested DNA and chlorpyrifos. The results indicated that chlorpyrifos significantly enhanced DNA degradation without affecting the enzyme activity of DNase I in an aqueous system. Spectroscopic experiments confirmed that chlorpyrifos and the analog chlorpyrifos-methyl could bind with DNA to cause the bases noncovalent stacking interaction. Molecular simulations further demonstrated that pesticide binding with DNA molecules caused widening of the DNA grooves and destruction of the hydrated layer, which enhanced DNA degradation. The findings presented herein provide novel insight into the genotoxicity and ecotoxicity of chlorpyrifos and chlorpyrifos-methyl, as well as their impacts on DNA persistence in aquatic environments.

Mapping interfacial hydration in ETS-family transcription factor complexes with DNA: a chimeric approach

Hydration of interfaces is a major determinant of target specificity in protein/DNA interactions. Interfacial hydration is a highly variable feature in DNA recognition by ETS transcription factors and functionally relates to cellular responses to osmotic stress. To understand how hydration is mediated in the conserved ETS/DNA binding interface, secondary structures comprising the DNA contact surface of the strongly hydrated ETS member PU.1 were substituted, one at a time, with corresponding elements from its sparsely hydrated relative Ets-1. The resultant PU.1/Ets-1 chimeras exhibited variably reduced sensitivity to osmotic pressure, indicative of a distributed pattern of interfacial hydration in wildt-ype PU.1. With the exception of the recognition helix H3, the chimeras retained substantially high affinities. Ets-1 residues could therefore offset the loss of favorable hydration contributions in PU.1 via low-water interactions, but at the cost of decreased selectivity at base positions flanking the 5'-GGA-3' core consensus. Substitutions within H3 alone, which contacts the core consensus, impaired binding affinity and PU.1 transactivation in accordance with the evolutionary separation of the chimeric residues involved. The combined biophysical, bioinformatics and functional data therefore supports hydration as an evolved specificity determinant that endows PU.1 with more stringent sequence selection over its ancestral relative Ets-1.

C5' omitted DNA enhances bendability and protein binding

Protein-DNA interactions are of great biological importance. The specificity and strength of these intimate contacts are crucial in the proper functioning of a cell, wherein the role of DNA dynamic bendability has been a matter of discussion. We relate DNA bendability to protein binding by introducing some simple modifications in the DNA structure. We removed C5' carbon in first modified structure and the second has an additional carbon between C3' and 3'-OH, hereby pronounced as C(-) and C(+) nucleic acids respectively. We observed that C(+) nucleic acid retains B-DNA duplex as seen by means of 500 ns long molecular dynamics (MD) simulations, structural and energetic calculations, while C(-) nucleic acid attains a highly bend structure. We transferred these observations to a protein-DNA system in order to monitor as to what extent the bendability enhances the protein binding. The energetics of binding is explored by performing 100 ns long MD simulations on control and modified DNA-protein complexes followed by running MM-PBSA/GBSA calculations on the resultant structures. It is observed that C(+) nucleic acid has protein binding in close correspondence to the control system (∼-14 kcal/mol) due to their relatable structure, while the C(-) nucleic acid displayed high binding to the protein (∼-18 kcal/mol). DelPhi based calculations reveal that the high binding could be the result of enhanced electrostatic interactions caused by exposed bases in the bend structure for protein recognition. Such modified oligonucleotides, due to their improved binding to protein and resistance to nuclease degradation, have a great therapeutic value.

Toward theoretical terahertz spectroscopy of glassy aqueous solutions: partially frozen solute-solvent couplings of glycine in water

The molecular-level understanding of THz spectra of aqueous solutions under ambient conditions has been greatly advanced in recent years. Here, we go beyond previous analyses by performing ab initio molecular dynamics simulations of glycine in water with artificially frozen solute or solvent molecules, respectively, while computing the total THz response as well as its decomposition into mode-specific resonances based on the "supermolecular solvation complex" technique. Clamping the water molecules and keeping glycine moving breaks the coupling of glycine to the structural dynamics of the solvent, however, the polarization and dielectric solvation effects in the static solvation cage are still at work since the full electronic structure of the quenched solvent is taken into account. The complementary approach of fixing glycine reveals both the dynamical and electronic response of the solvation cage at the level of its THz response. Moreover, to quantitatively account for the electronic contribution solely due to solvent embedding, the solute species is "vertically desolvated", thus preserving the fully coupled solute-solvent motion in terms of the solute's structural dynamics in solution, while its electronic structure is no longer subject to solute-solvent polarization and charge transfer effects. When referenced to the free simulation of Gly(aq), this three-fold approach allows us to decompose the THz spectral contributions due to the correlated solute-solvent dynamics into entirely structural and purely electronic effects. Beyond providing hitherto unknown insights, the observed systematic changes of THz spectra in terms of peak shifts and lineshape modulations due to conformational freezing and frozen solvation cages might be useful to investigate the solvation of molecules in highly viscous H-bonding solvents such as ionic liquids and even in cryogenic ices as relevant to polar stratospheric and dark interstellar clouds.

Ion-specificity and surface water dynamics in protein solutions

Ion-specific effects at the protein surface are investigated here in light of the changes they infer to surface water dynamics, as observed by 1H NMR relaxation (at 20 MHz). Two well-known proteins, hen egg-white lysozyme (LZM) and bovine serum albumin (BSA), show qualitatively opposite trends in the transverse relaxation rate, R2(1H), along a series of different monovalent salt anions in the solution. Presence of salt ions increases R2(1H) in the case of lysozyme and diminishes it in the case of BSA. The effect magnifies for larger and more polarizable ions. The same contrasting effect between the two proteins is observed for protein-solvent proton exchange. This hints at subtle effects ion-binding might have on the accessibility of water surface sites on the protein. We suggest that the combination of the density of surface charge residues and surface roughness, at the atomic scale, dictates the response to the presence of salt ions and is proper to each protein. Further, a dramatic increase in R2(1H) is found to correlate closely with the formation of protein aggregates. The same ordering of salts in their ability to aggregate lysozyme, as seen previously by cloud point measurements, is reproduced here by R2(1H). 1H NMR relaxation data is supplemented by 35Cl and 14N NMR relaxation for selected salt ions to probe the ion-binding itself.

Calcium Ions Affect Water Molecular Structures Surrounding an Oligonucleotide Duplex as Revealed by Sum Frequency Generation Vibrational Spectroscopy

The solvation of DNA in water facilitates the formation of a hydration layer surrounding it, thus stabilizing the DNA duplex in the biological aqueous environment. In this study, via using the lipid bilayer as a soft substrate to accommodate the duplex oligonucleotide, the structure of the water layer surrounding the oligonucleotide was detected under the perturbation of the calcium ions (Ca²⁺) with chiral and achiral sum frequency generation (SFG) vibrational spectroscopy. With increasing Ca²⁺ concentration, both the chiral and achiral water vibrational signals had similar concentration-dependent changes, i.e., an initial decreasing phase followed by an increasing phase. However, when the Ca²⁺ concentrations were adjusted to within the range comparable to those in the human serum, the chiral water vibrational signals remained nearly unchanged, whereas the achiral water vibrational signals still changed as a function of the Ca²⁺ concentration. Therefore, the current experimental result supports the possible protection function of the chiral hydration layer against the Ca²⁺ ions, which generally exist in the cell sap and play important roles in many biological functions.

Twist and turn: a revised structural view on the unpaired bubble of class II CPD photolyase in complex with damaged DNA

Cyclobutane pyrimidine dimer (CPD) photolyases harness the energy of blue light to repair UV-induced DNA CPDs. Upon binding, CPD photolyases cause the photodamage to flip out of the duplex DNA and into the catalytic site of the enzyme. This process, called base-flipping, induces a kink in the DNA, as well as an unpaired bubble, which are stabilized by a network of protein-nucleic acid interactions. Previously, several co-crystal structures have been reported in which the binding mode of CPD photolyases has been studied in detail. However, in all cases the internucleoside linkage of the photodamage site was a chemically synthesized formacetal analogue and not the natural phosphodiester. Here, the first crystal structure and conformational analysis via molecular-dynamics simulations of a class II CPD photolyase in complex with photodamaged DNA that contains a natural cyclobutane pyrimidine dimer with an intra-lesion phosphodiester linkage are presented. It is concluded that a highly conserved bubble-intruding region (BIR) mediates stabilization of the open form of CPD DNA when complexed with class II CPD photolyases.

Role of Macromolecular Crowding on the Intracellular Diffusion of DNA Binding Proteins

Recent experiments suggest that cellular crowding facilitates the target search dynamics of proteins on DNA, the mechanism of which is not yet known. By using large scale computer simulations, we show that two competing factors, namely the width of the depletion layer that separates the crowder cloud from the DNA molecule and the degree of protein-crowder crosstalk, act in harmony to affect the target search dynamics of proteins. The impacts vary from nonspecific to specific target search regime. During a nonspecific search, dynamics of a protein is only minimally affected, whereas, a significantly different behaviour is observed when the protein starts forming a specific protein-DNA complex. We also find that the severity of impacts largely depends upon physiological crowder concentration and deviation from it leads to attenuation in the binding kinetics. Based on extensive kinetic study and binding energy landscape analysis, we further present a comprehensive molecular description of the search process that allows us to interpret the experimental findings.

The mechanism and high-free-energy transition state of lac repressor-lac operator interaction

Significant, otherwise-unavailable information about mechanisms and transition states (TS) of protein folding and binding is obtained from solute effects on rate constants. Here we characterize TS for lac repressor(R)–lac operator(O) binding by analyzing effects of RO-stabilizing and RO-destabilizing solutes on association (k_a) and dissociation (k_d) rate constants. RO-destabilizing solutes (urea, KCl) reduce k_a comparably (urea) or more than (KCl) they increase k_d, demonstrating that they destabilize TS relative to reactants and RO, and that TS exhibits most of the Coulombic interactions between R and O. Strikingly, three solutes which stabilize RO by favoring burial/dehydration of amide oxygens and anionic phosphate oxygens all reduce k_d without affecting k_a significantly. The lack of stabilization of TS by these solutes indicates that O phosphates remain hydrated in TS and that TS preferentially buries aromatic carbons and amide nitrogens while leaving amide oxygens exposed. In our proposed mechanism, DNA-binding-domains (DBD) of R insert in major grooves of O pre-TS, forming most Coulombic interactions of RO and burying aromatic carbons. Nucleation of hinge helices creates TS, burying sidechain amide nitrogens. Post-TS, hinge helices assemble and the DBD-hinge helix-O-DNA module docks on core repressor, partially dehydrating phosphate oxygens and tightening all interfaces to form RO.

Temperature and osmotic stress dependence of the thermodynamics for binding linker histone H10, Its carboxyl domain (H10-C) or globular domain (H10-G) to B-DNA

Linker histones (H1) are the basic proteins in higher eukaryotes that are responsible for the final condensation of chromatin. In contrast to the nucleosome core histone proteins, the role of H1 in compacting DNA is not clearly understood. In this study ITC was used to measure the binding constant, enthalpy change, and binding site size for the interactions of H10, or its C-terminal (H10-C) and globular (H10-G) domains to highly polymerized calf-thymus DNA at temperatures from 288 K to 308 K. Heat capacity changes, ΔCp, for these same H10 binding interactions were estimated from the temperature dependence of the enthalpy changes. The enthalpy changes for binding H10, H10-C, or H10-G to CT-DNA are all endothermic at 298 K, becoming more exothermic as the temperature is increased. The ΔH for binding H10-G to CT-DNA is exothermic at temperatures above approximately 300 K. Osmotic stress experiments indicate that the binding of H10 is accompanied by the release of approximately 35 water molecules. We estimate from our naked DNA titration results that the binding of the H10 to the nucleosome places the H10 protein in close contact with approximately 41 DNA bp. The breakdown is that the H10 carboxyl terminus interacts with 28 bp of linker DNA on one side of the nucleosome, the H10 globular domain binds directly to 7 bp of core DNA, and shields another 6 linker DNA bases, 3 bp on either side of the nucleosome where the linker DNA exits the nucleosome core.

Evaluation of Sox2 binding affinities for distinct DNA patterns using steered molecular dynamics simulation

Transcription factors (TFs) are gene expression regulators that bind to DNA in a sequence‐specific manner and determine the functional characteristics of the gene. It is worthwhile to study the unique characteristics of such specific TF‐binding pattern in DNA. Sox2 recognizes a 6‐ to 7‐base pair consensus DNA sequence; the central four bases of the binding site are highly conserved, whereas the two to three flanking bases are variable. Here, we attempted to analyze the binding affinity and specificity of the Sox2 protein for distinct DNA sequence patterns via steered molecular dynamics, in which a pulling force is employed to dissociate Sox2 from Sox2–DNA during simulation to study the behavior of a complex under nonequilibrium conditions. The simulation results revealed that the first two stacking bases of the binding pattern have an exclusive impact on the binding affinity, with the corresponding mutant complexes showing greater binding and longer dissociation time than the experimental complexes do. In contrast, mutation of the conserved bases tends to reduce the affinity, and mutation of the complete conserved region disrupts the binding. It might pave the way to identify the most likely binding pattern recognized by Sox2 based on the affinity of each configuration. The α2‐helix of Sox2 was found to be the key player in the Sox2–DNA association. The characterization of Sox2's binding patterns for the target genes in the genome helps in understanding of its regulatory functions.

Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition

The Fox-1 RNA recognition motif (RRM) domain is an important member of the RRM protein family. We report a 1.8 Å X-ray structure of the free Fox-1 containing six distinct monomers. We use this and the nuclear magnetic resonance (NMR) structure of the Fox-1 protein/RNA complex for molecular dynamics (MD) analyses of the structured hydration. The individual monomers of the X-ray structure show diverse hydration patterns, however, MD excellently reproduces the most occupied hydration sites. Simulations of the protein/RNA complex show hydration consistent with the isolated protein complemented by hydration sites specific to the protein/RNA interface. MD predicts intricate hydration sites with water-binding times extending up to hundreds of nanoseconds. We characterize two of them using NMR spectroscopy, RNA binding with switchSENSE and free-energy calculations of mutant proteins. Both hydration sites are experimentally confirmed and their abolishment reduces the binding free-energy. A quantitative agreement between theory and experiment is achieved for the S155A substitution but not for the S122A mutant. The S155 hydration site is evolutionarily conserved within the RRM domains. In conclusion, MD is an effective tool for predicting and interpreting the hydration patterns of protein/RNA complexes. Hydration is not easily detectable in NMR experiments but can affect stability of protein/RNA complexes.

DNA's Chiral Spine of Hydration

The iconic helical structure of DNA is stabilized by the solvation environment, where a change in the hydration state can lead to dramatic changes to the DNA structure. X-ray diffraction experiments at cryogenic temperatures have shown crystallographic water molecules in the minor groove of DNA, which has led to the notion of a spine of hydration of DNA. Here, chiral nonlinear vibrational spectroscopy of two DNA sequences shows that not only do such structural water molecules exist in solution at ambient conditions but that they form a chiral superstructure: a chiral spine of hydration. This is the first observation of a chiral water superstructure templated by a biomolecule. While the biological relevance of a chiral spine of hydration is unknown, the method provides a direct way to interrogate the properties of the hydration environment of DNA and water in biological settings without the use of labels.

Turgor-responsive starch phosphorylation in Oryza sativa stems: A primary event of starch degradation associated with grain-filling ability

Grain filling ability is mainly affected by the translocation of carbohydrates generated from temporarily stored stem starch in most field crops including rice (Oryza sativa L.). The partitioning of non-structural stem carbohydrates has been recognized as an important trait for raising the yield ceiling, yet we still do not fully understand how carbohydrate partitioning occurs in the stems. In this study, two rice subspecies that exhibit different patterns of non-structural stem carbohydrates partitioning, a japonica-dominant cultivar, Momiroman, and an indica-dominant cultivar, Hokuriku 193, were used as the model system to study the relationship between turgor pressure and metabolic regulation of non-structural stem carbohydrates, by combining the water status measurement with gene expression analysis and a dynamic prefixed 13C tracer analysis using a mass spectrometer. Here, we report a clear varietal difference in turgor-associated starch phosphorylation occurred at the initiation of non-structural carbohydrate partitioning. The data indicated that starch degradation in Hokuriku 193 stems occurred at full-heading, 5 days earlier than in Momiroman, contributing to greater sink filling. Gene expression analysis revealed that expression pattern of the gene encoding α-glucan, water dikinase (GWD1) was similar between two varieties, and the maximum expression level in Hokuriku 193, reached at full heading (4 DAH), was greater than in Momiroman, leading to an earlier increase in a series of amylase-related gene expression in Hokuriku 193. In both varieties, peaks in turgor pressure preceded the increases in GWD1 expression, and changes in GWD1 expression was correlated with turgor pressure. Additionally, a threshold is likely to exist for GWD1 expression to facilitate starch degradation. Taken together, these results raise the possibility that turgor-associated starch phosphorylation in cells is responsible for the metabolism that leads to starch degradation. Because the two cultivars exhibited remarkable varietal differences in the pattern of non-structural carbohydrate partitioning, our findings propose that the observed difference in grain-filling ability originated from turgor-associated regulation of starch phosphorylation in stem parenchyma cells. Further understanding of the molecular mechanism of turgor-regulation may provide a new selection criterion for breaking the yield barriers in crop production.

The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery

The value of thoroughly understanding the thermodynamics specific to a drug discovery/design study is well known. Over the past decade, the crucial roles of water molecules in protein structure, function, and dynamics have also become increasingly appreciated. This Perspective explores water in the biological environment by adopting its point of view in such phenomena. The prevailing thermodynamic models of the past, where water was seen largely in terms of an entropic gain after its displacement by a ligand, are now known to be much too simplistic. We adopt a set of terminology that describes water molecules as being "hot" and "cold", which we have defined as being easy and difficult to displace, respectively. The basis of these designations, which involve both enthalpic and entropic water contributions, are explored in several classes of biomolecules and structural motifs. The hallmarks for characterizing water molecules are examined, and computational tools for evaluating water-centric thermodynamics are reviewed. This Perspective's summary features guidelines for exploiting water molecules in drug discovery.

Thermodynamics of complex structures formed between single-stranded DNA oligomers and the KH domains of the far upstream element binding protein

The noncovalent interaction between protein and DNA is responsible for regulating the genetic activities in living organisms. The most critical issue in this problem is to understand the underlying driving force for the formation and stability of the complex. To address this issue, we have performed atomistic molecular dynamics simulations of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein (FBP) complexed with two single-stranded DNA (ss-DNA) oligomers in aqueous media. Attempts have been made to calculate the individual components of the net entropy change for the complexation process by adopting suitable statistical mechanical approaches. Our calculations reveal that translational, rotational, and configurational entropy changes of the protein and the DNA components have unfavourable contributions for this protein-DNA association process and such entropy lost is compensated by the entropy gained due to the release of hydration layer water molecules. The free energy change corresponding to the association process has also been calculated using the Free Energy Perturbation (FEP) method. The free energy gain associated with the KH4-DNA complex formation has been found to be noticeably higher than that involving the formation of the KH3-DNA complex.