Role of the hydrophobic effect in stability of site-specific protein-DNA complexes

Evaluation of therapeutic role of harmaline: in vitro cytotoxicity targeting nucleic acids

Use of small molecules as valuable drugs against diseases is still an indefinable purpose due to the lack of in-detail knowledge regarding proper bio-target identification, specificity aspects, mode-mechanism of binding and proper in vitro study. Harmaline, an important beta-carboline alkaloid, shows effective anti-proliferative action against different types of human cancers and is also found to be a nucleic acid targeting natural molecule. This review sought to address the different signal pathways of apoptosis by harmaline in different cancer cell lines and simultaneously to characterize the structure activity aspects of the alkaloid with different motifs of nucleic acid to show its preference, biological efficacy and genotoxicity. The results open up new insights for the design and development of small molecule-based nucleic acid therapeutic agents.

A comparison on the biochemical activities of Fluorescein disodium, Rose Bengal and Rhodamine 101 in the light of DNA binding, antimicrobial and cytotoxic study

Biochemical activities of Fluorescein, Rose Bengal and Rhodamine 101 were studied by DNA binding, antibacterial and cytotoxic studies. DNA binding studies were done using spectroscopic, thermodynamic and molecular modeling techniques. Antibacterial activities were investigated against a gram-negative bacteria Escherichia coli and a gram-positive bacteria Staphylococcus aureus. Cytotoxic activities were studied against Wi-38 cell line. We observed these dyes bound to minor groove of DNA and structural diversity of dyes affect the phenomenon. No significant antibacterial and cytotoxic activities of these dyes were found in our observations.

The surface site interaction point approach to non-covalent interactions

The functional properties of molecular systems are generally determined by the sum of many weak non-covalent interactions, and therefore methods for predicting the relative magnitudes of these interactions is fundamental to understanding the relationship between function and structure in chemistry, biology and materials science. This review focuses on the Surface Site Interaction Point (SSIP) approach which describes molecules as a set of points that capture the properties of all possible non-covalent interactions that the molecule might make with another molecule. The first half of the review focuses on the empirical non-covalent interaction parameters, α and β, and provides simple rules of thumb to estimate free energy changes for interactions between different types of functional group. These parameters have been used to have been used to establish a quantitative understanding of the role of solvent in solution phase equilibria, and to describe non-covalent interactions at the interface between macroscopic surfaces as well as in the solid state. The second half of the review focuses on a computational approach for obtaining SSIPs and applications in multi-component systems where many different interactions compete. Ab initio calculation of the Molecular Electrostatic Potential (MEP) surface is used to derive an SSIP description of a molecule, where each SSIP is assigned a value equivalent to the corresponding empirical parameter, α or β. By considering the free energies of all possible pairing interactions between all SSIPs in a molecular ensemble, it is possible to calculate the speciation of all intermolecular interactions and hence predict thermodynamic properties using the SSIMPLE algorithm. SSIPs have been used to describe both the solution phase and the solid state and provide accurate predictions of partition coefficients, solvent effects on association constants for formation of intermolecular complexes, and the probability of cocrystal formation. SSIPs represent a simple and intuitive tool for describing the relationship between chemical structure and non-covalent interactions with sufficient accuracy to understand and predict the properties of complex molecular ensembles without the need for computationally expensive simulations.

Interaction of Heparin with Proteins: Hydration Effects

We present a thermodynamic investigation of the interaction of heparin with lysozyme in the presence of potassium glutamate (KGlu). The binding constant K_b is measured by isothermal titration calorimetry (ITC) in a temperature range from 288 to 310 K for concentrations of KGlu between 25 and 175 mM. The free energy of binding ΔG_b derived from K_b is strongly decreasing with increasing concentration of KGlu, whereas the dependence of ΔG_b on temperature T is found to be small. The decrease of ΔG_b can be explained in terms of counterion release: Binding of lysozyme to the strong polyelectrolyte heparin liberates approximately three of the condensed counterions of heparin, thus increasing the entropy of the system. The dependence of ΔG_b on T, on the other hand, is traced back to a change of hydration of the protein and the polyelectrolyte upon complex formation. This dependence is quantitatively described by the parameter Δw that depends on T and vanishes at a characteristic temperature T₀. A comparison of the complex formation in the presence of KGlu with the one in the presence of NaCl demonstrates that the parameters related to hydration are changed considerably. The characteristic temperature T₀ in the presence of KGlu solutions is considerably smaller than that in the presence of NaCl solutions. The change of specific heat Δc_p is found to become more negative with increasing salt concentration: This finding agrees with the model-free analysis by the generalized van't Hoff equation. The entire analysis reveals a small but important change of the free energy of binding by hydration. It shows that these ion-specific Hofmeister effects can be modeled quantitatively in terms of a characteristic temperature T₀ and a parameter describing the dependence of Δc_p on salt concentration.

Massively parallel, computationally guided design of a proenzyme

Proteins have shown promise as therapeutics and diagnostics, but their effectiveness is limited by our inability to spatially target their activity. To overcome this limitation, we developed a computationally guided method to design inactive proenzymes or zymogens, which are activated through cleavage by a protease. Since proteases are differentially expressed in various tissues and disease states, including cancer, these proenzymes could be targeted to the desired microenvironment. We tested our method on the therapeutically relevant protein carboxypeptidase G2 (CPG2). We designed Pro-CPG2s that are inhibited by 80 to 98% and are partially to fully reactivatable following protease treatment. The developed methodology, with further refinements, could pave the way for routinely designing protease-activated protein-based therapeutics and diagnostics that act in a spatially controlled manner.

Confining the activity of a designed protein to a specific microenvironment would have broad-ranging applications, such as enabling cell type-specific therapeutic action by enzymes while avoiding off-target effects. While many natural enzymes are synthesized as inactive zymogens that can be activated by proteolysis, it has been challenging to redesign any chosen enzyme to be similarly stimulus responsive. Here, we develop a massively parallel computational design, screening, and next-generation sequencing-based approach for proenzyme design. For a model system, we employ carboxypeptidase G2 (CPG2), a clinically approved enzyme that has applications in both the treatment of cancer and controlling drug toxicity. Detailed kinetic characterization of the most effectively designed variants shows that they are inhibited by ∼80% compared to the unmodified protein, and their activity is fully restored following incubation with site-specific proteases. Introducing disulfide bonds between the pro- and catalytic domains based on the design models increases the degree of inhibition to 98% but decreases the degree of restoration of activity by proteolysis. A selected disulfide-containing proenzyme exhibits significantly lower activity relative to the fully activated enzyme when evaluated in cell culture. Structural and thermodynamic characterization provides detailed insights into the prodomain binding and inhibition mechanisms. The described methodology is general and could enable the design of a variety of proproteins with precise spatial regulation.

Metal Ion Binding Induces Local Protein Unfolding and Destabilizes Human Carbonic Anhydrase II

Human carbonic anhydrase II (HCA) is a robust metalloprotein and an excellent biological model system to study the thermodynamics of metal ion coordination. Apo-HCA binds one zinc ion or two copper ions. We studied these binding processes at five temperatures (15-35 °C) using isothermal titration calorimetry, yielding thermodynamic parameters corrected for pH and buffer effects. We then sought to identify binding-induced structural changes. Our data suggest that binding at the active site organizes 6-8 residues; however, copper binding near the N-terminus results in a net unfolding of 6-7 residues. This surprising destabilization was confirmed using circular dichroism and protein stability measurements. Metal binding induced unfolding may represent an important regulatory mechanism, but it may be easily missed by NMR and X-ray crystallography. Thus, in addition to highlighting a highly novel binding-induced unfolding event, we demonstrate the value of calorimetry for studying the structural implications of metal binding.

Interaction of Linear Polyelectrolytes with Proteins: Role of Specific Charge-Charge Interaction and Ionic Strength

We present a thermodynamic study of the interaction of synthetic, linear polyelectrolytes with bovine serum albumin (BSA). All polyelectrolytes are based on poly(allyl glycidyl ether) which has been modified by polymer-analogous reaction with anionic (-SO₃Na), cationic (-NH₃Cl or -NHMe₂Cl) or zwitterionic groups (-NMe₂(CH₂)₃SO₃). While the anionic polymer shows a very weak interaction, the zwitterionic polymer exhibits no interaction with BSA (pI = 4.7) under the applied pH = 7.4, ionic strength (I = 23–80 mM) and temperature conditions (T = 20–37 °C). A strong binding, however, was observed for the polycations bearing primary amino or tertiary dimethyl amino groups, which could be analysed in detail by isothermal titration calorimetry (ITC). The analysis was done using an expression which describes the free energy of binding, ΔG_b, as the function of the two decisive variables, temperature, T, and salt concentration, c_s. The underlying model splits ΔG_b into a term related to counterion release and a term related to water release. While the number of released counter ions is similar for both systems, the release of bound water is more important for the primary amine compared to the tertiary N,N-dimethyl amine presenting polymer. This finding is further traced back to a closer contact of the polymers’ protonated primary amino groups in the complex with oppositely charged moieties of BSA as compared to the bulkier protonated tertiary amine groups. We thus present an investigation that quantifies both driving forces for electrostatic binding, namely counterion release and change of hydration, which contribute to a deeper understanding with direct impact on future advancements in the biomedical field.

Substitutions at Nonconserved Rheostat Positions Modulate Function by Rewiring Long-Range, Dynamic Interactions

Amino acid substitutions at nonconserved protein positions can have noncanonical and "long-distance" outcomes on protein function. Such outcomes might arise from changes in the internal protein communication network, which is often accompanied by changes in structural flexibility. To test this, we calculated flexibilities and dynamic coupling for positions in the linker region of the lactose repressor protein. This region contains nonconserved positions for which substitutions alter DNA-binding affinity. We first chose to study 11 substitutions at position 52. In computations, substitutions showed long-range effects on flexibilities of DNA-binding positions, and the degree of flexibility change correlated with experimentally measured changes in DNA binding. Substitutions also altered dynamic coupling to DNA-binding positions in a manner that captured other experimentally determined functional changes. Next, we broadened calculations to consider the dynamic coupling between 17 linker positions and the DNA-binding domain. Experimentally, these linker positions exhibited a wide range of substitution outcomes: Four conserved positions tolerated hardly any substitutions ("toggle"), ten nonconserved positions showed progressive changes from a range of substitutions ("rheostat"), and three nonconserved positions tolerated almost all substitutions ("neutral"). In computations with wild-type lactose repressor protein, the dynamic couplings between the DNA-binding domain and these linker positions showed varied degrees of asymmetry that correlated with the observed toggle/rheostat/neutral substitution outcomes. Thus, we propose that long-range and noncanonical substitutions outcomes at nonconserved positions arise from rewiring long-range communication among functionally important positions. Such calculations might enable predictions for substitution outcomes at a range of nonconserved positions.

Interaction of Polyelectrolytes with Proteins: Quantifying the Role of Water

A theoretical model is presented for the free energy ΔGb of complex formation between a highly charged polyelectrolyte and a protein. The model introduced here comprises both the effect of released counterions and the uptake or release of water molecules during complex formation. The resulting expression for ΔGb is hence capable of describing the dependence of ΔGb on temperature as well as on the concentration of salt in the system: An increase of the salt concentration in the solution increases the activity of the ions and counterion release becomes less effective for binding. On the other hand, an increased salt concentration leads to the decrease of the activity of water in bulk. Hence, release of water molecules during complex formation will be more advantageous and lead to an increase of the magnitude of ΔGb and the binding constant. It is furthermore demonstrated that the release or uptake of water molecules is the origin of the marked enthalpy-entropy cancellation observed during complex formation of polyelectrolytes with proteins. The comparison with experimental data on complex formation between a synthetic (sulfated dendritic polyglycerol) and natural polyelectrolytes (DNA; heparin) with proteins shows full agreement with theory.

Understanding the Interaction of Polyelectrolyte Architectures with Proteins and Biosystems

The counterions neutralizing the charges on polyelectrolytes such as DNA or heparin may dissociate in water and greatly influence the interaction of such polyelectrolytes with biomolecules, particularly proteins. In this Review we give an overview of studies on the interaction of proteins with polyelectrolytes and how this knowledge can be used for medical applications. Counterion release was identified as the main driving force for the binding of proteins to polyelectrolytes: Patches of positive charge become multivalent counterions of the polyelectrolyte and lead to the release of counterions from the polyelectrolyte and a concomitant increase in entropy. This is shown from investigations on the interaction of proteins with natural and synthetic polyelectrolytes. Special emphasis is paid to sulfated dendritic polyglycerols (dPGS). The Review demonstrates that we are moving to a better understanding of charge-charge interactions in systems of biological relevance. Research along these lines will aid and promote the design of synthetic polyelectrolytes for medical applications.

Evidence for Dual Site Binding of Nile Blue A toward DNA: Spectroscopic, Thermodynamic, and Molecular Modeling Studies

Binding of Nile Blue (NB) with calf thymus DNA has been studied using molecular modeling, spectroscopic, and thermodynamic techniques. Our study revealed that NB binds to the DNA helix by two types of modes (groove binding and intercalation) simultaneously. The thermodynamic study showed that the overall binding free energy is a combination of several negative and positive free energy changes. The binding was favored by negative enthalpy and positive entropy changes (due to the release of water from the DNA helix). The docking study validated all experimental evidence and showed that NB binds to a DNA minor groove at low concentrations and switches to intercalation mode at higher concentrations.

Conformational Plasticity and DNA-Binding Specificity of the Eukaryotic Transcription Factor Pax5

The eukaryotic transcription factor Pax5 has a DNA-binding Paired domain composed of two independent helical bundle subdomains joined by a flexible linker. Previously, we showed distinct biophysical properties of the N-terminal (NTD) and C-terminal (CTD) subdomains, with implications for how these two regions cooperate to distinguish nonspecific and cognate DNA sites [Perez-Borrajero, C., et al. (2016) J. Mol. Biol. 428, 2372-2391]. In this study, we combined experimental methods and molecular dynamics (MD) simulations to dissect the mechanisms underlying the functional differences between the Pax5 subdomains. Both subdomains showed a similar dependence of DNA-binding affinity on ionic strength. However, due to a greater contribution of non-ionic interactions, the NTD bound its cognate DNA half-site with an affinity approximately 10-fold higher than that of the CTD with its half-site. These interactions involve base-mediated contacts as evidenced by nuclear magnetic resonance spectroscopy-monitored chemical shift perturbations. Isothermal titration calorimetry revealed that favorable enthalpic and compensating unfavorable entropic changes were substantially larger for DNA binding by the NTD than by the CTD. Complementary MD simulations indicated that the DNA recognition helix H3 of the NTD is particularly flexible in the absence of DNA and undergoes the largest changes in conformational dynamics upon binding. Overall, these data suggest that the differences observed for the subdomains of Pax5 are due to the coupling of DNA binding with dampening of motions in the NTD required for specific base contacts. Thus, the conformational plasticity of the Pax5 Paired domain underpins the differing roles of its subdomains in association with nonspecific versus cognate DNA sites.

Quadruplex-Duplex Junction: A High-Affinity Binding Site for Indoloquinoline Ligands

A parallel quadruplex derived from the Myc promoter sequence was extended by a stem-loop duplex at either its 5'- or 3'-terminus to mimic a quadruplex-duplex (Q-D) junction as a potential genomic target. High-resolution structures of the hybrids demonstrate continuous stacking of the duplex on the quadruplex core without significant perturbations. An indoloquinoline ligand carrying an aminoalkyl side chain was shown to bind the Q-D hybrids with a very high affinity in the order K_a ≈10⁷  m^-1 irrespective of the duplex location at the quadruplex 3'- or 5'-end. NMR chemical shift perturbations identified the tetrad face of the Q-D junction as specific binding site for the ligand. However, calorimetric analyses revealed significant differences in the thermodynamic profiles upon binding to hybrids with either a duplex extension at the quadruplex 3'- or 5'-terminus. A large enthalpic gain and considerable hydrophobic effects are accompanied by the binding of one ligand to the 3'-Q-D junction, whereas non-hydrophobic entropic contributions favor binding with formation of a 2:1 ligand-quadruplex complex in case of the 5'-Q-D hybrid.

Heat Capacity Changes (ΔCp) for Interconversions between Differentially-Ordered DNA States within Physiological Temperature Domains: Implications for Biological Regulatory Switches

Knowledge of differences in heat capacity changes (ΔC_p) between biopolymer states provides essential information about the temperature dependence of the thermodynamic properties of these states, while also revealing insights into the nature of the forces that drive the formation of functional and dysfunctional biopolymer "order." In contrast to proteins, for nucleic acids there is a dearth of direct experimental determination of this information-rich parameter, a deficiency that compromises interpretations of the ever-increasing thermodynamic analyses of nucleic acid properties; particularly as they relate to differential nucleic acid (meta)stability states and their potential biological functions. Here we demonstrate that such heat capacity differences, in fact, exist not only between traditionally measured native to fully unfolded (assumed "random coil") DNA states, but also between competing order-to-order transformations. We illustrate the experimental approach by measuring the heat capacity change between "native"/ordered, sequence homologous, "isomeric" DNA states that differ in conformation but not sequence. Importantly, these heat capacity differences occur within biologically relevant temperature ranges. In short, we describe a new and general method to measure the value of such heat capacity differences anywhere in experimentally accessible conformational and temperature space; in this case, between two metastable bulge loop states, implicated in DNA expansion diseases, and their competing, fully paired, thermodynamically more stable duplex states. This measurement reveals a ΔC_p of 61 ± 7 cal mol_bp ^-1 K ^-1. Such heat capacity differences between competing DNA "native" ensemble states must be considered when evaluating equilibria between different DNA "ordered" conformations, including the assessment of the differential stabilizing forces and potential biological functions of competing DNA "structured" motifs.

H/D Exchange Characterization of Silent Coupling: Entropy-Enthalpy Compensation in Allostery

The allosteric coupling constant in K-type allosteric systems is defined as a ratio of the binding of substrate in the absence of effector to the binding of the substrate in the presence of a saturating concentration of effector. As a result, the coupling constant is itself an equilibrium value comprised of a ΔH and a TΔS component. In the scenario in which TΔS completely compensates ΔH, no allosteric influence of effector binding on substrate affinity is observed. However, in this "silent coupling" scenario, the presence of effector causes a change in the ΔH associated with substrate binding. A suggestion has now been made that "silent modulators" are ideal drug leads because they can be modified to act as either allosteric activators or inhibitors. Any attempt to rationally design the effector to be an allosteric activator or inhibitor is likely to be benefitted by knowledge of the mechanism that gives rise to coupling. Hydrogen/deuterium exchange with mass spectrometry detection has now been used to identify regions of proteins that experience conformational and/or dynamic changes in the allosteric regulation. Here, we demonstrate the expected temperature dependence of the allosteric regulation of rabbit muscle pyruvate kinase by Ala to demonstrate that this effector reduces substrate (phosphoenolpyruvate) affinity at 35°C and at 10°C but is silent at intermediate temperatures. We then explore the use of hydrogen/deuterium exchange with mass spectrometry to evaluate the areas of the protein that are modified in the mechanism that gives rise to the silent coupling between Ala and phosphoenolpyruvate. Many of the peptide regions of the protein identified as changing in this silent system (Ala as the effector) were included in changes previously identified for allosteric inhibition by Phe.

A Disorder-to-Order Transition Mediates RNA Binding of the Caenorhabditis elegans Protein MEX-5

CCCH-type tandem zinc finger (TZF) domains are found in many RNA-binding proteins (RBPs) that regulate the essential processes of post-transcriptional gene expression and splicing through direct protein-RNA interactions. In Caenorhabditis elegans, RBPs control the translation, stability, or localization of maternal messenger RNAs required for patterning decisions before zygotic gene activation. MEX-5 (Muscle EXcess) is a C. elegans protein that leads a cascade of RBP localization events that is essential for axis polarization and germline differentiation after fertilization. Here, we report that at room temperature, the CCCH-type TZF domain of MEX-5 contains an unstructured zinc finger that folds upon binding of its RNA target. We have characterized the structure and dynamics of the TZF domain of MEX-5 and designed a variant MEX-5 in which both fingers are fully folded in the absence of RNA. Within the thermal range experienced by C. elegans, the population of the unfolded state of the TZF domain of MEX-5 varies. We observe that the TZF domain becomes less disordered at lower temperatures and more disordered at higher temperatures. However, in the temperature range in which C. elegans is fertile, when MEX-5 needs to be functional, only one of the two zinc fingers is folded.

Polyamines and its analogue modulates amyloid fibrillation in lysozyme: A comparative investigation

BACKGROUND

Polyamines can induce protein aggregation that can be related to the physiology of the cellular function. Polyamines have been implicated in protein aggregation which may lead to neuropathic and non neuropathic amyloidosis.

SCOPE OF REVIEW

Change in the level of polyamine concentration has been associated with ageing and neurodegeneration such as Parkinson's disease, Alzheimer's disease. Lysozyme aggregation in the presence of polyamines leads to non neuropathic amyloidosis. Polyamine analogues can suppress or inhibit protein aggregation suggesting their efficacy against amyloidogenic protein aggregates.

MAJOR CONCLUSIONS

In this study we report the comparative interactions of lysozyme with the polyamine analogue, 1-naphthyl acetyl spermine in comparison with the biogenic polyamines through spectroscopy, calorimetry, imaging and docking techniques. The findings revealed that the affinity of binding varied as spermidine > 1-naphthyl acetyl spermine > spermine. The biogenic polyamines accelerated the rate of fibrillation significantly, whereas the analogue inhibited the rate of fibrillation to a considerable extent. The polyamines bind near the catalytic diad residues viz. Glu35 and Asp52, and in close proximity of Trp62 residue. However, the analogue showed dual nature of interaction where its alkyl amine region bind in same way as the biogenic polyamines bind to the catalytic site, while the naphthyl group makes hydrophobic contacts with Trp62 and Trp63, thereby suggesting its direct influence on fibrillation.

GENERAL SIGNIFICANCE

This study, thus, potentiates, the development of a polyamine analogue that can perform as an effective inhibitor targeted towards aggregation of amyloidogenic proteins.

Signatures of Specific DNA Binding by the AT-Rich Interaction Domain of BAF250a

The AT-rich interaction domain (ARID) containing BAF250a is a subunit of the BAF-A class of SWI/SNF chromatin remodeling complexes. The ARID belongs to a family of conserved DNA binding domains found in several eukaryotic proteins; however, its exact contribution to BAF250a function and the mechanism of its DNA binding are not well understood. Here we have probed the interaction of the BAF250a ARID with three different double-stranded DNA (dsDNA) sequences to understand its DNA binding properties. A comprehensive biophysical and thermodynamic study using nuclear magnetic resonance (NMR) spectroscopy and isothermal titration calorimetry revealed the complex nature of BAF250a ARID-DNA interactions. The thermodynamic signatures of the BAF250a ARID with 12 A-T bp dsDNA (AT-12) are distinct from those of 12 G-C bp dsDNA (GC-12) or 12 bp Dickerson dodecamer DNA (DD-12) sequences. We observed that the binding of the BAF250a ARID with AT-12 DNA is enthalpically driven in a tested temperature range of 5-25 °C. BAF250a ARID/AT-12 DNA interaction exhibited a larger negative calorimetric specific heat change (ΔC_p) compared to that of BAF250a ARID/GC-12 DNA or BAF250a ARID/DD-12 DNA interactions. In the presence of salt (NaCl), ARID/AT-12 DNA binding was less perturbed than ARID/GC-12 DNA or ARID/DD-12 DNA binding. Overall, these results show that BAF250a ARID/AT-12 DNA interaction has signatures of "specific" binding. Furthermore, using NMR chemical shift perturbation experiments, we have identified DNA binding residues on the BAF250a ARID and generated a data-driven HADDOCK model of the ARID/DNA complex that was further supported by mutating key lysine residues that were found to be important for DNA binding.

Energetic funnel facilitates facilitated diffusion

Transcription factors (TFs) are able to associate to their binding sites on DNA faster than the physical limit posed by diffusion. Such high association rates can be achieved by alternating between three-dimensional diffusion and one-dimensional sliding along the DNA chain, a mechanism-dubbed facilitated diffusion. By studying a collection of TF binding sites of Escherichia coli from the RegulonDB database and of Bacillus subtilis from DBTBS, we reveal a funnel in the binding energy landscape around the target sequences. We show that such a funnel is linked to the presence of gradients of AT in the base composition of the DNA region around the binding sites. An extensive computational study of the stochastic sliding process along the energetic landscapes obtained from the database shows that the funnel can significantly enhance the probability of TFs to find their target sequences when sliding in their proximity. We demonstrate that this enhancement leads to a speed-up of the association process.

Interaction of proflavine with the RNA polynucleotide polyriboadenylic acid-polyribouridylic acid: photophysical and calorimetric studies

The binding of proflavine, an acriflavine derivative, with the RNA polynucletodide polyadenylic acid-polyuridylic acid is investigated here to understand the structural and thermodynamic basis of the binding process. Such binding data are crucial for designing viable theraperutic agents. Spectroscopic studies clearly suggest a strong binding interaction between proflavine and polyadenylic acid-polyuridylic acid leading to efficient energy transfer between the poly AU base pairs and proflavine. The stoichiometry of proflavine polyadenylic acid-polyuridylic acid binding was independently estimated by continuous variation analysis of Job. An intercalative binding model is envisaged for the binding from hydrodynamic studies. Circular dichroism experiments revealed that the binding induced conformational changes in the RNA, and also led to induction of optical activity in the bound dye molecules. The binding affinity of the complex was deduced to be (6.57 ± 0.75) 10⁵ M^-1 at (298.15 ± 0.10) K from isothermal titration calorimetry experiment. Positive entropy and negative enthalpy changes characterized the complexation. The binding was observed to be weaker both at higher temperatures and increased [Na⁺]. The affinity of binding decreased with increasing [Na⁺]. When the Gibbs energy was parsed between polyelectrolytic and nonpolyelectropytic components, it surprisingly revealed a higher role for the non-polyelectrolytic forces. These results present new data for developing RNA targeted ligands.Communicated by Ramaswamy H. Sarma.

Chemical and Physicochemical Properties of Gangliosides

In this chapter, we briefly describe the structural features of gangliosides, and focus on the peculiar chemicophysical features of gangliosides, an important class of membrane amphipathic lipids that represent an important driving force determining the organization and properties of cellular membranes.

Revealing the Energetics of Ligand-Quadruplex Interactions Using Isothermal Titration Calorimetry

The thermodynamic characterization of G4-ligand interactions has shown to be a powerful adjunct to structural information in the rational design and optimization of potent G-quadruplex ligands for use in therapeutics, diagnostics, or other technological applications. Isothermal titration calorimetry (ITC) can resolve energetic contributions to complex formation and constitutes the only available experimental method to directly measure binding enthalpies. A general protocol for using ITC in studies on quadruplex-ligand interactions with details on the experimental setup, data analysis, and potential pitfalls is presented. The methodologies used are illustrated on results obtained from the targeting of a parallel DNA G-quadruplex with a G4-binding indoloquinoline derivative.

Hydration differences between the major and minor grooves of DNA revealed from heat capacity measurements

The nature of water on the surface of a macromolecule is reflected in the temperature dependence of the heat effect, i.e., the heat capacity change, ΔCp, that accompanies its removal on forming a complex. The relationship between ΔCp and the nature of the surface dehydrated cannot be modeled for DNA by the use of small molecules, as previously done for proteins, since the contiguous surfaces of the grooves cannot be treated as the sum of small component molecules such as nucleotides. An alternative approach is used here in which ΔCp is measured for the formation of several protein/DNA complexes and the calculated contribution from protein dehydration subtracted to yield the heat capacity change attributable to dehydration of the DNA. The polar and apolar surface areas of the DNA dehydrated on complex formation were calculated from the known structures of the complexes, allowing heat capacity coefficients to be derived representing dehydration of unit surface area of polar and apolar surface in both grooves. Dehydration of apolar surfaces in both grooves is essentially identical and accompanied by a reduction in ΔCp by about 3 J K⁻¹ mol⁻¹ (Ų)⁻¹, a value of somewhat greater magnitude than observed for proteins {ΔCp = − 1.79 J K⁻¹ mol⁻¹ (Ų)⁻¹}. In contrast, dehydration of polar surfaces is very different in the two grooves: in the minor groove ΔCp increases by 2.7 J K⁻¹ mol⁻¹ (Ų)⁻¹, but in the major groove, although ΔCp is also positive, it is low in value: + 0.4 J K⁻¹ mol⁻¹ (Ų)⁻¹. Physical explanations for the magnitudes of ΔCp are discussed.

Thermodynamic signature of indoloquinolines interacting with G-quadruplexes: Impact of ligand side chain

Binding of indoloquinolines with different aliphatic side chains to a parallel G-quadruplex derived from the MYC promoter sequence was characterized by optical and calorimetric measurements. ITC experiments performed at different temperatures enabled the determination of molar heat capacity changes upon quadruplex binding and a partitioning of the total binding free enthalpy into contributing terms with hydrophobic effects being major driving forces for all derivatives. Whereas affinities increase for indoloquinolines equipped with a long and positively charged side arm, the highest contribution of specific intermolecular interactions anticipated to impart enhanced specificity is found for a ligand with an uncharged ether aliphatic tail. Obtained thermodynamic signatures may considerably aid in the rational selection of ligand side chains for G-quadruplex binders with enhanced affinity or selectivity.

RheoScale: A tool to aggregate and quantify experimentally determined substitution outcomes for multiple variants at individual protein positions

Human mutations often cause amino acid changes (variants) that can alter protein function or stability. Some variants fall at protein positions that experimentally exhibit "rheostatic" mutation outcomes (different amino acid substitutions lead to a range of functional outcomes). In ongoing studies of rheostat positions, we encountered the need to aggregate experimental results from multiple variants, to describe the overall roles of individual positions. Here, we present "RheoScale" which generates quantitative scores to discriminate rheostat positions from those with "toggle" (most substitutions abolish function) or "neutral" (most substitutions have wild-type function) outcomes. RheoScale scores facilitate correlations of experimental data (such as binding affinity or stability) with structural and bioinformatic analyses. The RheoScale calculator is encoded into a Microsoft Excel workbook and an R script. Example analyses are shown for three model protein systems, including one assessed via deep mutational scanning. The RheoScale calculator quickly and efficiently provided quantitative descriptions that were in good agreement with prior qualitative observations. As an example application, scores were compared to the example proteins' structures; strong rheostat positions tended to occur in dynamic locations. In the future, RheoScale scores can be easily integrated into computational studies to facilitate improved algorithms for predicting outcomes of human variants.

Comparative Study of Toluidine Blue O and Methylene Blue Binding to Lysozyme and Their Inhibitory Effects on Protein Aggregation

A comparative binding interaction of toluidine blue O (TBO) and methylene blue (MB) with lysozyme was investigated by multifaceted biophysical approaches as well as from the aspects of in silico biophysics. The bindings were static, and it occurred via ground-state complex formation as confirmed from time-resolved fluorescence experiments. From steady-state fluorescence and anisotropy, binding constants were calculated, and it was found that TBO binds more effectively than MB. Synchronous fluorescence spectra revealed that binding of dyes to lysozyme causes polarity changes around the tryptophan (Trp) moiety, most likely at Trp 62 and 63. Calorimetric titration also depicts the higher binding affinity of TBO over MB, and the interactions were exothermic and entropy-driven. In silico studies revealed the potential binding pockets in lysozyme and the participation of residues Trp 62 and 63 in ligand binding. Furthermore, calculations of thermodynamic parameters from the theoretical docking studies were in compliance with experimental observations. Moreover, an inhibitory effect of these dyes to lysozyme fibrillogenesis was examined, and the morphology of the formed fibril was scanned by atomic force microscopy imaging. TBO was observed to exhibit higher potential in inhibiting the fibrillogenesis than MB, and this phenomenon stands out as a promising antiamyloid therapeutic strategy.

Gangliosides in Membrane Organization

Since the structure of GM1 was elucidated 55years ago, researchers have been attracted by the sialylated glycans of gangliosides. Gangliosides head groups, protruding toward the extracellular space, significantly contribute to the cell glycocalyx; and in certain cells, such as neurons, are major determinants of the features of the cell surface. Expression of glycosyltransferases involved in the de novo biosynthesis of gangliosides is tightly regulated along cell differentiation and activation, and is regarded as the main metabolic mechanism responsible for the acquisition of cell-specific ganglioside patterns. The resulting sialooligosaccharides are characterized by a high degree of geometrical complexity and by highly dynamic properties, which seem to be functional for complex interactions with other molecules sitting on the same cellular membrane (cis-interactions) or soluble molecules present in the extracellular environment, or molecules associated with the surface of other cells (trans-interactions). There is no doubt that the multifaceted biological functions of gangliosides are largely dependent on oligosaccharide-mediated molecular interactions. However, gangliosides are amphipathic membrane lipids, and their chemicophysical, aggregational, and, consequently, biological properties are dictated by the properties of the monomers as a whole, which are not merely dependent on the structures of their polar head groups. In this chapter, we would like to focus on the peculiar chemicophysical features of gangliosides (in particular, those of the nervous system), that represent an important driving force determining the organization and properties of cellular membranes, and to emphasize the causal connections between altered ganglioside-dependent membrane organization and relevant pathological conditions.

Deciphering the complexation process of a fluoroquinolone antibiotic, levofloxacin, with bovine serum albumin in the presence of additives

The current work aims to explore the thermodynamic and conformational aspects for the binding of fluoroquinolone antibacterial drug, levofloxacin (LFC), with bovine serum albumin (BSA) using calorimetric, spectroscopic (UV-visible, fluorescence, circular dichroism, and ¹H NMR), dynamic light scattering (DLS) and computational methods (molecular docking). The binding of LFC with BSA at two sequential sites with higher affinity (~10³M^-1) at the first site has been explored by calorimetry whereas the binding at a single site with affinity of the order of ~10⁴M^-1 has been observed from fluorescence spectroscopy. The calorimetric study in the presence of additives along with docking analysis reveals the significant role of electrostatic, hydrogen bonding, and hydrophobic interactions in the association process. The slight conformational changes in protein as well as the changes in the water network structure around the binding cavity of protein have been observed from spectroscopic and DLS measurements. The LFC induced quenching of BSA fluorescence was observed to be initiated mainly through the static quenching process and this suggests the formation of ground state LFC-BSA association complex. The stronger interactions of LFC in the cavity of Sudlow site I (subdomain IIA) of protein have been explored from site marker calorimetric and molecular docking study.

Ground- and Excited-State Interactions of a Psoralen Derivative with Human Telomeric G-Quadruplex DNA

G-quadruplex DNA has been a recent target for anticancer agents, and its binding interactions with small molecules, often used as anticancer drugs, have become an important area of research. Considering that psoralens have long been studied in the context of duplex DNA but that very little is known about their potential as G-quadruplex binders and their excited-state interaction with the latter has not been explored, we have studied herein the binding of a planar water-soluble psoralen derivative, 4'-aminomethyl-4,5',8-trimethylpsoralen (AMT), with the 22-mer human telomeric G-quadruplex-forming sequence, AGGG(TTAGGG)₃, labeled here as (hTel22), and investigated the consequences of photoexcitation of AMT by calorimetric and spectroscopic techniques. The results show an enthalpy-driven 1:1 binding of AMT with hTel22 via end-stacking mode. Fluorescence quenching experiments on 6-fluorescein amidite-labeled oligomers indicate that the binding site is nearer to the 3' end of hTel22 in the diagonal loop region. Femtosecond time-resolved transient absorption measurements indicate electron transfer from the guanine moiety of hTel22 to photoexcited AMT, leading to the formation of a radical pair species (AMT^•-G^•+), which survives for 30 ps and is favored by a parallel/quasi-parallel orientation between the two. The findings reveal psoralens as a prospective class of compounds for the development of anticancer therapeutics by targeting the G-quadruplex DNA.

Comparative analyses of the thermodynamic RNA binding signatures of different types of RNA recognition motifs

RNA recognition motifs (RRMs) are structurally versatile domains important in regulation of alternative splicing. Structural mechanisms of sequence-specific recognition of single-stranded RNAs (ssRNAs) by RRMs are well understood. The thermodynamic strategies are however unclear. Therefore, we utilized microcalorimetry and semi-empirical analyses to comparatively analyze the cognate ssRNA binding thermodynamics of four different RRM domains, each with a different RNA binding mode. The different binding modes are: canonical binding to the β-sheet surface; canonical binding with involvement of N- and C-termini; binding to conserved loops; and binding to an α-helix. Our results identify enthalpy as the sole and general force driving association at physiological temperatures. Also, networks of weak interactions are a general feature regulating stability of the different RRM–ssRNA complexes. In agreement, non-polyelectrolyte effects contributed between ∼75 and 90% of the overall free energy of binding in the considered complexes. The various RNA binding modes also displayed enormous heat capacity differences, that upon dissection revealed large differential changes in hydration, conformations and dynamics upon binding RNA. Altogether, different modes employed by RRMs to bind cognate ssRNAs utilize various thermodynamics strategies during the association process.

Wing 1 of protein HOP2 is as important as helix 3 in DNA binding by MD simulation

The repair of programmed DNA double-strand breaks through recombination is required for proper association and disjunction of the meiotic homologous chromosomes. Meiosis-specific protein HOP2 plays essential roles in recombination by promoting recombinase activities. The N-terminal domain of HOP2 interacts with DNA through helix 3 (H3) and wing 1 (W1). Mutations in wing 1 (Y65A/K67A/Q68A) slightly weakened the binding but mutations in helices 2 and 3 (Q30A/K44A/K49A) nearly abolished the binding. To better understand such differential effects at atomic level, molecular dynamics simulations were employed. Despite losing some hydrogen bonds, the W1-mutant DNA complex was rescued by stronger hydrophobic interactions. For the wild type and W1-mutant, the protein was found to slide along the DNA grooves as the DNA rolls along its double-helix axis. This motion could be functionally important to facilitate the precise positioning of the single-stranded DNA with the homologous double-stranded DNA. The sliding motion was reduced in the W1-mutant. The H-mutant nearly lost all intermolecular interactions. Moreover, an additional mutation in wing 1 (Y65A/K67A/Q68A/K69A) also caused complete complex dissociation. Therefore, both wing 1 and helix 3 make important contribution to the DNA binding, which could be important to the strand invasion function of HOP2 homodimer and HOP2-MND1 heterodimer. Similar to cocking a medieval crossbow with the archer's foot placed in the stirrup, wing 1 may push the minor groove to cause distortion while helix 3 grabs the major groove.

A Review of Spectroscopic and Biophysical-Chemical Studies of the Complex of Cyclobutane Pyrimidine Dimer Photolyase and Cryptochrome DASH with Substrate DNA

Cyclobutane pyrimidine dimer (CPD) photolyase (PL) is a structure-specific DNA repair enzyme that uses blue light to repair CPD on DNA. Cryptochrome (CRY) DASH enzymes use blue light for the repair of CPD lesions on single-stranded (ss) DNA, although some may also repair these lesions on double-stranded (ds) DNA. In addition, CRY DASH may be involved in blue light signaling, similar to cryptochromes. The focus of this review is on spectroscopic and biophysical-chemical experiments of the enzyme-substrate complex that have contributed to a more detailed understanding of all the aspects of the CPD repair mechanism of CPD photolyase and CRY DASH. This will be performed in the backdrop of the available X-ray crystal structures of these enzymes bound to a CPD-like lesion. These structures helped to confirm conclusions that were drawn earlier from spectroscopic and biophysical-chemical experiments, and they have a critical function as a framework to design new experiments and to interpret new experimental data. This review will show the important synergy between X-ray crystallography and spectroscopic/biophysical-chemical investigations that is essential to obtain a sufficiently detailed picture of the overall mechanism of CPD photolyases and CRY DASH proteins.

Exploring the interaction of phenothiazinium dyes methylene blue, new methylene blue, azure A and azure B with tRNAPhe: spectroscopic, thermodynamic, voltammetric and molecular modeling approach

RNA targeting by small molecules.

Binding interaction of phenothiazinium dyes with double stranded RNAs: Spectroscopic and calorimetric investigation

RNA targeting through small molecules is an emerging and promising therapeutic route that necessitates identification of small molecules that can selectively target specific RNA structures. In this context a comparative study of the interaction of two phenothiazinium dyes thionine (THN) and toluidine blue O (TBO) with three double stranded RNA polynucleotides (ds RNAs) viz. poly(I).poly(C), poly(A).poly(U) and poly(C).poly(G) was conducted by various biophysical techniques. A higher binding of THN with poly(I).poly(C) over poly(A).poly(U) and poly(C).poly(G) was observed. The intercalative binding and RNA induced fluorescence quenching of the dyes through a static mechanism was confirmed by viscosity studies and steady state polarization anisotropy experiments. Binding induced structural perturbation in the RNA polynucleotides was confirmed from circular dichroism spectroscopy. DSC and thermal melting experiments confirmed that the binding resulted in strong thermal stabilization. The binding affinity of THN with poly(I).poly(C) was the highest followed by that to poly(A).poly(U) and poly(C).poly(G). The trend was the same for TBO also, but THN bound stronger than TBO. The binding of the dyes was characterized by strong negative enthalpy changes with minimum positive entropy changes indicating typical intercalative interaction. The results presented here may be useful to design new types of RNA binding antitumor, antibacterial and anticancer agents.

Mechanisms of Protein Translocation on DNA Are Differentially Responsive to Water Activity

Water plays important but poorly understood roles in the functions of most biomolecules. We are interested in understanding how proteins use diverse search mechanisms to locate specific sites on DNA; here we present a study of the role of closely associated waters in diverse translocation mechanisms. The bacterial DNA adenine methyltransferase, Dam, moves across large segments of DNA using an intersegmental hopping mechanism, relying in part on movement through bulk water. In contrast, other proteins, such as the bacterial restriction endonuclease EcoRI, rely on a sliding mechanism, requiring the protein to stay closely associated with DNA. Here we probed how these two mechanistically distinct proteins respond to well-characterized osmolytes, dimethyl sulfoxide (DMSO), and glycerol. The ability of Dam to move over large segments of DNA is not impacted by either osmolyte, consistent with its minimal reliance on a sliding mechanism. In contrast, EcoRI endonuclease translocation is significantly enhanced by DMSO and inhibited by glycerol, providing further corroboration that these proteins rely on distinct translocation mechanisms. The well-established similar effects of these osmolytes on bulk water, and their differential effects on macromolecule-associated waters, support our results and provide further evidence of the importance of water in interactions between macromolecules and their ligands.

Multispectroscopic and calorimetric studies on the binding of the food colorant tartrazine with human hemoglobin

Interaction of the food colorant tartrazine with human hemoglobin was studied using multispectroscopic and microcalorimetric techniques to gain insights into the binding mechanism and thereby the toxicity aspects. Hemoglobin spectrum showed hypochromic changes in the presence of tartrazine. Quenching of the fluorescence of hemoglobin occurred and the quenching mechanism was through a static mode as revealed from temperature dependent and time-resolved fluorescence studies. According to the FRET theory the distance between β-Trp37 of hemoglobin and bound tartrazine was evaluated to be 3.44nm. Synchronous fluorescence studies showed that tartrazine binding led to alteration of the microenvironment around the tryptophans more in comparison to tyrosines. 3D fluorescence and FTIR data provided evidence for conformational changes in the protein on binding. Circular dichroism studies revealed that the binding led to significant loss in the helicity of hemoglobin. The esterase activity assay further complemented the circular dichroism data. Microcalorimetric study using isothermal titration calorimetry revealed the binding to be exothermic and driven largely by positive entropic contribution. Dissection of the Gibbs energy change proposed the protein-dye complexation to be dominated by non-polyelectrolytic forces. Negative heat capacity change also corroborated the involvement of hydrophobic forces in the binding process.

Molecular Recognition of tRNA with 1-Naphthyl Acetyl Spermine, Spermine, and Spermidine: A Thermodynamic, Biophysical, and Molecular Docking Investigative Approach

The role of tRNA in protein translational machinery and the influence of polyamines on the interaction of acylated and deacylated tRNA with ribosomes make polyamine-tRNA interaction conspicuous. We studied the interaction of two biogenic polyamines, spermine (SPM) and spermidine (SPD), with tRNA^Phe and compared the results to those of the analogue 1-naphthyl acetyl spermine (NASPM). The binding affinity of SPM was comparable to that of NASPM; both were higher than that of SPD. The interactions led to significant thermal stabilization of tRNA^Phe and an increase in the enthalpy of transition. All the interactions were exothermic in nature and displayed prominent enthalpy-entropy compensation behavior. The entropy-driven nature of the interaction, the structural perturbations observed, and docking results proved that the polyamines were bound in the groove of the anticodon arm of tRNA^Phe. The amine groups of polyamines were involved in extensive electrostatic, H-bonding, and van der Waals interactions with tRNA^Phe. The naphthyl group of NASPM showed an additional stacking interaction with G24 and G26 of tRNA^Phe, which was absent in others. The results demonstrate that 1-naphthyl acetyl spermine can target the same binding sites as the biogenic polyamines without substituting for the functions played by them, which may lead to exhibition of selective anticancer cytotoxicity.

Spectroscopic and calorimetric investigations on the binding of phenazinium dyes safranine-O and phenosafranine to double stranded RNA polynucleotides

RNA targeting through small molecules that can selectively bind specific RNA structures is an important current strategy in therapeutic drug development. Towards this strategy a comparative study on the interaction of two phenazinium dyes, safranine-O and phenosafranine to double stranded RNAs, poly(I).poly(C), poly(A).poly(U) and poly(C).poly(G) was performed. Spectrophotometric and spectrofluorimetric studies revealed non-cooperative binding of the dyes to the duplex RNA with binding constants of the order 10(5)M(-1) with a higher affinity of safranine-O to poly(I).poly(C) followed by poly(A).poly(U) and poly(C).poly(G). Anisotropy and fluorescence quenching results confirmed an intercalation mode of binding for the dyes on these RNAs. Binding induced conformational changes in the RNA polynucleotides were revealed from circular dichroism data. Thermal melting study and DSC experiments demonstrated stabilization of dye-RNA complexes. Calorimetric studies revealed that the binding was accompanied by a large positive entropy term with a small negative enthalpy contributions. Significant hydrophobic forces in the complexation of the double stranded RNAs with the dyes were confirmed from the negative heat capacity changes. Enthalpy-entropy compensation was also observed in the binding. Parsing of the Gibbs energy suggested a larger non-electrostatic contribution in all the cases. The results presented here may be helpful to design new types of RNA-based therapeutic agents.

Structure and dynamics of the tetrameric mnt repressor and a model for its DNA complex

Abstract The tetrameric Mnt repressor of bacteriophage P22 consists of two dimeric DNA-binding domains and a tetramerization domain. The NOE and chemical shift data demonstrate that the structures of the domains in the wild-type repressor protein are similar to those of the separate domains, the three-dimensional structures of which have been determined previously. (15)N relaxation measurements show that the linker that connects the anti-parallel four-helix bundle with the two β-sheet DNA-binding dimers is highly flexible. No evidence was found for interactions between the distinct modules. The (15)N relaxation properties of the two domains differ substantially, confirming their structural independence. A model in which one two-stranded coiled coil of the four-helix bundle is attached to one N-terminal dimer is most consistent with the biochemical data and (15)N relaxation data. For the Mnt-DNA complex this geometry fits with a model in which the two β-sheet DNA-binding domains are bound at two successive major grooves of the Mnt operator and the tetramerization domain is packed between these two DNA-bound dimers. In such a model the two-fold symmetry axis of the four-helix bundle coincides with that of the operator sequence and the two bound dimers. Bending of the Mnt operator of approximately 30° upon binding of the tetramer, as measured by gel-shift assays, is in agreement with this model of the Mnt-DNA complex.