The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations

Systematic enhancement of protein crystallization efficiency by bulk lysine-to-arginine (KR) substitution

Structural genomics consortia established that protein crystallization is the primary obstacle to structure determination using x-ray crystallography. We previously demonstrated that crystallization propensity is systematically related to primary sequence, and we subsequently performed computational analyses showing that arginine is the most overrepresented amino acid in crystal-packing interfaces in the Protein Data Bank. Given the similar physicochemical characteristics of arginine and lysine, we hypothesized that multiple lysine-to-arginine (KR) substitutions should improve crystallization. To test this hypothesis, we developed software that ranks lysine sites in a target protein based on the redundancy-corrected KR substitution frequency in homologs. This software can be run interactively on the worldwide web at https://www.pxengineering.org/. We demonstrate that three unrelated single-domain proteins can tolerate 5-11 KR substitutions with at most minor destabilization, and, for two of these three proteins, the construct with the largest number of KR substitutions exhibits significantly enhanced crystallization propensity. This approach rapidly produced a 1.9 Å crystal structure of a human protein domain refractory to crystallization with its native sequence. Structures from Bulk KR-substituted domains show the engineered arginine residues frequently make hydrogen-bonds across crystal-packing interfaces. We thus demonstrate that Bulk KR substitution represents a rational and efficient method for probabilistic engineering of protein surface properties to improve crystallization.

Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions

The interactions of amino acid side-chains confer diverse energetic contributions and physical properties to a protein's stability and function. Various computational tools estimate the effect of changing a given amino acid on the protein's stability based on parametrized (free) energy functions. When parametrized for the prediction of protein stability in water, such energy functions can lead to suboptimal results for other solvents, such as ionic liquids (IL), aqueous ionic liquids (aIL), or salt solutions. However, to our knowledge, no comprehensive data are available describing the energetic effects of aIL on intramolecular protein interactions. Here, we present the most comprehensive set of potential of mean force (PMF) profiles of pairwise protein-residue interactions to date, covering 50 relevant interactions in water, the two biotechnologically relevant aIL [BMIM/Cl] and [BMIM/TfO], and [Na/Cl]. These results are based on a cumulated simulation time of >1 ms. aIL and salt ions can weaken, but also strengthen, specific residue interactions by more than 3 kcal mol^-1, depending on the residue pair, residue-residue configuration, participating ions, and concentration, necessitating considering such interactions specifically. These changes originate from a complex interplay of competitive or cooperative noncovalent ion-residue interactions, changes in solvent structural dynamics, or unspecific charge screening effects and occur at the contact distance but also at larger, solvent-separated distances. This data provide explanations at the atomistic and energetic levels for complex IL effects on protein stability and should help improve the prediction accuracies of computational tools that estimate protein stability based on (free) energy functions.

Diclofenac Ion Hydration: Experimental and Theoretical Search for Anion Pairs

Self-assembly of organic ions in aqueous solutions is a hot topic at the present time, and substances that are well-soluble in water are usually studied. In this work, aqueous solutions of sodium diclofenac are investigated, which, like most medicinal compounds, is poorly soluble in water. Classical MD modeling of an aqueous solution of diclofenac sodium showed equilibrium between the hydrated anion and the hydrated dimer of the diclofenac anion. The assignment and interpretation of the bands in the UV, NIR, and IR spectra are based on DFT calculations in the discrete-continuum approximation. It has been shown that the combined use of spectroscopic methods in various frequency ranges with classical MD simulations and DFT calculations provides valuable information on the association processes of medical compounds in aqueous solutions. Additionally, such a combined application of experimental and calculation methods allowed us to put forward a hypothesis about the mechanism of the effect of diclofenac sodium in high dilutions on a solution of diclofenac sodium.

The Effects of Arginine Glutamate (RE:pair) on Wound Healing and Skin Elasticity Improvement After CO2 Laser Irradiation

BACKGROUND

Glutamic acid is known to be effective for keratinocyte proliferation, but its dermatological application is limited due to its poor solubility in water and various solvents.

AIM

Here, the efficacy of the arginine glutamate ion pair (named as RE:pair) for recovering damaged skin and improving skin elasticity was investigated through the analysis of keratinocyte proliferation and collagen synthesis.

METHODS

Following the structural analysis of RE:pair using spectroscopic methods, a scratch assay, and Pro-Collagen I ELISA, skin tissue changes in wound-induced artificial skin, changes in wound area after laser wound induction, and the sensory evaluation of skin improvement were investigated.

RESULTS

As a result of scratch assay, wound recovery of 94.55±9.57% was confirmed at 10 ppm RE:pair treatment. When evaluation of expression efficacy of procollagen type I, it was found that the expression rate was increased by 32.47±5.62% compared to the control group. Further, the upregulation of the proliferation marker Ki-67 and filaggrin expression in the damage-induced artificial skin was verified. Clinically, the improvement was subjectively verified in terms of the reduction of the wound area, the restoration of the barrier, the improvement of skin elasticity, and through the sensory experience of skin improvement.

CONCLUSION

RE:pair shows a greater therapeutic effect than the individual effects of its constituent amino acids and those of the simple mixtures of these compounds. RE:pair exerts its therapeutic action by promoting the proliferation of keratinocytes and enhancing collagen synthesis in fibroblasts. Accordingly, it can be used throughout the cosmetic industry as an effective amino acid wound healing and skin elasticity improving material.

Colorimetric determination of lead(II) or mercury(II) based on target induced switching of the enzyme-like activity of metallothionein-stabilized copper nanoclusters

It is shown that metallothionein-stabilized copper nanoclusters (MT-CuNCs) display catalase-like activity. In the presence of either lead(II) or mercury(II), the catalase-like activity is converted to a peroxidase-like activity. On addition of Pb(II) or Hg(II), the inhibitory effect of MT-CuNCs on the chromogenic reaction of 3,3',5,5'-tetramethylbenzidine (TMB) with H₂O₂ is weakened. On the other hand, the catalytic effect of the nanoclusters on the chromogenic reaction is increased. The system MT-CuNCs-Pb(II)/Hg(II) exhibits high affinity for the substrates TMB and H₂O₂. Their catalytic behavior follows Michaelis-Menten kinetics. Based on these findings, a method was developed for visual detection (via the blue coloration formed) and spectrophotometric determination (at 450 nm) of Pb(II) and Hg(II). The linear range for Pb(II) extends from 0.7 to 96 μM, and the linear ranges for Hg(II) from 97 nM to 2.3 μM and from 3.1 μM to 15.6 μM. The detection limits are 142 nM for Pb(II) and 43.8 nM for Hg(II). Graphical abstract Metallothionein-stabilized copper nanoclusters (MT-CuNCs) display catalase-like activity. On addition of Pb(II) or Hg(II), the catalase-like activity is converted to a peroxidase-like activity. The latter catalyzes the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) by H₂O₂.

Cyclic dipeptide peroxosolvates: first direct evidence for hydrogen bonding between hydrogen peroxide and a peptide backbone

The crystal structures of cyclic dipeptide peroxosolvates provide valuable insight into the non-redox interaction of hydrogen peroxide with the peptide backbone.

Protamine-gold nanoclusters as peroxidase mimics and the selective enhancement of their activity by mercury ions for highly sensitive colorimetric assay of Hg(II)

We certify that protamine-gold nanoclusters (PRT-AuNCs) synthesized by one-pot method exhibit peroxidase-like activity. The catalytic activity of PRT-AuNCs followed typical Michaelis-Menten kinetics and exhibited higher affinity to 3,3',5,5'-tetramethylbenzidine (TMB) as the substrate compared to that of natural horseradish peroxidase. Meanwhile, we found that Hg(II) could dramatically and selectively enhance the peroxidase-like activity of PRT-AuNCs, and the enhanced mechanism by Hg(II) was demonstrated to be generation of the cationic Au species and the partly oxidized Au species (Au^δ+) by Hg²⁺-Au⁰/Au⁺ interaction. Based on this finding, quantitative determinations of Hg(II) via visual observation and absorption spectra were achieved. The proposed strategy displays high selectivity that arises from the strong aurophilic interaction of mercury towards gold. Moreover, the developed method is highly sensitive with a wide linear range and low detection limit of 1.16 nM. This strategy is not only helpful to develop effective nanomaterials-based artificial enzyme mimics but also irradiative to discover new applications of artificial mimic enzymes in bio-detection, medical diagnostics, and biotechnology. Graphical abstract Protamine-gold nanoclusters (PRT-AuNCs) synthesized by one-pot method exhibit peroxidase-like activity. Hg(II) can stimulate the peroxidase-like activity of PRT-AuNCs selectively, enhancing their ability to catalyze the chromogenic reaction of TMB by H₂O₂.

Hydration of the Carboxylate Group in Anti-Inflammatory Drugs: ATR-IR and Computational Studies of Aqueous Solution of Sodium Diclofenac

Diclofenac (active ingredient of Voltaren) has a significant, multifaceted role in medicine, pharmacy, and biochemistry. Its physical properties and impact on biomolecular structures still attract essential scientific interest. However, its interaction with water has not been described yet at the molecular level. In the present study, we shed light on the interaction between the steric hindrance (the intramolecular N-H···O bond, etc.) carboxylate group (-CO₂^-) with water. Aqueous solution of sodium declofenac is investigated using attenuated total reflection-infrared (ATR-IR) and computational approaches, i.e., classical molecular dynamics (MD) simulations and density functional theory (DFT). Our coupled classical MD simulations, DFT calculations, and ATR-IR spectroscopy results indicated that the -CO₂^- group of the diclofenac anion undergoes strong specific interactions with the water molecules. The combined experimental and theoretical techniques provide significant insights into the spectroscopic manifestation of these interactions and the structure of the hydration shell of the -CO₂^- group. Moreover, the developed methodology for the theoretical analysis of the ATR-IR spectrum could serve as a template for the future IR/Raman studies of the strong interaction between the steric hindrance -CO₂^- group of bioactive molecules with the water molecules in dilute aqueous solutions.

Explaining urokinase type plasminogen activator inhibition by amino-5-hydroxybenzimidazole and two naphthamidine-based compounds through quantum biochemistry

Urokinase plasminogen activator (uPA) is a biomarker and therapeutic target for several cancer types whose inhibition has been shown to slow tumor growth and metastasis.

Conversion of an instantaneous activating K+ channel into a slow activating inward rectifier

The miniature channel, Kcv, is a structural equivalent of the pore of all K⁺ channels. Here, we follow up on a previous observation that a largely voltage-insensitive channel can be converted into a slow activating inward rectifier after extending the outer transmembrane domain by one Ala. This gain of rectification can be rationalized by dynamic salt bridges at the cytosolic entrance to the channel; opening is favored by voltage-sensitive formation of salt bridges and counteracted by their disruption. Such latent voltage sensitivity in the pore could be relevant for the understanding of voltage gating in complex Kv channels.

Inactivation of urease by catechol: Kinetics and structure

Urease is a Ni(II)-containing enzyme that catalyzes the hydrolysis of urea to yield ammonia and carbamate at a rate 10¹⁵ times higher than the uncatalyzed reaction. Urease is a virulence factor of several human pathogens, in addition to decreasing the efficiency of soil organic nitrogen fertilization. Therefore, efficient urease inhibitors are actively sought. In this study, we describe a molecular characterization of the interaction between urease from Sporosarcina pasteurii (SPU) and Canavalia ensiformis (jack bean, JBU) with catechol, a model polyphenol. In particular, catechol irreversibly inactivates both SPU and JBU with a complex radical-based autocatalytic multistep mechanism. The crystal structure of the SPU-catechol complex, determined at 1.50Å resolution, reveals the structural details of the enzyme inhibition.