Theoretical Study on the Alkaline and Neutral Hydrolysis of Succinimide Derivatives in Deamidation Reactions

Structural basis for the hyperthermostability of an archaeal enzyme induced by succinimide formation

Stability of proteins from hyperthermophiles (organisms existing under boiling water conditions) enabled by a reduction of conformational flexibility is realized through various mechanisms. A succinimide (SNN) arising from the post-translational cyclization of the side chains of aspartyl/asparaginyl residues with the backbone amide -NH of the succeeding residue would restrain the torsion angle Ψ and can serve as a new route for hyperthermostability. However, such a succinimide is typically prone to hydrolysis, transforming to either an aspartyl or β-isoaspartyl residue. Here, we present the crystal structure of Methanocaldococcus jannaschii glutamine amidotransferase and, using enhanced sampling molecular dynamics simulations, address the mechanism of its increased thermostability, up to 100°C, imparted by an unexpectedly stable succinimidyl residue at position 109. The stability of SNN109 to hydrolysis is seen to arise from its electrostatic shielding by the side-chain carboxylate group of its succeeding residue Asp110, as well as through n → π^∗ interactions between SNN109 and its preceding residue Glu108, both of which prevent water access to SNN. The stable succinimidyl residue induces the formation of an α-turn structure involving 13-atom hydrogen bonding, which locks the local conformation, reducing protein flexibility. The destabilization of the protein upon replacement of SNN with a Φ-restricted prolyl residue highlights the specificity of the succinimidyl residue in imparting hyperthermostability to the enzyme. The conservation of the succinimide-forming tripeptide sequence (E(N/D)(E/D)) in several archaeal GATases strongly suggests an adaptation of this otherwise detrimental post-translational modification as a harbinger of thermostability.

Protein asparagine deamidation prediction based on structures with machine learning methods

Chemical stability is a major concern in the development of protein therapeutics due to its impact on both efficacy and safety. Protein "hotspots" are amino acid residues that are subject to various chemical modifications, including deamidation, isomerization, glycosylation, oxidation etc. A more accurate prediction method for potential hotspot residues would allow their elimination or reduction as early as possible in the drug discovery process. In this work, we focus on prediction models for asparagine (Asn) deamidation. Sequence-based prediction method simply identifies the NG motif (amino acid asparagine followed by a glycine) to be liable to deamidation. It still dominates deamidation evaluation process in most pharmaceutical setup due to its convenience. However, the simple sequence-based method is less accurate and often causes over-engineering a protein. We introduce structure-based prediction models by mining available experimental and structural data of deamidated proteins. Our training set contains 194 Asn residues from 25 proteins that all have available high-resolution crystal structures. Experimentally measured deamidation half-life of Asn in penta-peptides as well as 3D structure-based properties, such as solvent exposure, crystallographic B-factors, local secondary structure and dihedral angles etc., were used to train prediction models with several machine learning algorithms. The prediction tools were cross-validated as well as tested with an external test data set. The random forest model had high enrichment in ranking deamidated residues higher than non-deamidated residues while effectively eliminated false positive predictions. It is possible that such quantitative protein structure-function relationship tools can also be applied to other protein hotspot predictions. In addition, we extensively discussed metrics being used to evaluate the performance of predicting unbalanced data sets such as the deamidation case.

Racemization of the Succinimide Intermediate Formed in Proteins and Peptides: A Computational Study of the Mechanism Catalyzed by Dihydrogen Phosphate Ion

In proteins and peptides, d-aspartic acid (d-Asp) and d-β-Asp residues can be spontaneously formed via racemization of the succinimide intermediate formed from l-Asp and l-asparagine (l-Asn) residues. These biologically uncommon amino acid residues are known to have relevance to aging and pathologies. Although nonenzymatic, the succinimide racemization will not occur without a catalyst at room or biological temperature. In the present study, we computationally investigated the mechanism of succinimide racemization catalyzed by dihydrogen phosphate ion, H₂PO₄⁻, by B3LYP/6-31+G(d,p) density functional theory calculations, using a model compound in which an aminosuccinyl (Asu) residue is capped with acetyl (Ace) and NCH₃ (Nme) groups on the N- and C-termini, respectively (Ace–Asu–Nme). It was shown that an H₂PO₄⁻ ion can catalyze the enolization of the H_α–C_α–C=O portion of the Asu residue by acting as a proton-transfer mediator. The resulting complex between the enol form and H₂PO₄⁻ corresponds to a very flat intermediate region on the potential energy surface lying between the initial reactant complex and its mirror-image geometry. The calculated activation barrier (18.8 kcal·mol⁻¹ after corrections for the zero-point energy and the Gibbs energy of hydration) for the enolization was consistent with the experimental activation energies of Asp racemization.

Free Energy Barriers for the N-Terminal Asparagine to Succinimide Conversion: Quantum Molecular Dynamics Simulations for the Fully Solvated Model

Deamidation of asparagine residues represents one of the main routes for the post-translational modification of protein sequences. We computed the estimates of the free energy barriers for three stages of the deamidation process, deprotonation, cyclization, and deamination, of the conversion of asparagine to the succinimide intermediate within the fully solvated model with explicit water molecules. The Born-Oppenheimer molecular dynamics in the Gaussian and Plane Wave (GPW) approximation as implemented in the CP2K quantum chemistry package was utilized to sample the configurational space. By applying the metadynamics technique, the estimates of the free energy barriers were obtained for three separated stages of the reaction. In agreement with the experimental kinetic measurements, the estimated activation barriers do not exceed 21 kcal/mol. We demonstrate that the use of fully solvated models is the critical issue in theoretical studies of these reactions. We also conclude that more extensive sampling is necessary to obtain full free energy profiles and accurate barriers for the reaction stages.

Theoretical study on HF elimination and aromatization mechanisms: a case of pyridoxal 5' phosphate-dependent enzyme

Pyridoxal 5-phosphate (PLP), the phosphorylated and the oxidized form of vitamin B6 is an organic cofactor. PLP forms a Schiff base with the ϵ-amino group of a lysine residue of PLP-dependent enzymes. γ-Aminobutyric acid (GABA) aminotransferase is a PLP-dependent enzyme that degrades GABA to succinic semialdehyde, while reduction of GABA concentration in the brain causes convolution besides several neurological diseases. The fluorine-containing substrate analogues for the inactivation of the GABA-AT are synthesized extensively in cases where the inactivation mechanisms involve HF elimination. Although two proposed mechanisms are present for the HF elimination, the details of the base-induced HF elimination are not well identified. In this density functional theory (DFT) study, fluorine-containing substrate analogue, 5-amino-2-fluorocyclohex-3-enecarboxylic acid, is particularly chosen in order to explain the details of the HF elimination reactions. On the other hand, the experimental studies revealed that aromatization competes with Michael addition mechanism in the presence of 5-amino-2-fluorocyclohex-3-enecarboxylic acid. The results allowed us to draw a conclusion for the nature of HF elimination, besides the elucidation of the mechanism preference for the inactivation mechanism. Furthermore, the solvent phase calculations carried out in this study ensure that the proton transfer steps should be assisted either by a water molecule or a base for lower activation energy barriers.

Initiation of the reaction of deamidation in triosephosphate isomerase: investigations by means of molecular dynamics simulations

Deamidation of asparagine is the spontaneous degradation of this residue into aspartic acid. The kinetics of this slow reaction is mainly dependent on the nature of the adjacent amino acid that follows asparagine in a peptide or protein primary sequence. In the homodimer triosephosphate isomerase (TPI), there are two main deamidation sites per subunit: Asn15-Gly16 and Asn71-Gly72 for which deamidation dynamics are known to be interrelated. In this study, we investigate the initiation of the deamidation reaction in TPI by means of molecular dynamics. Simulations based on classical AMBER force field are performed in a 60 to 90 ns time scale for six distinct samples. Conformational changes, desolvation effects, and hydrogen bond networks are analyzed to interpret the experimental findings and previous quantum mechanical (QM) results. Results that are based on desolvation analysis clarify the assignments in the literature about the different behaviors of two deamidating sites in TPI. Conformational analysis supports findings suggested by QM studies: the most favorable reaction mechanism is the one that yields to succinimide intermediate via one or two step routes. The mechanism leading to the succinimide intermediate most likely involves the formation of a tetrahedral intermediate that is formed either directly from asparagine or via a side chain tautomer intermediate. In all cases, surrounding water molecules are present to assist the reaction.

Development of novel linkers to conjugate pharmacophores to a carrier antibody

We have developed modified maleimide novel linkers with improved chemical stability that could potentially be used in conjugating various pharmacophores such as oligo nucleotides, peptides, and proteins to antibodies to afford novel biologics with well-defined therapeutic benefits and improved pharmacokinetic properties. These linkers expand the array of tools available for bioconjugation of pharmacophores to antibodies.

Mechanism of C-terminal intein cleavage in protein splicing from QM/MM molecular dynamics simulations

Protein splicing is a post-translational process in which a biologically inactive protein is activated by the release of a segment denoted as an intein. The process involves four steps. In the third, the scission of the intein takes place after the cyclization of the last amino acid of the segment, an asparagine. Little is known about the chemical reaction necessary for this cyclization. Experiments demonstrate that two histidines (the penultimate amino acid of the intein, and a histidine located 10 amino acids upstream) are relevant in the cyclization of the asparagine. We have investigated the mechanism and determinants of reaction in the GyrA intein focusing on the requirements for asparagine activation for its cyclization. First, the influence that the protonation states of these two histidines have on the orientation of the asparagine side chain is investigated by means of molecular dynamics simulation. Molecular dynamics simulations using the CHARMM27 force field were carried out on the three possible protonation states for each of these two histidines. The results indicate that the only protonation state in which the conformation of the system is suitable for cyclization is when the penultimate histidine is fully protonated (positively charged), and the upstream histidine is in the His(ε) neutral tautomeric form. The free energy profile for the reaction in which the asparagine is activated by a proton transfer to the upstream histidine is presented, computed by hybrid quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics at the SCCDFTB/CHARMM27 level of theory. The calculated free energy barrier for the reaction is 19.0 kcal mol(-1). B3LYP/6-31+G(d) QM/MM single-point calculations give a qualitatively a similar energy profile, although with somewhat higher energy barriers, in good agreement with the value derived from experiment of 25 kcal mol(-1) at 60 °C. QM/MM molecular dynamics simulations of the reactant, activated reactant and intermediate states highlight the importance of the Arg181-Val182-Asp183 segment in catalysing the reaction. Overall, the results indicate that nucleophilic activation of the asparagine for its cyclization by the upstream histidine acting as the base is a plausible mechanism for the C-terminal cleavage in protein splicing.

Stability of protein pharmaceuticals: an update

In 1989, Manning, Patel, and Borchardt wrote a review of protein stability (Manning et al., Pharm. Res. 6:903-918, 1989), which has been widely referenced ever since. At the time, recombinant protein therapy was still in its infancy. This review summarizes the advances that have been made since then regarding protein stabilization and formulation. In addition to a discussion of the current understanding of chemical and physical instability, sections are included on stabilization in aqueous solution and the dried state, the use of chemical modification and mutagenesis to improve stability, and the interrelationship between chemical and physical instability.

Modeling protein splicing: reaction pathway for C-terminal splice and intein scission

Protein splicing is a post-translational process where a biologically inactive protein is activated after the release of a so-called intein domain. In spite of the importance of this type of process, the specific molecular mechanism for the catalysis is still uncertain. In this work, we present a computational study of one of the key steps in protein splicing: the release of the intein due to the cyclization of an asparagine, the last amino acid of the intein. Density functional theory (DFT) calculations using the B3LYP functional in conjunction with the polarizable continuum model (PCM) were used to study the main stationary points along various possible reaction pathways. The results are compared with other DFT functionals and the MP2 ab initio method. In the first part of this work, the Asn-Thr dipeptide is analyzed with the aim of determining the specific requirements for the activation of the intrinsically slow Asn cyclization. The results show that the nucleophilic activation of the Asn side chain by removing one of its proton decreases the free energy barrier by approximately 20 kcal/mol. A full pathway of the reaction was also characterized in a larger model, including two imidazole molecules and two water molecules. The proposed reaction mechanism consists of two main steps: Asn side chain activation by a proton transfer to one of the imidazole groups, and cleavage of the peptide bond upon protonation of its nitrogen atom by the other imidazole. The overall free energy barrier in solution was determined to be 29.3 kcal/mol, in reasonable agreement with the apparent experimental barrier in the enzyme. The proposed mechanism suggests that the penultimate histidine stabilizes the tetrahedral intermediate and protonates the nitrogen of the scissile peptide bond, while a second histidine (located 10 amino acids upstream) activates the Asn side chain by deprotonating it.

Deamidation of asparagine residues: direct hydrolysis versus succinimide-mediated deamidation mechanisms

Quantum chemical calculations are reported to provide new insights on plausible mechanisms leading to the deamidation of asparagine residues in proteins and peptides. Direct hydrolysis to aspartic acid and several succinimide-mediated mechanisms have been described. The catalytic effect of water molecules has been explicitly analyzed. Calculations have been carried out at the density functional level (B3LYP/6-31+G**). Comparisons of free energy profiles show that the most favorable reaction mechanism goes through formation of a succinimide intermediate and involves tautomerization of the asparagine amide to the corresponding imidic acid as the initial reaction step. Another striking result is that direct water-assisted hydrolysis is competitive with the succinimide-mediated deamidation routes even in the absence of acid or base catalysis. The rate-determining step for the formation of the succinimide intermediate is cyclization, regardless of the mechanism. The rate-determining step for the complete deamidation is the hydrolysis of the succinimide intermediate. These results allow clarification of some well-known facts, such as the isolation of succinimide or the absence of iso-Asp among the reaction products observed in some experiments.

Computational study on nonenzymatic peptide bond cleavage at asparagine and aspartic acid

Nonenzymatic peptide bond cleavage at asparagine (Asn) and glutamine (Gln) residues has been observed during peptide deamidation experiments; cleavage has also been reported at aspartic acid (Asp) and glutamic acid (Glu) residues. Although peptide backbone cleavage at Asn is known to be slower than deamidation, fragmentation products are often observed during peptide deamidation experiments. In this study, mechanisms leading to the cleavage of the carboxyl-side peptide bond of Asn and Asp residues were investigated using computational methods (B3LYP/6-31+G**). Single-point solvent calculations at the B3LYP/6-31++G** level were carried out in water, utilizing the integral equation formalism-polarizable continuum (IEF-PCM) model. Mechanism and energetics of peptide fragmentation at Asn were comparatively analyzed with previous calculations on deamidation of Asn. When deamidation proceeds through direct hydrolysis of the Asn side chain or through cyclic imide formationvia a tautomerization routeit exhibits lower activation barriers than peptide bond cleavage at Asn. The fundamental distinction between the mechanisms leading to deamidationvia a succinimideand backbone cleavage was found to be the difference in nucleophilic entities involved in the cyclization process (backbone versus side-chain amide nitrogen). If deamidation is prevented by protein three-dimensional structure, cleavage may become a competing pathway. Fragmentation of the peptide backbone at Asp was also computationally studied to understand the likelihood of Asn deamidation preceding backbone cleavage. The activation barrier for backbone cleavage at Asp residues is much lower (approximately 10 kcal/mol) than that at Asn. This suggests that peptide bond cleavage at Asn residues is more likely to take place after it has deamidated into Asp.

The role of the cyclic imide in alternate degradation pathways for asparagine-containing peptides and proteins

Peptides and proteins exhibit enhanced reactivity at asparagine residues due to the formation of a reactive succinimide intermediate that produces normal and isoaspartyl deamidation products along with significant racemization. This study examines the potential for attack of amine nucleophiles at the succinimide carbonyls to generate alternate decomposition products, depending on the nucleophile involved in the reaction. The reactions of the model peptides Phe-Asn-Gly (FNG) and Phe-isoAsn-Gly (FisoNG) were explored as a function of pH (8.5-10.5) in the presence and absence of ammonia buffer (0.2-2 M) using an isocratic HPLC method to monitor reactant disappearance and product formation. In addition to deamidation to form isoAsp and Asp peptides, two additional types of reactions were found to occur via the succinimide intermediate under these conditions. Back-reaction of the succinimide with ammonia led to peptide backbone isomerization while intramolecular attack by the amino terminus produced diketopiperazines. A kinetic model assuming a central role for the succinimide intermediate was derived to fit the concentration versus time data. These studies implicate the cyclic imide as a key intermediate in the formation of alternate peptide and protein degradants, including possible covalent amide-linked aggregates that may form from intermolecular attack of the cyclic imide by neighboring amino groups.

Reaction mechanism of deamidation of asparaginyl residues in peptides: effect of solvent molecules

Deamidation of proteins occurs spontaneously under physiological conditions. Asparaginyl (Asn) residues may deamidate into aspartyl (Asp) residues, causing a change in both the charge and the conformation of peptides. It has been previously proposed by Capasso et al. that deamidation of relatively unrestrained Asn residues proceeds through a succinimide intermediate. This mechanism has been modeled by Konuklar et al. and the rate determining step for the deamidation process in neutral media has been shown to be the cyclization step leading to the succinimide intermediate. In the present study, possible water-assisted mechanisms, for both concerted and stepwise succinimide formation, were computationally explored using the B3LYP method with 6-31+G* basis set. Single point solvent calculations were carried out in water, by means of integral equation formalism-polarizable continuum model (IEF-PCM) at the B3LYP/6-31++G* level of theory. A novel route leading to the succinimide intermediate via tautomerization of the Asn side chain amide functionality has been proposed. The energetics of these pathways have been subject to a comparative study to identify the most probable mechanism for the deamidation of peptides in solution.

Asparagine Deamidation: pH-Dependent Mechanism from Density Functional Theory

Asparagine deamidation is a decisive event in chemotherapy-induced apoptosis and a major obstacle in the formulation of monoclonal antibodies. Despite the importance of deamidation, little is known about the elementary reactions involved. B3LYP/6-31+G(d,p)/COSMO-RS calculations were used to obtain stable structures and transition states for a network of reactions. Calculated rate constants were incorporated into a kinetic model of the pH dependence and compared to a pseudo-steady-state model. At low pH, the calculations show that deamidation occurs by direct acid-catalyzed hydrolysis to aspartate. At neutral to basic pH, deamidation proceeds by the initial formation of a tetrahedral intermediate. The intermediate can be converted to succinimide by two pathways and three rate-determining steps that shift in relative importance with pH. The calculated pH-dependent rate constant qualitatively agrees with the experimental pH dependence. The rate-determining transition state structures may help to understand chemotherapy-induced apoptosis and improve protein formulations.

Polyelectrolyte multilayers with a tunable Young's modulus: influence of film stiffness on cell adhesion

Mechanical properties of model and natural gels have recently been demonstrated to play an important role in various cellular processes such as adhesion, proliferation, and differentiation, besides events triggered by chemical ligands. Understanding the biomaterial/cell interface is particularly important in many tissue engineering applications and in implant surgery. One of the final goals would be to control cellular processes precisely at the biomaterial surface and to guide tissue regeneration. In this work, we investigate the substrate mechanical effect on cell adhesion for thin polyelectrolyte multilayer (PEM) films, which can be easily deposited on any type of material. The films were cross linked by means of a water-soluble carbodiimide (EDC), and the film elastic modulus was determined using the AFM nanoindentation technique with a colloidal probe. The Young's modulus could be varied over 2 orders of magnitude (from 3 to 400 kPa) for wet poly(L-lysine)/hyaluronan (PLL/HA) films by changing the EDC concentration. The chemical changes upon cross linking were characterized by means of Fourier transform infrared spectroscopy (FTIR). We demonstrated that the adhesion and spreading of human chondrosarcoma cells directly depend on the Young's modulus. These data indicate that, besides the chemical properties of the polyelectrolytes, the substrate mechanics of PEM films is an important parameter influencing cell adhesion and that PEM offer a new way to prepare thin films of tunable mechanical properties with large potential biomedical applications including drug release.