Neutral Amino Group Research Articles

Transformation of Supramolecular Membranes to Vesicles Driven by Spontaneous Gradual Deprotonation on Membrane Surfaces

The various proteins and asymmetric lipid bilayers present in cell membranes form curvatures, resulting in structural transformations to generate vesicles. Fission and fusion processes between vesicles and cell membranes are reversible in living organisms. Although the transformation of a two-dimensional membrane to a three-dimensional vesicle structure is a common natural phenomenon, the lack of a detailed understanding at the molecular level limits the development of synthetic systems for functional materials. Herein, we report a supramolecular membrane system through donor-acceptor interactions using a π-deficient acceptor and π-rich donor as building blocks. The reduced electrostatic repulsion between ammonium cations and the spontaneously deprotonated neutral amino group induced anisotropic membrane curvature, resulting in membrane fission to form vesicles with a detailed understanding at the molecular level. Furthermore, the reversible transformation of vesicles to membranes upon changing the pH provides a novel synthetic system exhibiting both fission and fusion processes.

Modified mesoporous silica nanoparticles coated by polymer complex as novel curcumin delivery carriers

The synthesis of mesoporous KIL-2 and KIT-6 nanoparticles (40 and 60 nm, respectively) was performed. Post synthesis procedure was applied for the modification of the initial mesoporous silicas with amino groups. Incipient wetness impregnation or solid state reaction were used for curcumin loading in the parent and amino-modified nanoporous supports. Polymer coating of alternating polymer layers with complementary functionality (k-carrageenan and chitosan) was formed. The parent and drug loaded formulations were characterized by XRD, N2 physisorption, thermal analysis, TEM, AFM, ATR-FT-IR and solid state NMR spectroscopy. Loading of curcumin in the nanocarriers followed by polymer coating made the sustained delivery of curcumin possible. A comparative study on anti-proliferative effect of curcumin loaded into NH2-modified KIT-6 and KIL-2 carriers vs. free drug was performed on a panel of three human cell lines. The most stable complexes of curcumin with protonated amino group ((CH2)3NH3+) are formed when the ammonia group interacts with an O center from the carbonyl group irrespectively of the form of curcumin, while curcumin (in both enol and keto forms) interacts most strongly with the neutral amino group ((CH2)3NH2) via phenolic OH group. On the basis of the obtained results it can be concluded that modified silica particles are promising carriers for controlled delivery of curcumin.

Surface complexation modeling of interactions between freshwater and marine diatom species and trace elements (Mo, W, Cr, Ge, Ga, Al)

Towards a better understanding of photosynthetic algae interaction with less common trace elements, we performed adsorption experiments of Al, Ga, Ge, Cr (VI), Mo, and W onto four diatom species typical for marine, estuarine, and freshwater aquatic systems. Using a surface complexation approach, we tentatively identified the nature of functional groups involved in the complexation of trace elements with diatom surface moieties and we quantified the stability of surface complexes formed at the diatom – solution interface. The differences in binding properties between freshwater and marine species are linked to variable proportion of three main binding groups at the diatom surfaces, namely amine, carboxylate and silanol. Under acidic conditions, the oxyanion (MoO42−, WO42−, CrO42−) sorption occurred electrostatically with a 1:1 ratio to the protonated amino groups. Trivalent cations (Ga3+ and Al3+) were complexed by deprotonated carboxyl groups, while the anionic hydroxylated forms of these metals (Ga(OH)4− and Al(OH)4−) formed mononuclear monodentate complex with positively charged amino groups at higher pH. Finally, Ge(IV) sorption was controlled by interaction with neutral carboxylic, silanol and amino groups. Taken together, the surface complexation model developed in this study allows rigorous description of anions and trivalent hydrolysates adsorption onto diatom surfaces and demonstrates potential importance of diatoms for the control of trace element transfer in aquatic settings.

Polymer Solar Cells Exceeding 10% Efficiency Enabled via a Facile Star‐Shaped Molecular Cathode Interlayer with Variable Counterions

A series of star‐shaped small molecular cathode interlayer materials are synthesized for PTB7:PC71BM based polymer solar cells (PSCs), comprising neutral amino groups, quaternary ammonium ions, amino N‐oxides, and sulfobetaine ions as pendant polar functionalities, respectively. For the first time, the effect of these different pendant functional groups with or without mobile counterions on the cells' photovoltaic properties is investigated in detail. A large improvement in device performance is observed by inserting these cathode interfacial layers (CILs) between the PTB7:PC71BM active layer and the Al electrode. The CILs could effectively lower the work function of the Al cathode, increase the built‐in potential, and decrease the series resistance of the related PSCs. poly(9,9‐dioctylfluorene‐co‐N‐[4‐(3‐methyl‐propyl)]‐diphenylamine) with pendant quaternary ammonium ions shows the best cathode modification ability, giving rise to the highest power conversion efficiency of 10.1%, even better than that of the typical poly[(9,9‐bis(3′‐(N,N‐dimethylamino)propyl)‐2,7‐fluorene)‐alt‐2,7‐(9,9‐dioctylfluorene)] based device. The design strategy and structure–property relationships concluded in this work will be helpful to develop more efficient cathode interface materials for high‐performance PSCs in the future.

The Unusual Heme Coordination of THB1, a Hemoglobin from Chlamydomonas Reinhardtii

THB1 is a ∼15 kDa “truncated” hemoglobin (Hb) found in the cytoplasm of the unicellular green alga Chlamydomonas reinhardtii. As for other Hbs within photosynthetic microbes, THB1 is thought to be involved in the management of reactive oxygen/nitrogen species. To complement physiological studies aimed at determining the function of THB1, we are pursuing the characterization of the recombinant protein (rTHB1) [1] with special attention to the heme environment. At pH ∼ 5, ferric rTHB1 has an optical spectrum characteristic of a six-coordinate, high-spin complex with a histidine and a water molecule as axial ligands to the heme iron. When the pH is raised near neutrality, the protein undergoes a transition (apparent pKa of 6.5) to a six-coordinate, low-spin complex. Mutagenesis and NMR data collected in the diamagnetic ferrous state provide direct evidence for the ligation of a lysine (K53) on the distal side of the heme [1]. Here, we continue the study of this unusual iron coordination scheme. The distal lysine, like the distal histidine of cyanobacterial globins (GlbNs), facilitates electron transfer. However, unlike the histidine of GlbN, the distal lysine of THB1 does not protect ferric heme from oxidative damage caused by H2O2. Analysis of ferrous THB1 NMR data reveals a neutral lysine amino group with highly upfield-shifted 15N signal. Fast-exchange averaging of the two amino protons is a further indication of a dynamic distal coordination. Additional structural information was obtained from diffraction data collected at beamline X25 (National Synchrotron Light Source, Brookhaven National laboratory). Crystals of ferric rTHB1 grown at pH 9.5 diffracted to 1.9 A resolution (P6122 space group) and the data were used to inspect the structural factors allowing lysine coordination.[1] Johnson et al. (2014) Biochemistry 53:4573Supported by NSF grant MCB-1330488

Heme Coordination Versatility in a Truncated Hemoglobin

GlbN, the “truncated” hemoglobin from Synechocystis sp. PCC 6803, coordinates the heme iron with His46 (E10, distal) and His70 (F8, proximal). Displacement of His E10 by an exogenous ligand (e.g., cyanide in the ferric state) drives a significant conformational change allowing Tyr22 (B10), Gln43 (E7) and Gln47 (E11) to establish a hydrogen bond network stabilizing the distal ligand.THB1, a closely related hemoglobin from Chlamydomonas reinhardtii, also binds cyanide and forms the same network of interactions. However, in the absence of an exogenous ligand, the neutral amino group of Lys53 (E10) coordinates the heme iron on the distal side [1]. Because of the importance of the coordination scheme in controlling the reactivity of heme proteins, the flexibility of the truncated hemoglobin fold, and the rarity of lysine coordination, we explored the ability of GlbN to use lysine at position E10 as an axial ligand. The His46Lys replacement yielded a protein with UV-Vis and NMR spectra similar to those of His46Leu and comparable pH response, suggesting that GlbN does not accommodate lysine coordination at position E10. However, the spectra were incompatible with water coordination and suggested that in the ferric state these variants were low-spin endogenously hexacoordinate complexes. We performed amino acid replacements within the distal H-bond network to characterize the perturbed heme environment and ligand sets. A combination of pH titrations and NMR experiments illustrates the delicate balance of interactions governing the heme pocket conformation of GlbN.[1] Johnson et al. (2014) Biochemistry 53:4573Supported by NSF grant MCB-1330488

CORROSION INHIBITION OF ALUMINUM IN 0.1 M HCL SOLUTION BY GLUTAMIC ACID

The inhibition effect of glutamic acid (Glu) on corrosion of aluminum in 0.1 M HCl solution was investigated using linear polarization (LPR), potentiodynamic polarization, and electrochemical impedance spectroscopy (EIS) methods. Polarization curves revealed that Glu acted as a mixed-type inhibitor. The values of polarization resistance obtained by LPR and EIS were consistent in showing that inhibition efficiency increased with increasing concentration of Glu. The inhibition occurs by adsorption of Glu on the metal surface, and evidence of this was given by the equivalent circuit analysis of EIS results. The adsorption process was found to obey the Hill-de Boer isotherm with a standard free energy of adsorption of −60.45 kJ mol−1. Surface analysis by means of X-ray photoelectron spectroscopy (XPS) was performed to provide chemical characterization of the adsorbed layer. The N 1 s spectrum showed the presence of ionized () and neutral (NH2) amino group. The corrosion inhibition was attributed to a chemisorption process with Glu molecules forming a stable chelate on the metal surface.

Effect of Amino Group Charge on the Photooxidation Kinetics of Aromatic Amino Acids

The kinetics of the photooxidation of aromatic amino acids histidine (His), tyrosine (Tyr), and tryptophan (Trp) by 3,3',4,4'-benzophenonetetracarboxylic acid (TCBP) has been investigated in aqueous solutions using time-resolved laser flash photolysis and time-resolved chemically induced dynamic nuclear polarization. The pH dependence of quenching rate constants is measured within a large pH range. The chemical reactivities of free His, Trp, and Tyr and of their acetylated derivatives, N-AcHis, N-AcTyr, and N-AcTrp, toward TCBP triplets are compared to reveal the influence of amino group charge on the oxidation of aromatic amino acids. The bimolecular rate constants of quenching reactions between the triplet-excited TCBP in the fully deprotonated state and tryptophan, histidine, and tyrosine with a positively charged amino group are kq = 2.2 × 10(9) M(-1) s(-1) (4.9 < pH < 9.4), kq = 1.6 × 10(9) M(-1) s(-1) (6.0 < pH < 9.2), and kq = 1.5 × 10(9) M(-1) s(-1) (4.9 < pH < 9.0), respectively. Tryptophan, histidine, and tyrosine with a neutral amino group quench the TCBP triplets with the corresponding rate constants kq = 8.0 × 10(8) M(-1) s(-1) (pH > 9.4), kq = 3.0 × 10(8) M(-1) s(-1) (pH > 9.2), and kq = (4.0-10.0) × 10(8) M(-1) s(-1) (9.0 < pH < 10.1) that are close to those for the N-acetylated derivatives. Thus, it has been established that the presence of charged amino group changes oxidation rates by a significant factor; i.e., His with a positively charged amino group quenches the TCBP triplets 5 times more effectively than N-AcHis and His with a neutral amino group. The efficiency of quenching reaction between the TCBP triplets and Tyr and Trp with a positively charged amino group is about 3 times as high as that of both Tyr and Trp with a neutral amino group, N-AcTyr and N-AcTrp.

DNA Damage Processing by Human 8-Oxoguanine-DNA Glycosylase Mutants with the Occluded Active Site

8-Oxoguanine-DNA glycosylase (OGG1) removes premutagenic lesion 8-oxoguanine (8-oxo-G) from DNA and then nicks the nascent abasic (apurinic/apyrimidinic) site by β-elimination. Although the structure of OGG1 bound to damaged DNA is known, the dynamic aspects of 8-oxo-G recognition are not well understood. To comprehend the mechanisms of substrate recognition and processing, we have constructed OGG1 mutants with the active site occluded by replacement of Cys-253, which forms a wall of the base-binding pocket, with bulky leucine or isoleucine. The conformational dynamics of OGG1 mutants were characterized by single-turnover kinetics and stopped-flow kinetics with fluorescent detection. Additionally, the conformational mobility of wild type and the mutant OGG1 substrate complex was assessed using molecular dynamics simulations. Although pocket occlusion distorted the active site and greatly decreased the catalytic activity of OGG1, it did not fully prevent processing of 8-oxo-G and apurinic/apyrimidinic sites. Both mutants were notably stimulated in the presence of free 8-bromoguanine, indicating that this base can bind to the distorted OGG1 and facilitate β-elimination. The results agree with the concept of enzyme plasticity, suggesting that the active site of OGG1 is flexible enough to compensate partially for distortions caused by mutation.

Molecular dynamics and quantum chemical approaches in the study of the hydration of protonated cyclohexyldiamines

Explicit hydration of the neutral and charged cyclohexylamine and of the cyclohexyldiamine isomers in their mono- or diprotonated forms is investigated through classical molecular dynamics (MD) simulations in aqueous solutions combined with DFT calculations in amine–water complexes. The MD studies performed in the monoamines reveal that the structure of the hydration shell around the neutral amino group (NH2) is quite distinct from that around the charged one (NH3+). On average, the number of water molecules surrounding the two groups is calculated to be ∼2 and 3–4, respectively. The variation of the hydration structure prompted by the groups’ proximity is discussed based on the data found for the mono- and diprotonated diamines. To have a more detailed picture of the water molecules’ arrangement around the amino groups and of the amine–water hydrogen bonds, geometry optimisations in hydrates with up to six water molecules are carried out at the B3LYP/aug-cc-pVDZ level. Complexation energies are also computed. The main findings emerging from these calculations are found to be very helpful to rationalise the mutual influence of the amino groups and therefore to better elucidate the MD findings. The complementary nature of the two research methods is emphasised as an excellent tool in order to closely examine the hydration of polyamines, as exemplified for the cyclohexyldiamines.

Theoretical and experimental study of the pH-dependent interaction of amino acids and MFI-type zeolite

The separation and purification of peptides and proteins using chromatography can make up more than half the amount of the total purification costs of a biotechnological process [1]. The development of cost-efficient processes still suffers from the lack of understanding on a molecular level of adsorption mechanisms of biomolecules on materials surfaces. To explore the power of computer science in supporting experimentally based process development, we applied a combined force field approach with subsequent Density Functional Theory (DFT) calculations. As a first step, we examined the adsorption of the amino acids glycine (gly), l-alanine (ala) and l-lysine (lys) on MFI-type zeolite (MFI). Experimental data from adsorption isotherms and Isothermal Titration Calorimetry (ITC) have proved the adsorption to be strongly pH-dependent. Therefore, we applied the amino acids in their protonated and neutral state in order to simulate low and medium pH values in our computational study. A T33 cluster containing all potential binding regions was used as a model of MFI. Initial geometries for DFT calculations were prepared with force field methods in order to speed up the search in conformational space. Low energy adsorption sites were determined using Adsorption Locator and Forcite modules of Materials Studio 6.0 (Accelrys Inc.). Subsequently, the structures were optimized with DMol3 code (Accelrys Inc.) using the generalized-gradient approximation (GGA) with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional and the double numerical plus polarization (DNP) basis set. Calculated energies strongly mirror the adsorption affinities derived from experimental adsorption isotherms: (lyslow_pH >> ((ala > gly)low_pH ~ lysmedium_pH)) >> (ala > gly)medium_pH. Furthermore, calculated adsorption energy ratios between protonated amino acids agree very well with the enthalpy ratios derived from low pH ITC experiments: ([ala:gly] = 1.12exp = 1.14calc), ([lys:ala] = 1.72 exp = 1.75 calc), ([lys:gly] = 1.92exp = 1.97calc). Additionally, the adsorption mechanisms of neutral and protonated amino acids were found to be qualitatively different. Neutral amino acids bind via neutral amino group and proton transfer to the active site in zeolite, whereas protonated amino acids bind via carboxyl group. These results illustrate that a judiciously designed combination of atomistic modeling methods can be used as a reliable first step in the design of cost-efficient industrial processes.

A comparative DFT study of the Schiff base formation from acetaldehyde and butylamine, glycine and phosphatidylethanolamine

Mechanisms for the formation of the Schiff base from acetaldehyde and butylamine, glycine and phosphatidylethanolamine based on Dmol3/DFT calculations were realized. For the case of phosphatidylethanolamine, calculations were done under periodic boundary conditions, in an amine-phospholipid monolayer model with two molecules of phosphatidylethanolamine by cell. All models contained explicit aqueous solvent. In the three cases, a neutral amino group is used to model the nucleophilic attack on the carbonyl group of acetaldehyde, and water molecules form hydrogen bond networks. These networks were involved in the reactions by performing as proton-transfer carriers, important in some steps of reactions, and stabilizing reaction intermediates. In all the studied reactions, they take place in two steps, namely: (1) formation of a carbinolamine and (2) its dehydration to the Schiff base, being the dehydration the rate-determining step of the process, consistent with available experimental evidence for similar reactions. The main difference between the studied reactions is found in the value for relative free energy for the intermediates and transition states in the second step; these values are lower in the cases of glycine and phosphatidylethanolamine in comparison with butylamine, due the influence of their molecular environments. Based on the results, the aminophospholipid surface environment and carboxylic group of glycine may boost Schiff base formation via a neighboring catalyst effect.

The α-amino group of the threonine substrate as the general base during tRNA aminoacylation: a new version of substrate-assisted catalysis predicted by hybrid DFT.

Density functional theory-based methods in combination with large chemical models have been used to investigate the mechanism of the second half-reaction catalyzed by Thr-tRNA synthetase: aminoacyl transfer from Thr-AMP onto the (A76)3'OH of the cognate tRNA. In particular, we have examined pathways in which an active site His309 residue is either protonated or neutral (i.e., potentially able to act as a base). In the protonated His309-assisted mechanism, the rate-limiting step is formation of the tetrahedral intermediate. The barrier for this step is 155.0 kJ mol(-1), and thus, such a pathway is concluded to not be enzymatically feasible. For the neutral His309-assisted mechanism, two models were used with the difference being whether Lys465 was included. For either model, the barrier of the rate-limiting step is below the upper thermodynamic enzymatic limit of ~125 kJ mol(-1). Specifically, without Lys465, the rate-limiting barrier is 122.1 kJ mol(-1) and corresponds to a rotation about the tetrahedral intermediate C(carb)-OH bond. For the model with Lys465, the rate-limiting barrier is slightly lower and corresponds to the formation of the tetrahedral intermediate. Importantly, for both "neutral His309" models, the neutral amino group of the threonyl substrate directly acts as the proton acceptor; in the formation of the tetrahedral intermediate, the (A76)3'OH proton is directly transferred onto the Thr-NH(2). Therefore, the overall mechanism follows a general substrate-assisted catalytic mechanism.

Curing Induced Structural Reorganization and Enhanced Reactivity of Amino-Terminated Organic Thin Films on Solid Substrates: Observations of Two Types of Chemically and Structurally Unique Amino Groups on the Surface

Infrared-visible sum frequency generation vibrational spectroscopy (SFG) was used to characterize the structure of 3-aminopropyltriethoxysilane (APTES) films deposited on solid substrates under controlled experimental conditions for the first time. Our SFG spectra in combination with complementary analytical data showed that APTES films undergo structural changes when cured at an elevated temperature. Before the films are cured, well-ordered hydrophobic ethoxy groups are dominantly present on the surface. A majority of hydrophilic surface amino groups are protonated, and they are either buried or randomly oriented at the interface. After the films are cured, chemically and structurally different neutral amino groups are detected on the surface. Unlike the protonated amino groups, a new class of neutral amino groups is ordered at the interface and shows enhanced reactivity.

Stereospecificity of isotopic exchange of C-α-protons of glycine catalyzed by three PLP-dependent lyases: the unusual case of tyrosine phenol-lyase

A comparative study of the kinetics and stereospecificity of isotopic exchange of the pro-2R- and pro-2S protons of glycine in (2)H(2)O under the action of tyrosine phenol-lyase (TPL), tryptophan indole-lyase (TIL) and methionine γ-lyase (MGL) was undertaken. The kinetics of exchange was monitored using both (1)H- and (13)C-NMR. In the three compared lyases the stereospecificities of the main reactions with natural substrates dictate orthogonal orientation of the pro-2R proton of glycine with respect to the cofactor pyridoxal 5'-phosphate (PLP) plane. Consequently, according to Dunathan's postulate with all the three enzymes pro-2R proton should exchange faster than does the pro-2S one. In fact the found ratios of 2R:2S reactivities are 1:20 for TPL, 108:1 for TIL, and 1,440:1 for MGL. Thus, TPL displays an unprecedented inversion of stereospecificity. A probable mechanism of the observed phenomenon is suggested, which is based on the X-ray data for the quinonoid intermediate, formed in the reaction of TPL with L-alanine. The mechanism implies different conformational changes in the active site upon binding of glycine and alanine. These changes can lead to relative stabilization of either the neutral amino group, accepting the α-proton, or the respective ammonium group, which is formed after the proton abstraction.

Reactivity of a Phospholipid Monolayer Model under Periodic Boundary Conditions: A Density Functional Theory Study of the Schiff Base Formation between Phosphatidylethanolamine and Acetaldehyde

A mechanism for the formation of the Schiff base between an acetaldehyde and an amine-phospholipid monolayer model based on Dmol3/density functional theory calculations under periodic boundary conditions was constructed. This is the first time such a system has been modeled to examine its chemical reactivity at this computation level. Each unit cell contains two phospholipid molecules, one acetaldehyde molecule, and nine water molecules. One of the amine-phospholipid molecules in the cell possesses a neutral amino group that is used to model the nucleophilic attack on the carboxyl group of acetaldehyde, whereas the other has a charged amino group acting as a proton donor. The nine water molecules form a hydrogen bond network along the polar heads of the phospholipids that facilitates very fast proton conduction at the interface. Using periodic boundary conditions afforded proton transfer between different cells. The reaction takes place in two steps, namely, (1) formation of a carbinolamine and (2) its dehydration to the Schiff base. The carbinolamine is the primary reaction intermediate, and dehydration is the rate-determining step of the process, consistent with available experimental evidence for similar reactions. On the basis of the results, the cell membrane surface environment may boost phospholipid glycation via a neighboring catalyst effect.

The Cu(II) complex of a C-lipophilized 13aneN4 macrocycle with an additional protonable amino group as micellar anion receptor

Three 13aneN4 macrocyclic ligands have been prepared bearing a -CH(2)NHR side arm (R = H, n-C(5)H(11), n-C(10)H(21)) on a carbon atom. When Cu(2+) is complexed in the macrocyclic ring, the amino group of the side arm undergoes an acid-base protonation equilibrium but it is not able to coordinate apically the metal cation even when it is deprotonated. The Cu(2+) complex with the ligand bearing the longest appended aliphatic chain is fully confined inside Triton X-100 micelles, and its ability to bind and sequestrate a series of anions inside micelles has been studied at two different pH values, i.e. both with protonated and neutral side-arm amino group. The favourable role played by the protonated amino group in the side arm has been demonstrated.

Adsorption of a tripeptide, GSH, on Au(1 1 1) under UHV conditions; PM-RAIRS and low T-XPS characterisation

Adsorption of the tripeptide, l-glutathione or GSH, was performed from vapour phase on Au(1 1 1) and monitored in situ by polarisation modulation reflection absorption infrared spectroscopy (PM-RAIRS). The surface was analysed by photoelectron spectroscopy (XPS) at two stages of adsorption, 5 or 50 min of exposure at P = 1 × 10 −7 Pa; to do so, the sample was cooled down to 100 K before X-ray analysis; it was then warmed up to RT, and analysed again, in order to discriminate between strongly and weakly bound molecules. From the beginning of exposure and up to 55 min, the molecule is mainly adsorbed under a dimeric or cluster form, leading to an average coverage close to one monolayer. Compared to adsorption from aqueous phase that favours the anchoring of GSH molecules via the S atoms under a zwitterionic form, here one observes that part of the molecules bears neutral acid and amino groups and keeps their SH group intact. XPS data show the coexistence of unbound and Au-bound sulphur, the former type of species slightly decreasing upon warming the sample to RT. Heating to 500 K leads to an almost total desorption of the GSH layer.

Molecular simulation of protein adsorption and desorption on hydroxyapatite surfaces

Protein adsorption and desorption on material surfaces play a key role in the biocompatibility of medical implants, biomineralization and protein separation. In this report, the adsorption and desorption behavior of the 10th type III module of fibronectin (FN-III 10) with different orientations on hydroxyapatite (HAP) (0 0 1) surface were systematically studied by molecular dynamics (MD) and steered MD simulations. These studies show that the electrostatic energy plays a dominant role in the interaction between the model protein and the HAP surface. The values of the interaction energy not only relates to the number of adsorbed sites but also the type. The charged –COO − and –NH 3 + are the strongest groups that interact with the surface, while other groups like charged guanido group, neutral amino and hydroxyl groups have considerable interactions with the surface. The effects of these groups on interaction energy were quantitatively investigated.

Insights into the Base Catalysis Exerted by the DD-Transpeptidase from Streptomyces K15: A Molecular Dynamics Study

Herein, we present results from molecular dynamics simulations of the DD-transpeptidase/penicillin-binding protein from Streptomyces K15 and its Michaelis complex with benzylpenicillin. For the apo-enzyme, six different configurations of the active site were modeled in aqueous solution and their relative stabilities were estimated by means of quantum mechanical energy calculations. The energetically most stable configuration has a neutral Lys(213) residue. In this configuration, the nucleophilic Ser(35) hydroxyl group interchanges with a water molecule in the "oxy-anion hole" and the Lys(38)/Lys(213) ammonium/amino groups are connected through the Ser(96) hydroxyl group. Subsequently, the enzyme-penicillin complexes corresponding to the four most stable configurations of the apo-enzyme were modeled. In the presence of the beta-lactam antibiotic, the configuration with a neutral Lys(38) residue is favored energetically and shows the best orientation for nucleophilic attack. In addition, a very stable contact between the Ser(35) hydroxyl group and the neutral amino group of Lys(38) supports the assignation of Lys(38) as the base catalyst for the acylation step. Finally, some mechanistic implications of enzyme-inhibitor contacts involving the benzylpenicillin carboxylate group are also discussed.