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1.
Modified Poisson-Boltzmann (MPB) equations have been numerically solved to study ionic distributions and mean electrostatic potentials around a macromolecule of arbitrarily complex shape and charge distribution. Results for DNA are compared with those obtained by classical Poisson-Boltzmann (PB) calculations. The comparisons were made for 1:1 and 2:1 electrolytes at ionic strengths up to 1 M. It is found that ion-image charge interactions and interionic correlations, which are neglected by the PB equation, have relatively weak effects on the electrostatic potential at charged groups of the DNA. The PB equation predicts errors in the long-range electrostatic part of the free energy that are only ∼1.5 kJ/mol per nucleotide even in the case of an asymmetrical electrolyte. In contrast, the spatial correlations between ions drastically affect the electrostatic potential at significant separations from the macromolecule leading to a clearly predicted effect of charge overneutralization.  相似文献   

2.
The cold shock protein Bc-Csp from the thermophile Bacillus caldolyticus differs from its mesophilic homolog Bs-CspB from Bacillus subtilis by 15.8 kJ mol(-1) in the Gibbs free energy of denaturation (DeltaG(D)). The two proteins vary in sequence at 12 positions but only two of them, Arg3 and Leu66 of Bc-Csp, which replace Glu3 and Glu66 of Bs-CspB, are responsible for the additional stability of Bc-Csp. These two positions are near the ends of the protein chain, but close to each other in the three-dimensional structure. The Glu3Arg exchange alone changed the stability by more than 11 kJ mol(-1). Here, we elucidated the molecular origins of the stability difference between the two proteins by a mutational analysis. Electrostatic contributions to stability were characterized by measuring the thermodynamic stabilities of many variants as a function of salt concentration. Double and triple mutant analyses indicate that the stabilization by the Glu3Arg exchange originates from three sources. Improved hydrophobic interactions of the aliphatic moiety of Arg3 contribute about 4 kJ mol(-1). Another 4 kJ mol(-1) is gained from the relief of a pairwise electrostatic repulsion between Glu3 and Glu66, as in the mesophilic protein, and 3 kJ mol(-1) originate from a general electrostatic stabilization by the positive charge of Arg3, which is not caused by a pairwise interaction. Mutations of all potential partners for an ion pair within a radius of 10 A around Arg3 had only marginal effects on stability. The Glu3-->Arg3 charge reversal thus optimizes ionic interactions at the protein surface by both local and global effects. However, it cannot convert the coulombic repulsion with another Glu residue into a corresponding attraction. Avoidance of unfavorable coulombic repulsions is probably a much simpler route to thermostability than the creation of stabilizing surface ion pairs, which can form only at the expense of conformational entropy.  相似文献   

3.
The drying of reduced glutathione from a series of aqueous–ethanol binary solutions at 300 K (below human body temperature) and 330 K (above human body temperature) was investigated in detail by steered molecular simulation and an umbrella sampling method with the Gromacs software package and Gromos96(53a6) united atomic force field. The results show that electrostatic interactions between glutathione and solvent represent the main resistance to drying. When the aqueous solution was gradually changed to pure ethanol, the energy of electrostatic interaction between glutathione and solvent molecules increased by 445.088 kJ/mol, and the drying potential of mean force (PMF) free energy also fell by 253.040 kJ/mol. However, an increase in temperature from 300 to 330 K in the aqueous solution only results in an increase of 23.013 kJ/mol in electrostatic interaction energy and a decrease of 34.956 kJ/mol in drying PMF free energy. Furthermore, we show that hydrogen bonding is the major form of electrostatic interaction involved, and directly affects the drying of glutathione. Therefore, choosing water-miscible solvents that minimise hydrogen-bond formation with glutathione will enhance its drying rate, and this is likely to be more efficient than increasing the temperature of the process. Thus, a power-saving technology can be used to produce the high bioactivity medicines.  相似文献   

4.
恶臭假单胞菌扁桃酸消旋酶的Val22位于20 s环状结构上, 是与底物结合相关的氨基酸之一。其中Val被替换为Arg后酶活性下降了75.9%。除了酶与底物疏水作用减弱以外, 静电排斥作用增强也可能引起活性的下降。利用分子动力学模拟对酶与底物的米氏复合物进行分析, 结果表明: 突变后第22位氨基酸侧链与底物的静电势从0.036 kJ/mol升高至0.124 kJ/mol。这说明氨基酸侧链极性的改变增加了侧链与底物分子之间的静电排斥作用, 因而静电排斥作用也是导致突变体活性下降的原因之一。同时, 突变后系统势能增加了283 kJ/mol, 进一步证实了第22位氨基酸侧链极性和带电性质的改变导致酶与底物结合状态的势能增大, 从而引起活性大幅下降。因此, 将来对酶的结合口袋区域进行理性设计时, 除了考虑空间位阻效应外, 还需考虑疏水作用和静电作用。  相似文献   

5.
Factor VIII (FVIII) is a glycoprotein that plays an important role in the intrinsic pathway of coagulation. In circulation, FVIII is protected upon binding to von Willebrand factor (VWF), a chaperone molecule that regulates its half-life, distribution, and activity. Despite the biological significance of this interaction, its molecular mechanisms are not fully characterized. We determined the equilibrium and activation thermodynamics of the interaction between FVIII and VWF. The equilibrium affinity determined by surface plasmon resonance was temperature-dependent with a value of 0.8 nM at 35 °C. The FVIII-VWF interaction was characterized by very fast association (8.56 × 10(6) M(-1) s(-1)) and fast dissociation (6.89 × 10(-3) s(-1)) rates. Both the equilibrium association and association rate constants, but not the dissociation rate constant, were dependent on temperature. Binding of FVIII to VWF was characterized by favorable changes in the equilibrium and activation entropy (TΔS° = 89.4 kJ/mol, and -TΔS(++) = -8.9 kJ/mol) and unfavorable changes in the equilibrium and activation enthalpy (ΔH° = 39.1 kJ/mol, and ΔH(++) = 44.1 kJ/mol), yielding a negative change in the equilibrium Gibbs energy. Binding of FVIII to VWF in solid-phase assays demonstrated a high sensitivity to acidic pH and a sensitivity to ionic strength. Our data indicate that the interaction between FVIII and VWF is mediated mainly by electrostatic forces, and that it is not accompanied by entropic constraints, suggesting the absence of conformational adaptation but the presence of rigid "pre-optimized" binding surfaces.  相似文献   

6.
The magnitude of the dipole potential of lipid membranes is often estimated from the difference in conductance between the hydrophobic ions, tetraphenylborate, and tetraphenylarsonium or tetraphenylphosphonium. The calculation is based on the tetraphenylarsonium-tetraphenylborate hypothesis that the magnitude of the hydration energies of the anions and cations are equal (i.e., charge independent), so that their different rates of transport across the membrane are solely due to differential interactions with the membrane phase. Here we investigate the validity of this assumption by quantum mechanical calculations of the hydration energies. Tetraphenylborate (Delta G(hydr) = -168 kJ mol(-1)) was found to have a significantly stronger interaction with water than either tetraphenylarsonium (Delta G(hydr) = -145 kJ mol(-1)) or tetraphenylphosphonium (Delta G(hydr) = -157 kJ mol(-1)). Taking these differences into account, literature conductance data were recalculated to yield values of the dipole potential 57 to 119 mV more positive in the membrane interior than previous estimates. This may partly account for the discrepancy of at least 100 mV generally observed between dipole potential values calculated from lipid monolayers and those determined on bilayers.  相似文献   

7.
Cha T  Guo A  Zhu XY 《Biophysical journal》2006,90(4):1270-1274
Electrostatic interaction is known to play important roles in the adsorption of charged lipids on oppositely charged surfaces. Here we show that, even for charge neutral (zwitterionic) lipids, electrostatic interaction is critical in controlling the adsorption and fusion of lipid vesicles to form supported phospholipid bilayers (SPBs) on surfaces. We use terminally functionalized alkanethiol self-assembled monolayers (SAMs) to systematically control the surface charge density. Charge neutral egg phophatidylcholine (eggPC) vesicles readily fuse into SPBs on either a positively charged 11-aminino-1-undecanethiol SAM or a negatively charged 10-carboxy-1-decanethiol SAM when the density of surface charge groups is > or = 80%. These processes depend critically on the buffer environment: fusion of adsorbed vesicles to form SPBs on each charged molecular surface does not occur when the molecular ion of the buffer used is of the opposite charge type. We attribute this to the high entropic repulsion (electric double layer repulsion) due to the large size of molecular counterions. On the other hand, such a critical dependence on buffer type is not observed when charged lipids are used. This study suggests the general importance of controlling electrostatic interaction in the formation of stable SPBs.  相似文献   

8.
Combined quantum chemical and molecular mechanics geometry optimisations have been performed on myoglobin without or with O(2) or CO bound to the haem group. The results show that the distal histidine residue is protonated on the N(epsilon 2) atom and forms a hydrogen bond to the haem ligand both in the O(2) and the CO complexes. We have also re-refined the crystal structure of CO[bond]myoglobin by a combined quantum chemical and crystallographic refinement. Thereby, we probably obtain the most accurate available structure of the active site of this complex, showing a Fe[bond]C[bond]O angle of 171 degrees, and Fe[bond]C and C[bond]O bond lengths of 170-171 and 116-117 pm. The resulting structures have been used to calculate the strength of the hydrogen bond between the distal histidine residue and O(2) or CO in the protein. This amounts to 31-33 kJ/mol for O(2) and 2-3 kJ/mol for CO. The difference in hydrogen-bond strength is 21-22 kJ/mol when corrected for entropy effects. This is slightly larger than the observed discrimination between O(2) or CO by myoglobin, 17 kJ/mol. We have also estimated the strain of the active site inside the protein. It is 2-4 kJ/mol larger for the O(2) complex than for the CO complex, independent of which crystal structure the calculations are based on. Together, these results clearly show that myoglobin discriminates between O(2) and CO mainly by electrostatic interactions, rather than by steric strain.  相似文献   

9.
The interaction of Ce(3+) to bovine serum albumin (BSA) has been investigated mainly by fluorescence spectra, UV-vis absorption spectra, and circular dichroism (CD) under simulative physiological conditions. Fluorescence data revealed that the quenching mechanism of BSA by Ce(3+) was a static quenching process, the binding constant is 6.70 × 10(5) , and the number of binding site is 1. The thermodynamic parameters (ΔH = -29.94 kJ mol(-1) , ΔG = -32.38 kJ mol(-1) , and ΔS = 8.05 J mol(-1) K(-1) ) indicate that electrostatic effect between the protein and the Ce(3+) is the main binding force. In addition, UV-vis, CD, and synchronous fluorescence results showed that the addition of Ce(3+) changed the conformation of BSA.  相似文献   

10.
The elemental surface composition of eleven microorganisms was determined by X-ray photoelectron spectroscopy. Bacteria could be distinguished from yeasts by higher nitrogen and phosphate concentrations. Overall physico-chemical properties, electrical charge and hydrophobicity, were also investigated: the former by electrophoretic mobility measurements, the latter by contact angle and by hydrophobic interaction chromatography. Phosphate plays the major role in determining the surface electrostatic charge. A correlation is observed between the N/P atomic concentration ratio and the electrostatic charge. In bacteria, hydrophobicity is directly related to concentration of carbon in hydrocarbon form and inversely related to oxygen concentration or to the N/P ratio. For yeasts, a positive correlation is found between hydrophobicity and the N/P ratio, pointing at the role of proteins in determining the hydrophobicity.  相似文献   

11.
H Wiesinger  H J Hinz 《Biochemistry》1984,23(21):4921-4928
The energetics of binding of the coenzyme pyridoxal 5'-phosphate (PLP) to both the apo beta 2 subunit and the apo alpha 2 beta 2 complex of tryptophan synthase from Escherichia coli has been investigated as a function of pH and temperature by direct microcalorimetric methods. At 25 degrees C, pH 7.5, the binding process proceeds in the time range of minutes and shows a biphasic heat output which permits resolution of the overall reaction into different reaction steps. Binding studies on the coenzyme analogues pyridoxal (PAL), pyridoxine 5'-phosphate (PNP), and pyridoxine (POL) to the protein as well as a comparison of these results with data from studies on PLP binding to epsilon-aminocaproic acid have led to a deconvolution of the complex heat vs. time curves into fast endothermic contributions from electrostatic interaction and Schiff base formation and slow exothermic contributions from the interactions between PLP and the binding domain. The pH-independent, large negative change in heat capacity of about -9.1 kJ/(mol of beta 2 X K) when binding PLP to beta 2 is indicative of major structural changes resulting from complex formation. The much smaller value of delta Cp = -1.7 kJ/(mol of beta 2 X K) for binding of PLP to alpha 2 beta 2 clearly demonstrates the energetic linkage of protein-protein and protein-ligand interactions. Calorimetric titrations of the apo beta 2 subunit with PLP at 35 degrees C have shown that also at this temperature positive cooperativity between the two binding sites occurs. On the basis of these measurements a complete set of site-specific thermodynamic parameters has been established.(ABSTRACT TRUNCATED AT 250 WORDS)  相似文献   

12.
Marti DN  Bosshard HR 《Biochemistry》2004,43(39):12436-12447
The pH-dependent stability of a protein is strongly affected by electrostatic interactions between ionizable residues in the folded as well as unfolded state. Here we characterize the individual contributions of charged Glu and His residues to stability and determine the NMR structure of the designed, heterodimeric leucine zipper AB consisting of an acidic A chain and a basic B chain. Thermodynamic parameters are compared with those of the homologous leucine zipper AB(SS) in which the A and B chains are disulfide-linked. NMR structures of AB based on (1)H NMR data collected at 600 MHz converge, and formation of the same six interchain salt bridges found previously in disulfide-linked AB(SS) [Marti, D. N., and Bosshard, H. R. (2003) J. Mol. Biol. 330, 621-637] is indicated. While the structures of AB and AB(SS) are very similar, their pH-dependent relative stabilities are strikingly different. The stability of AB peaks at pH approximately 4.5 and is higher at pH 8 than at pH 2. In contrast, AB(SS) is most stable at acidic pH where no interhelical salt bridges are formed. The different energetic contributions of charged Glu and His residues to stability of the two coiled coil structures were evaluated from pK(a) shifts induced by folding. The six charged Glu residues involved in salt bridges stabilize leucine zipper AB by 4.5 kJ/mol yet destabilize disulfide-linked AB(SS) by -1.1 kJ/mol. Two non-ion-paired Glu charges destabilize AB by only -1.8 kJ/mol but AB(SS) by -5.6 kJ/mol. The higher relative stability of AB at neutral pH is not caused by more favorable electrostatic interactions in the folded leucine zipper. It is due mainly to unfavorable electrostatic interactions in the unfolded A and B chains and may therefore be called an inverse electrostatic effect. This study illustrates the importance of residual interactions in the unfolded state and how the energetics of the unfolded state affect the stability of the folded protein.  相似文献   

13.
Electrostatic stabilization in four-helix bundle proteins.   总被引:5,自引:3,他引:2       下载免费PDF全文
Charge substitutions generated by site-directed mutagenesis at the termini of adjacent anti-parallel alpha-helices in a four-helix bundle protein were used to determine a precise value for the contribution of indirect charge-charge interactions to overall protein stability, and to simulate the electrostatic effects of alpha-helix macrodipoles. Thermodynamic double mutant cycles were constructed to measure the interaction energy between such charges on adjacent anti-parallel helices in the four-helix bundle cytochrome b562 from Escherichia coli. Previously, theoretical calculations of helix macrodipole interactions using modeled four-helix bundle proteins have predicted values ranging over an order of magnitude from 0.2 to 2.5 kcal/mol. Our system represents the first experimental evidence for electrostatic interactions such as those between partial charges due to helix macrodipole charges. At the positions mutated, we have measured a favorable interaction energy of 0.6 kcal/mol between opposite charges simulating an anti-parallel helix pair. Pairs of negative or positive charges simulating a parallel orientation of helices produce an unfavorable interaction of similar magnitude. The interaction energies show a strong dependence upon ionic strength, consistent with an electrostatic effect. Indirect electrostatic contacts do appear to confer a limited stabilization upon the association of anti-parallel packing of helices, favoring this orientation by as much as 1 kcal/mol at 20 mM K phosphate.  相似文献   

14.
The calculations have been done for CH/π interaction with π-system of Ni(II)-acetylacetonato chelate ring. The results show that there is an attractive electrostatic interaction, while dispersion component is a major source of attractive interacting energies. The interaction was compared with CH/π interaction between two benzene rings. The comparison shows that two interactions are quite similar, enabling to estimate the energy of CH/π interaction with π-system of Ni(II)-acetylacetonato chelate ring to be about 10.5 kJ/mol. The results indicate that CH/π interactions of chelate ring in various molecular systems can be as important as CH/π interactions of phenyl ring.  相似文献   

15.
The binding reactions of lomefloxacin-copper(II) complex (LMF-Cu) or LMF to bovine serum albumin (BSA) in physiological solution were investigated by multi-spectroscopy. The binding constant, the number of binding sites and the binding distance between LMF-Cu or LMF and BSA were obtained by a fluorescence quenching method and according to the mechanism of Forster-type dipole-dipole non-radioactive energy-transfer, respectively. Enthalpy and entropy changes for two systems were calculated to be -7.970 kJ mol(-1) and 47.438 J mol(-1)K(-1) for LMF-BSA, -12.469 kJ mol(-1) and 33.542 J mol(-1)K(-1) for LMF-Cu-BSA, respectively. The highly positive values observed for the entropy give evidence for a strong interaction. The values of DeltaH and DeltaS in two systems are similar, indicating that electrostatic interactions in two systems play major role. The effect of LMF-Cu or LMF on the conformation of BSA was also analyzed by synchronous fluorescence, three-dimensional fluorescence and circular dichroism spectra. The results showed that the presence of Cu ion in LMF-Cu can affect the conformation of BSA to some degree. All the results revealed that the addition of copper ion promotes the interaction of lomefloxacin with bovine serum albumin.  相似文献   

16.
Maturational cleavage of the hepatitis C virus polyprotein involves the viral chymotrypsin-like serine protease NS3. The substrate binding site of this enzyme is unusually flat and featureless. We here show that NS3 has a highly asymmetric charge distribution that is characterized by strong positive potentials in the vicinity of its active site and in the S5/S6 region. Using electrostatic potential calculations, we identified determinants of this positive potential, and the role of six different residues was explored by site-directed mutagenesis. Mutation of residues in the vicinity of the active site led to changes in k(cat) values of a peptide substrate indicating that basic amino acids play a role in the stabilization of the transition state. Charge neutralization in the S5/S6 region increased the K(m) values of peptide substrates in a manner that depended on the presence of negatively charged residues in the P5 and P6 positions. K(i) values of hexapeptide acids spanning P6-P1 (product inhibitors) were affected by charge neutralization in both the active site region and the S5/S6 region. Pre-steady-state kinetic data showed that the electrostatic surface potential is used by this enzyme to enhance collision rates between peptidic ligands and the active site. Calculations of the interaction energies of protease-substrate or protease-inhibitor complexes showed that electrostatic interaction energies oppose the formation of a tightly bound complex due to an unfavorable change in the desolvation energy. We propose that desolvation costs are minimized by avoiding the formation of individual ion pair interactions through the use of clusters of positively charged residues in the generation of local electrostatic potentials.  相似文献   

17.
In vitro channel activity of the C-terminal colicin E1 channel polypeptide under conditions of variable electrostatic interaction with synthetic lipid membranes showed distinct maxima with respect to pH and membrane surface potential. The membrane binding energy was determined from fluorescence quenching of the intrinsic tryptophans of the channel polypeptide by liposomes containing N-trinitrophenyl-phosphatidylethanolamine. Maximum in vitro colicin channel activity correlated with an intermediate magnitude of the electrostatic interaction. For conditions associated with maximum activity (40% anionic lipid, I = 0.12 M, pH 4.0), the free energy of binding was delta G approximately -9 kcal/mol, with nonelectrostatic and electrostatic components, delta Gnel approximately -5 kcal/mol and delta Gel approximately -4 kcal/mol, and an effective binding charge of +7 at pH 4.0. Binding of the channel polypeptide to negative membranes at pH 8 is minimal, whereas initial binding at pH 4 followed by a shift to pH 8 causes only 3-10% reversal of binding, implying that it is kinetically trapped, probably by a hydrophobic interaction. It was inferred that membrane binding and insertion involves an initial electrostatic interaction responsible for concentration and binding to the membrane surface. This is followed by insertion into the bilayer driven by hydrophobic forces, which are countered in the case of excessive electrostatic binding.  相似文献   

18.
T Kiho  C E Ballou 《Biochemistry》1988,27(15):5824-5828
Properties of the mycobacterial polymethylpolysaccharide-lipid complex have been investigated by fluorometric techniques. From the dissociation constant for the O-methyglucose polysaccharide-parinaric acid complex at 293 K, a Gibbs free energy (delta G degree) of -33.65 kJ/mol was obtained. The Kd decreased with increasing temperature, giving an enthalpy (delta H degree) of 15.4 kJ/mol. From these data, a molar entropy (delta S degree) of 167.4 J K-1 was obtained. Thus, the reaction is slightly endothermic, but the large positive entropy change leads to an overall negative free energy favoring complex formation. From fluorescence depolarization measurements, the methylglucose polysaccharide-parinaric acid complex appears to display isotropic rotation with a correlation time of 2.55 ns at 23 degrees C. This may be compared to a rotational correlation time of 6.17 ps for free parinaric acid in water at 23 degrees C calculated from the value determined in cyclohexanol at the same temperature, which demonstrates that the mobility of the fatty acid in the complex is restricted. Assuming the complex is spherical, it was calculated to have a diameter of 23-26 A, whereas a helical methyglucose polysaccharide molecule assembled from space-filling models has the dimensions of a cylinder of 18 X 24 A. The polysaccharide and fatty acid chain-length dependence of the interaction shows a discontinuity for helical polysaccharide segments shorter than 12 sugars and for fatty acids shorter than palmitate.  相似文献   

19.
A better understanding of the nature of the interaction between various cationic lipids used for gene delivery and DNA would lend insight into their structural and physical properties that may modulate their efficacy. We therefore separated the protonation and binding events which occur upon complexation of 1:1 DOTAP (1,2-dioleoyl-3-trimethylammonium propane):DOPE (1,2-dioleoylphosphatidylethanolamine) liposomes to DNA using proton linkage theory and isothermal titration calorimetry (ITC). The enthalpy of DOPE protonation was estimated as -45.0+/-0.7 kJ/mol and the intrinsic binding enthalpy of lipid to DNA as +2.8+/-0.3 kJ/mol. The pK(a) of DOPE was calculated to shift from 7.7+/-0.1 in the free state to 8.8+/-0.1 in the complex. At physiological ionic strength, proton linkage was not observed upon complex formation and the buffer-independent binding enthalpy was +1.0+/-0.4 kJ/mol. These studies indicate that the intrinsic interaction between 1:1 DOTAP/DOPE and DNA is an entropy-driven process and that the affinities of cationic lipids that are formulated with and without DOPE for DNA are controlled by the positive entropic changes that occur upon complex formation.  相似文献   

20.
Quantum chemical calculations have been performed to study the all-metal π halogen bonding in Al(4)(2-)···halohydrocarbon complexes. The result shows the existence of the all-metal π halogen bond in the complexes. There are three interaction modes (top, corner, and side) between Al(4)(2-) and halohydrocarbon. The interaction energy of this interaction varies from a positive value to -90.54 kJ mol(-1) in Al(4)(2-)···I-ethyne-s complex. The interaction strength is affected greatly by the hybridization of C atom and follows the order of C(sp(3)) < C(sp(2)) < C(sp) in most complexes. The methyl group in the halogen donor plays a negative contribution to the formation of halogen bond. The halogen bonding becomes stronger for the heavier halogen atom. The effect of binding site on the strength of halogen bond is related with the nature of halogen atom. The complexes have been analyzed with electrostatic potential, NICS, ELF, NBO, and AIM.  相似文献   

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