Molecular hydrophobic attraction and ion-specific effects studied by molecular dynamics

Much is written about "hydrophobic forces" that act between solvated molecules and nonpolar interfaces, but it is not always clear what causes these forces and whether they should be labeled as hydrophobic. Hydrophobic effects roughly fall in two classes, those that are influenced by the addition of salt and those that are not. Bubble adsorption and cavitation effects plague experiments and simulations of interacting extended hydrophobic surfaces and lead to a strong, almost irreversible attraction that has little or no dependence on salt type and concentration. In this paper, we are concerned with hydrophobic interactions between single molecules and extended surfaces and try to elucidate the relation to electrostatic and ion-specific effects. For these nanoscopic hydrophobic forces, bubbles and cavitation effects play only a minor role and even if present cause no equilibration problems. In specific, we study the forced desorption of peptides from nonpolar interfaces by means of molecular dynamics simulations and determine the adsorption potential of mean force. The simulation results for peptides compare well with corresponding AFM experiments. An analysis of the various contributions to the total peptide-surface interactions shows that structural effects of water as well as van der Waals interactions between surface and peptide are important. Hofmeister ion effects are studied by separately determining the effective interaction of various ions with hydrophobic surfaces. An extension of the Poisson-Boltzmann equation that includes the ion-specific potential of mean force yields surface potentials, interfacial tensions, and effective interactions between hydrophobic surfaces. There, we also analyze the energetic contributions to the potential of mean force and find that the most important factor determining ion-specific adsorption at hydrophobic surfaces can best be described as surface-modified ion hydration.     

Dielectric decrement as a source of ion-specific effects

Many theoretical studies were devoted in the past to ion-specific effects trying to interpret a large body of experimental evidence, such as surface tension at air/water interfaces and force measurements between charged objects. Although several mechanisms were suggested to explain the results, such as dispersion forces and specific surface-ion interactions, we would like to suggest another source of ion-specificity originating from the local variations of the dielectric constant due to the presence of ions in the solution. We present a mean-field model to account for the heterogeneity of the dielectric constant caused by the ions. In particular, for ions that decrease the dielectric constant we find a depletion of ions from the vicinity of charged surfaces. For a two-plate system, the same effect leads to an increase of the pressure in between two surfaces. Our results suggest that the effect of ions on the local dielectric constant should be taken into account when interpreting experiments that address ion-specific effects.     

A Molecular Dynamics study of short-chain polyelectrolytes in explicit water: Toward the origin of ion-specific effects

We present all atom explicit water Molecular Dynamics simulation results for the structure of short (six monomer units) aliphatic ionenes in mixtures with a low-molecular weight electrolyte. The SPC/E model was used to describe water. Long-range effects were taken into account via the Ewald summation procedure. The results indicate that strongly hydrated ions such as F⁻ cannot approach the nitrogen atom on the oligoion. In contrast, weakly hydrated I⁻ ions accumulate close to the oligoion. These findings are consistent with the thermodynamic data and ongoing measurements of the dielectric relaxation in ionene solutions.     

顺铂耐药的分子机制

顺铂被广泛用于多种类型的实体肿瘤的临床治疗.DNA是顺铂的主要靶点,顺铂结合会导致DNA损伤并诱发细胞凋亡.然而,顺铂化疗常常受到内在的和获得性的耐药性的限制.在过去30多年里,大量的研究致力于对顺铂耐药性的理解,并且提出了几种导致顺铂耐药性的分子机制.这些机制显示顺铂的耐药性具有多因素特征.本文系统描述和讨论了顺铂的耐药性机制,包括细胞内药物积累的减少,药物去活作用的增强,DNA修复作用,DNA损伤反应和凋亡通路的变化以及一些间接信号通路的调控影响.     

Molecular mechanisms of antibiotic resistance

Over the past decade, resistance to antibiotics has emerged as a crisis of global proportion. Microbes resistant to many and even all clinically approved antibiotics are increasingly common and easily spread across continents. At the same time there are fewer new antibiotic drugs coming to market. We are reaching a point where we are no longer able to confidently treat a growing number of bacterial infections. The molecular mechanisms of drug resistance provide the essential knowledge on new drug development and clinical use. These mechanisms include enzyme catalyzed antibiotic modifications, bypass of antibiotic targets and active efflux of drugs from the cell. Understanding the chemical rationale and underpinnings of resistance is an essential component of our response to this clinical challenge.     

Molecular mechanisms characterizing cone photoresponses

In the vertebrate retina, rods mediate twilight vision and cones mediate daylight vision. Their photoresponse characteristics are different. The light-sensitivity of a cone is 10(2)-10(3) times lower than that of a rod. In addition, the photoresponse time course is much faster in cones. The mechanism characterizing cone photoresponses has not been known mainly because of the difficulty in isolating cones in large quantities to perform biochemistry. Recently, we developed a method to purify cones from carp retina using a density gradient, which made it possible to analyze the differences in the molecular mechanism of phototransduction between rods and cones. The results showed that signal amplification in cones is less effective, which explains the lower light-sensitivity of cones. The results also showed that visual pigment phosphorylation, a quenching mechanism of light-activated visual pigment, is much more rapid in cones than in rods. The rapid phosphorylation in cones is attributed to a very high total kinase activity in cones. Because of this high activity, cone pigment is readily phosphorylated even at very high bleaching levels, which probably explains why cone photoresponses recover quickly. Based on these findings, the molecular mechanisms of the differences in the photoresponse characteristics between rods and cones are outlined.     

Molecular mechanisms of hydrogen-loaded beta-hydroquinone clathrate

Molecular dynamics simulations are used to investigate the molecular interactions of hydrogen-loaded beta-hydroquinone clathrate. It is found that, at lower temperatures, higher loadings are more stable, whereas at higher temperatures, lower loadings are more stable. Attractive forces between the guest and host molecules lead to a stabilized minimum-energy configuration at low temperatures. At higher temperatures, greater displacements take the system away from the shallow energy minimum, and the trend reverses. The nature of the cavity structure is nearly spherical for a loading of one, leads to preferential occupation near the hydroxyl ring crowns of the cavity with a loading of two, and at higher loadings, leads to occupation of the interstitial sites (the hydroxyl rings) between cages by a single H(2) molecule with the remaining molecules occupying the equatorial plane of the cavity. Occupation of the interstitial positions of the cavities leads to facile diffusion.     

Molecular biosensing system based on intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) that undergo structural transition upon binding their target molecules are becoming increasingly known. IDPs, because of their binding specificity and induced folding properties, can serve as biological recognition elements for sensing applications. In this paper, BRCA1, an IDP, was utilized as the biological recognition element to detect tumor suppressor protein p53 through the BRCA1/p53 binding interaction to serve as a proof-of-concept for the use of IDPs as recognition elements. The binding resulted in a disordered-to-ordered BRCA1 conformational change, as seen in our circular dichroism (CD) measurements. This conformational change in BRCA1 (residues 219-498) was utilized in the detection of p53 (residues 311-393) via both intrinsic and extrinsic fluorescent probes. Intrinsic tryptophan residues within the BRCA1 sequence detected p53 (311-393) with a detection limit of 0.559 nM (0.112 pmol). Two environmentally sensitive fluorophores, tetramethylrhodamine-5-maleimide (TMR) and 6-((5-dimethylaminonaphthalene-1-sulfonyl)amino)hexanoic acid, succinimidyl ester (dansyl-X, SE) were conjugated to BRCA1 (219-498). Dansyl-X, SE-conjugated BRCA1 (219-498) detected p53 (311-393) with a detection limit of 1.50 nM (0.300 pmol). The sensitivities for TMR and dansyl-X, SE-conjugated BRCA1 for the detection of p53 were nearly threefold and twofold higher, respectively, than the sensitivity reported using intrinsic BRCA1 tryptophan fluorescence. CD measurements did not reveal a disruption of p53/dye-conjugated BRCA1 binding, thus validating the applicability of environmentally sensitive fluorophores as transduction moieties to detect molecules which bind to IDPs and induce a structural change.     

Molecular mechanisms of the photostability of indigo

The photophysics of indigo as well as of bispyrroleindigo, the basic chromophore of indigo, has been investigated with ab initio electronic-structure calculations. Vertical electronic excitation energies and excited-state potential-energy profiles have been calculated with the CASSCF, CASPT2 and CC2 methods. The calculations reveal that indigo and bispyrroleindigo undergo intramolecular single-proton transfer between adjacent N-H and C=O groups in the (1)ππ* excited state. The nearly barrierless proton transfer provides the pathway for a very efficient deactivation of the (1)ππ* state via a conical intersection with the ground state. While a low-lying S(1)-S(0) conical intersection exists also after double-proton transfer, the latter reaction path exhibits a much higher barrier. The reaction path for trans→cis photoisomerization via the twisting of the central C=C bond has been investigated for bispyrroleindigo. It has been found that the twisting of the central C=C bond is unlikely to play a role in the photochemistry of indigo, because of a large potential-energy barrier and a rather high energy of the S(1)-S(0) conical intersection of the twisted structure. These findings indicate that the exceptional photostability of indigo is the result of rapid internal conversion via intramolecular single-proton transfer, combined with the absence of a low-barrier reaction path for the generation of the cis isomer via trans→cis photoisomerization.     

Molecular thin films on solid surfaces: mechanisms of melting

We use molecular dynamics simulations to study the melting of pentane and hexane monolayers adsorbed on the basal plane of graphite. For both of these systems, the temperature-dependent structures and the melting temperatures agree well with experiment. A detailed analysis reveals that a mechanism involving the promotion of molecules to the second layer underlies melting in these systems. In the second-layer promotion mechanism, a small fraction of molecules transition into the second layer around the melting temperature, leaving vacant space in the first layer to facilitate disordering. The second-layer promotion mechanism arises because of the weaker molecule-surface interaction in our study than that in previous studies. The weaker molecule-surface interaction is consistent with experimental temperature-programmed desorption studies.     

Molecular orbital calculations on the conformation of polypeptides and proteins

Quantum-mechanical calculations, by the PCILO method, on the conformations of the amino-acid residues of proteins have been extended to the seryl and threonyl residues. The conformationally stable regions, within 5 Kcal/mole above the global minima, represent 57% of the total available space for the seryl residue and 27% for the threonyl one. They are appreciably wider than those permitted by the empirical studies. The quantum-mechanical calculations account much more satisfactorily for the limiting contour of the distribution of the experimental conformations, as observed in lysozyme, myoglobin and -lactalbumin, than do the empirical computations. The situation is less satisfactory as concerns the position of the global minima which imply two intramolecular hydrogen bonds. This may be attributed to the fact that this position is more sensitive to the model employed in the calculations than the general contours. Experiments made on a seryl-containing dipeptide agree completely with our prediction on the two most stable conformations of that residue. The calculations indicate also that the seryl and threonyl residues should have a reduced tendency to assume theR conformation, which, however, is not forbidden to any of them.

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Zusammenfassung Die quantenmechanischen Berechnungen von Aminosäure-Anteilen in Proteinen mit Hilfe der PCILO-Methode wurden auf den Seryl- und Threonyl-Anteil ausgedehnt. Die Gebiete stabiler Konformation — innerhalb 5 Kcal/mol über dem absoluten Minimum — stellen 57 % des insgesamt möglichen Bereichs für den Seryl-Anteil und 27% für den Threonyl-Anteil dar. Diese Gebiete sind beträchtlich größer als diejenigen, die auf Grund empirischer Verfahren möglich sind. Die quantenmechanischen Rechnungen genügen dem Bereich der experimentellen Verteilung der Konformationen besser als die empirischen Rechnungen. Im Hinblick auf die Lage der absoluten Minima, die zu innermolekularen Wasserstoffbindungen gehören, ist die Beschreibung weniger befriedigend. Dies kann der Tatsache zugeschrieben werden, daß diese Werte empfindlicher bezüglich der verwendeten Modellverbindung sind als dies bei der allgemeinen Stabilitätskarte der Fall ist. Die Experimente mit einem Dipeptid mit Seryl-Anteil stimmen völlig mit unseren Voraussagen der stabilsten Konformation dieses Anteils überein. Die Berechnungen zeigen weiterhin, daß sowohl der Seryl- als auch der Threonyl-Anteil eine verhältnismäßig geringe Tendenz zur Aufnahme derR -Konformation haben sollten; sie ist jedoch für beide Anteile nicht verboten.

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Resume Les calculs quantiques par la méthode PCILO sur les conformations des résidus amino-acides des protéines ont été étendus au cas des résidus séryle et thréonyle. Les zones conformationnelles stables, dans la limite de 5 Kcal/mole au dessus du plus has minimum, répresentent 57%, de l'espace disponible pour le residue séryle et 27% de cet espace pour le résidu thréonyle. Elles sont nettement plus larges que celles permises par les calculs empiriques. Les calculs quantiques rendent compte d'une façon beaucoup satisfaisante que les calculs mpiriques des limites de la répartition sur la carte conformationnelle des points représentatifs des conformations des résidus séryle et thréonyle dans le lysozyme, la myoglobine et l'-lactalbumine. La situation est plus délicate en ce qui concerne la position du plus has minimum qui comporte deux liaisons hydrogéne intramoléculaires. Ceci pent être attribué au fait que cette position parait être plus sensible au modèle utilisé dans les calculs que ne le sont les contours généraux. Les expériences effectuées sur un dipeptide à résidu séryle confirment complètement nos prédictions sur les conformations les plus stables de ce résidu. Les calculs indiquent aussi que les résidues séryle et thréonyle devraient avoir une tendance réduite pour assumer la conformationR sans que celle-ci leur soit toutefois interdite.

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This work was supported by grant n° 67-00-532 of the Délégation Générale à la Recherche Scientifique et Technique (Comité de Biologie Moléculaire).     

Molecular orbital calculations on the conformation of polypeptides and proteins

Quantum mechanical calculations using the PCILO method have been performed on the tripeptide model CH₃CO-X-Y-NHCH₃. Competition between C₅, C₇, C₁₀ rings and open structures has been investigated through mapping of the whole {φ, Ψ} conformational space and energy minimization. From these results, it appears that the C₁₀ ring simulating the folding named U-turn, involving a hydrogen bond between the i...i + 3 residues, is the most probable structure although not the most stable in energy. The results are used for predicting the frequency of U-turns in proteins, α-chymotrypsin is given as an example.     

Molecular recognition of amines and amino esters by zinc porphyrin receptors: binding mechanisms and solvent effects

Zinc porphyrin receptors bearing 12 ester groups in the meso phenyl groups (1-3) were prepared, and binding of amines and alpha-amino esters was studied with emphasis on the binding mechanisms. The X-ray crystallographic analysis of 5,10,15,20-tetrakis(2, 6-bis(carbomethoxymethoxy)-4-carbomethoxyphenyl)porphyrin (free base of 1) showed that the receptor has a binding pocket above the porphyrin plane. UV-visible titration experiments revealed that the zinc porphyrin receptors bound amines and alpha-amino esters with binding constants (K(a)) ranging from 0.5 to 52 700 M(-1) in CH(2)Cl(2) at 25 degrees C. The ester functional groups of 1 assisted the binding of aromatic alpha-amino esters (K(a) = 8 000-23 000 M(-1) in CH(2)Cl(2) at 25 degrees C) and inhibited the binding of bulky aliphatic alpha-amino esters (K(a) = 460 M(-1) for Leu-OMe in CH(2)Cl(2) at 25 degrees C), indicating that CH-pi type interactions and steric repulsions control the selectivity. The binding of amines and alpha-amino esters was tight both in a nonpolar solvent (CH(2)Cl(2)) and in a polar solvent (water) but loose in a solvent of intermediate polarity (H(2)O-MeOH (1:1)), demonstrating that two competitive driving forces are operating: (1) attractive electrostatic forces between host and guest such as coordination of the amino group to the zinc atom, and (2) entropic forces stemming from desolvation as well as enthalpic forces due to the host-guest dispersion forces. The former forces drive the binding in CH(2)Cl(2) while the latter forces drive the binding in water. The enthalpy changes in the binding in CH(2)Cl(2) and those in water range from -50 to -30 kJ mol(-1) and from -35 to 0 kJ mol(-1), respectively. The entropy changes in CH(2)Cl(2) and those in water range from -120 to -60 J K(-1) mol(-1) and from -50 to +60 J K(-1) mol(-1), respectively. Thus the binding in CH(2)Cl(2) is characterized by large negative enthalpy changes, while that in water by less negative entropy changes. These thermodynamic parameters also indicate that host-guest polar interactions (enthalpic forces) drive the binding in CH(2)Cl(2) while both host-guest dispersion interactions (an enthalpic force) and desolvation (an entropic force) drive the binding in water. Enthalpy-entropy compensation observed for the binding in water indicates that the binding of amines and amino esters in water by zinc porphyrins is associated with conformational changes as well as a high degree of dehydration. In CH(2)Cl(2), no clear compensation was observed, consistent with the mechanism that neither desolvation processes nor conformational changes contribute significantly to the binding energetics.     

Molecular orbital calculations on the conformation of polypeptides and proteins

The conformational energy maps are computed for the lysyl and the arginyl residues with the help of the quantum-mechanical method PCILO. Because of the relatively very large number of the possible combinations of the side chain rotational angles, sub-maps are constructed only for the most common such combinations as indicated from the X-rays study of ten globular proteins. These submaps are then combined for the construction of the general conformational energy map. The comparison of the theoretically allowed and experimentally observed values of backbone dihedral angles and for the lysyl and arginyl residues in the globular proteins indicates a very satisfactory agreement among the two. These results confirm that the contour of the stable zone on the conformational energy map depends primarily on ¹ but indicate also that its fine structure is sensitive to the remaining 's in particular to ².

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Zusammenfassung Diagramme der Konformationsenergie werden für den Lysyl- sowie den Arginylrest mit Hilfe der quantenmechanischen PCILO-Methode berechnet. Wegen der großen Zahl möglicher Kombinationen der Rotationswinkel der Seitenketten werden Teildiagramme nur für die wichtigsten derartigen Kombinationen, die bei Untersuchungen nach der Röntgenstrahlmethode an zehn globulären Proteinen gefunden wurden, konstruiert. Diese Teildiagramme werden dann zum Gesamtdiagramm der Konformationsenergie kombiniert. Die Übereinstimmung zwischen experimentellen und theoretisch erlaubten Winkeln und der Hauptkette und den Lysyl- und Arginylresten ist sehr zufriedenstellend. Diese Ergebnisse bestätigen, daß der stabile Bereich des Diagramms der Konformationsenergie hauptsächlich von ¹ abhängt; sie zeigen aber auch, daß seine genaue Struktur von den übrigen -Werten beeinflußt wird, insbesondere von ².

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Résumé Les cartes d'énergie conformationelle des résidus lysyle et arginyle sont construites à l'aide de la méthode PCILO de la Chimie Quantique. A cause du nombre très élevé des combinaisons possibles des angles rotationnels de la chaîne latérale, des sous-cartes sont construites pour les plus fréquentes seulement de ces combinaisons (selon les indications de l'étude aux rayons X de dix protéines globulaires). Ces sous-cartes sont ensuite combinées pour la construction de la carte générale d'énergie conformationnelle. La comparaison des valeurs théoriques et expérimentales des angles et de la chaîne principale pour les résidus lysyle et arginyle des protéines indique un accord très satisfaisant entre les deux. Ces résultats confirment que le contour de la zone stable sur la carte d'énergie conformationnelle est déterminé principalement par la valeur de ₁ mais indiquent aussi que la structure fine de cette zone est sensible aux valeurs des supérieurs, en particulier de ².

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This work was supported by grant n 67-00-532 of the Délégation Générale à la Recherche Scientifique et Technique (Comité de Biologie Moléculaire).     

Molecular orbital calculations on the conformation of polypeptides and proteins

An extensive comparison of empirical and quantum-mechanical computations on the conformation of the glycyl and alanyl residues indicates substantial differences between the two. The quantummechanical computations impose less restrictions upon the allowed or preferred conformational space than do the empirical ones. In the case of the alanyl residue they even introduce new zones of conformational stability, overlooked by the majority of the empirical computations. The experimental data coming from crystallographic studies on lysozyme, myoglobin and a number of smaller compounds are in better agreement with the quantum-mechanical results than with the empirical ones. Recent quantum-mechanical calculations on the conformational maps of the four aromatic residues of proteins having shown that these maps are, as far as their general contours are concerned, very similar to those of the alanyl residue, the conformational map for this last residue is considered as typical, roughly, for all C containing residues. It is shown that practically all experimentally known conformations for all the different amino-acid residues in lysozyme, myoglobin and a number of smaller compounds, fit into this scheme, the agreement being much better with the quantum-mechanical conformational map than with a typical empirical one.

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Zusammenfassung Ein detaillierter Vergleich der Resultate empirischer und quantenmechanischer Rechnungen für die Konformation des Glycyl- und Alanyl-Restes zeigt gro\e Divergenzen. Die nicht empirischen, nach der PCILO-Methode durchgeführten Rechnungen ergeben weniger BeschrÄnkungen als die empirischen. Im Fall des Alanylrestes führen erstere sogar zu neuen Bereichen der StabilitÄt, die bei der Mehrzahl der empirischen Rechnungen nicht auftreten, obwohl sie wesentlich zu sein scheinen. Die experimentellen Angaben aus kristallographischen Studien über Lysozym, Myoglobin und eine Anzahl kleinerer Moleküle sind in besserer übereinstimmung mit den Resultaten der quantenmechanischen als mit denen der empirischen Rechnungen. Kürzlich haben quantenmechanische Berechnungen für die Konformation von vier aromatischen Proteinresten gezeigt, da\ sie im gro\en und ganzen der des Alanylrestes sehr Ähnlich sind. Deshalb wurden dessen Konformationen als in den Grundzügen typisch für alle C enthaltenden Reste angesehen. Schlie\lich wird gezeigt, da\ praktisch alle bekannten Konformationen für die verschiedenen AminosÄure-Reste in Lysozym, Myoglobin und einer Anzahl kleinerer Verbindungen in dieses Schema passen, wobei die übereinstimmung mit den quantenmechanischen Ergebnissen besser als mit denen rein empirischer Rechnungen ist.

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Résumé Une comparaison détaillée des résultats des calculs empiriques avec ceux des calculs quantiques sur la conformation des résidus glycyle et alanyle indique l'existence des divergences profondes entre les deux. Les calculs quantiques, menés par la méthode PCILO, imposent nettement moins de restrictions que ne le font les calculs empiriques sur l'espace conformationnel préféré de ces résidus. Dans le cas du résidu alanyle les calculs quantiques introduisent mÊme des nouvelles zones de stabilité conformationnelle qui ont échappé à la majorité des calculs empiriques et dont la signification paraÎt essentielle. Les données expérimentales provenant des études cristallographiques sur le lysozyme, la myoglobine et un certain nombre de molécules plus petites sont en meilleur accord avec les résultats des calculs quantiques qu'avec ceux des calculs empiriques. Des calculs quantiques récents sur les cartes conformationelles des quatre résidus aromatiques des protéines ayant montré que ces cartes sont, pour autant que l'on s'intéresse à leurs contours généraux, très semblables à celle du résidu alanyle, la carte conformationelle de ce dernier a été considérée comme représentant, grosso modo, tous les résidus à carbone . On montre que pratiquement toutes les conformations connues expérimentalement de tous les acides aminés du lysozyme, de la myoglobine et d'un certain nombre de molécules plus petites sont en accord avec cette représentation, l'accord étant bien meilleur avec la carte conformationnelle résultant des calculs quantiques qu'avec celle représentant un calcul empirique typique.

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This work was supported by grant n 67-00-532 of the Délégation Générale á la Recherche Scientifique (Comité de Biologie Moléculaire).