The role of methyl groups in the formation of hydrogen bond in DMSO-methanol mixtures

When examining the formation energetics of a hydrogen-bonded complex R-X-H...Y-R', focus has been almost always on the atoms directly involved, namely the atoms X, Y, and H. Little attention has been paid to the effects of the secondary alkyl groups R and R'. Taking dimethyl sulfoxide (DMSO)-methanol binary system as an example, we have studied the roles of the alkyl groups in stabilizing the hydrogen bonds by employing FTIR and NMR techniques and quantum chemical calculations. We found that methyl groups play different roles in response to the hydrogen-bonding interactions. The methyl groups of DMSO are electron-donating, whereas that of methanol is electron-withdrawing, both making positive contributions. The findings reveal non-negligible effects of secondary alkyl groups in hydrogen bonding interaction and may shed light on the understanding of other more complicated hydrogen-bonded systems in chemical and biological systems.     

分子动力学研究F1-ATP合酶对三磷酸腺苷的稳定和定位作用

F₁-ATP合酶通过与ATP之间建立广泛的相互作用,实现对ATP的位置进行精确的定位.这些相互作用为ATP的合成/水解创造了稳定的环境.理解这些相互作用是理解ATP的合成/水解机理的基础.我们通过分子动力学模拟方法研究这些相互作用,找出在稳定化过程中起到重要作用的残基.通过检测ATP和F₁-ATP合酶之间的非键相互作用,发现残基段158-164所形成的loop区域及残基R189, Y345对ATP存在显著相互作用.其中,该loop区域对ATP的三磷酸部分形成一个半包围结构,封闭活性位点区域,并通过氢键网络约束ATP三磷酸的运动,为ATP合成/水解创造稳定的环境.此外,关键残基Y345通过π-π叠加相互作用对ATP的碱基进行约束,但是ATP的碱基可以在平行于Y345芳香环的平面内进行滑动,我们推断这种滑动运动有利于促进ATP的水解.     

Repeated two-hybrid screening detects transient protein–protein interactions

Yeast two-hybrid (Y2H) screening is a powerful method to detect protein–protein interactions (PPI) at the genomic-scale. A recently proposed framework for binary interactome mapping recommends the repeated screening approach to improve the quality of PPI data. Such repeated screening reveals Y2H interactions ranging from highly sampled to singleton interactions. The quality and the biological significance of interactions from distinguished sampling classes remain unknown. In order to systematically characterize such interactions, we have chosen a dataset of 1,262 interactions that were screened repeatedly four-times. The interactions were classified as highly sampled, weakly sampled, and singleton interactions. We assessed the quality of interactions in different sampling classes using features such as protein structural properties, conservation in yeast and presence of known domain–domain interactions that are previously associated with false positive rates. Our analysis reveals that the quality of singleton interactions is comparable to that of highly sampled interactions. Interestingly, singletons encompass a higher fraction of known domain–domain interactions than highly sampled ones. Furthermore, we observed that the singleton interactions are transient in nature, while the highly sampled interactions are predominantly part of stable complexes. Hence, the repeated Y2H screening method is ideal for detecting transient PPIs that are crucial in cellular signaling pathways.     

Conformational selectivity of peptides for single-walled carbon nanotubes

Carbon nanotubes show promising prospects for applications ranging from molecular electronics to ultrasensitive biosensors. An important aspect to understanding carbon nanotube properties is their interactions with biomolecules such as peptides and proteins, as these interactions are important in our understanding of nanotube interactions with the environment, their use in cellular systems, as well as their interface with biological materials for medical and diagnostic applications. Here we report the sequence and conformational requirements of peptides for high-affinity binding to single-walled carbon nanotubes (SWNTs). A new motif, X(1)THX(2)X(3)PWTX(4), where X(1) is G or H, X(2) is H or D or null, X(3) is null or R, and X4 is null or K, was identified from two classes of phage-displayed peptide libraries. The high affinity binding of the motif to SWNTs required constrained conformations which were achieved through either the extension of the amino acid sequence (e.g., LLADTTHHRPWT) or the addition of a constrained disulfide bond (e.g., CGHPWTKC). This motif shows specific high-affinity to the currently studied SWNTs, compared to previously reported peptides. The conformations of the identified peptides in complex with SWNTs were also characterized with a variety of biophysical methodologies including CD, fluorescence, NMR spectroscopy, and molecular modeling.     

Analysis and parametric optimization of 1H off-resonance relaxation NMR experiments designed to map polypeptide self-recognition and other noncovalent interactions

The measurement of 1H off-resonance nonselective relaxation rates (R(theta,ns)) has been recently proposed as an effective method to probe peptide self-recognition, opening new perspectives in the understanding of the prefibrillization oligomerization processes in amylodogenesis. However, a full analysis and parametric optimization of the NMR experiments designed to measure R(theta,ns) relaxation rates is still missing. Here we analyze the dependence of the R(theta,ns) rates upon three critical parameters: the tilt angle of the effective field during the spin lock, the static magnetic field, and finally the repetition delay. Our analysis reveals that the tilt angle theta = 35.5 degrees not only minimizes spin-diffusion, but also avoids experimental artifacts such as J-transfer and poor adiabaticity. In addition, we found that when the dominant relaxation mechanism is caused by uncorrelated pairwise 1H dipole-1H dipole interactions the R(35.5 degrees,ns) rate is not significantly affected by static field variations, suggesting a wide applicability of the 1H off-resonance nonselective relaxation experiment. Finally, we show that the self-recognition maps based on the comparative analysis of the R(35.5 degrees,ns) rates can tolerate decreases in the interscan delays without significantly compromising the identification of critical self-association loci. These considerations not only provide a better understanding of the 1H off-resonance nonselective relaxation, but they also serve as guidelines for the optimal setup of this experiment.     

Interactions of alkyltin salts with biological dithiols: dealkylation and induction of a regular beta-turn structure in peptides

Organotin compounds specifically target vicinal dithiols, thereby inhibiting the function of essential enzymes. Here, we present the NMR binding studies of trimethyltin (TMT) and dimethyltin (DMT) chlorides with a linear peptide (ILGCWCYLR) derived from the membrane protein stannin (SNN). We show that this peptide is able to dealkylate TMT and bind DMT, adopting a stable type-I beta-turn conformation. Both the NMR data and the calculated structures indicate that the two cysteines coordinate the tin atom in a distorted tetrahedral geometry. The molecular geometries and tin coordination state were confirmed using density functional theory (DFT). In addition, NMR spectral parameters back calculated from the DFT minimized structure compared well with experimental data. These results in conjunction with studies on peptide variants (i.e., C4S, C6S, and Y7F) demonstrate unequivocally the key role of biological dithiols in both the dealkylation and binding of organotin compounds. This peptide serves as a model system for alkyltin-protein interactions and gives new insights into the biological fate of alkyltin compounds.     

Development of Neuropeptide Y and Cell-Penetrating Peptide MAP Adsorbed onto Lipid Nanoparticle Surface

Functionalization of nanoparticles surfaces have been widely used to improve diagnostic and therapeutic biological outcome. Several methods can be applied to modify nanoparticle surface; however, in this article we focus toward a simple and less time-consuming method. We applied an adsorption method on already formulated nanostructured lipid carriers (NLC) to functionalize these nanoparticles with three distinct peptides sequences. We selected a cell-penetrating peptide (CPP), a lysine modified model amphipathic peptide (Lys(N₃)-MAP), CPP/drug complex, and the neuropeptide Y. The aim of this work is to evaluate the effect of several parameters such as peptide concentration, different types of NLC, different types of peptides, and incubation medium on the physicochemical proprieties of NLC and determine if adsorption occurs. The preliminary results from zeta potential analysis indicate some evidence that this method was successful in adsorbing three types of peptides onto NLC. Several non-covalent interactions appear to be involved in peptide adsorption with the possibility of three adsorption peptide hypothesis that may occur with NLC in solution. Moreover, and for the first time, in silico docking analysis demonstrated strong interaction between CPP MAP and NPY Y1 receptor with high score values when compared to standard antagonist and NPY.     

A novel, bio-reducible gene vector containing arginine and histidine enhances gene transfection and expression of plasmid DNA

We have engineered a novel, non-viral, multifunctional gene vector (STR-CH(2)R(4)H(2)C) that contained stearoyl (STR) and a block peptide consisting of Cys (C), His (H), and Arg (R). STR-CH(2)R(4)H(2)C can form a stable nano-complex with plasmid DNA (pDNA) based on electronic interactions and disulfide cross linkages. In this study, we evaluated the efficacy of STR-CH(2)R(4)H(2)C as a gene vector. We first determined the optimal weight ratio for STR-CH(2)R(4)H(2)C/pDNA complexes. The complexes with a weight ratio of 50 showed the highest transfection efficacy. We also examined the transfection efficacy of STR-CH(2)R(4)H(2)C/pDNA complexes with or without serum and compared STR-CH(2)R(4)H(2)C/pDNA transfection efficacy with that of Lipofectamine. Even in the presence of serum, STR-CH(2)R(4)H(2)C showed higher transfection efficacy than did Lipofectamine. In addition, we determined the mechanism of transfection of the STR-CH(2)R(4)H(2)C/pDNA complexes using various cellular uptake inhibitors and evaluated its endosomal escape ability using chloroquine. Macropinocytosis was main cellular uptake pathway of STR-CH(2)R(4)H(2)C/pDNA complexes. Our results suggested that STR-CH(2)R(4)H(2)C is a promising gene delivery system.     

Photoactive peptides for light-initiated tyrosyl radical generation and transport into ribonucleotide reductase

The mechanism of radical transport in the alpha2 (R1) subunit of class I E. coli ribonucleotide reductase (RNR) has been investigated by the phototriggered generation of a tyrosyl radical, *Y356, on a 20-mer peptide bound to alpha2. This peptide, Y-R2C19, is identical to the C-terminal peptide tail of the beta2 (R2) subunit and is a known competitive inhibitor of binding of the native beta2 protein to alpha2. *Y356 radical initiation is prompted by excitation (lambda >or= 300 nm) of a proximal anthraquinone, Anq, or benzophenone, BPA, chromophore on the peptide. Transient absorption spectroscopy has been employed to kinetically characterize the radical-producing step by time resolving the semiquinone anion (Anq*-), ketyl radical (*-BPA), and Y* photoproducts on (i) BPA-Y and Anq-Y dipeptides and (ii) BPA/Anq-Y-R2C19 peptides. Light-initiated, single-turnover assays have been carried out with the peptide/alpha2 complex in the presence of [14C]-labeled cytidine 5'-diphosphate substrate and ATP allosteric effector. We show that both the Anq- and BPA-containing peptides are competent in deoxycytidine diphosphate formation and turnover occurs via Y731 to Y730 to C439 pathway-dependent radical transport in alpha2. Experiments with the Y730F mutant exclude a direct superexchange mechanism between C439 and Y731 and are consistent with a PCET model for radical transport in which there is a unidirectional transport of the electron and proton transport among residues of alpha2.     

Anisotropic local motions and location of amide protons in proteins

A new method has been developed to obtain dynamic and structural information about peptide planes in proteins by a combination of measurements of weak short-range cross-correlation rates R(H(N)N/NC') that are due to concerted fluctuations of the H(N)-N and N-C' dipole-dipole interactions and stronger long-range cross-correlation rates R(C'H(N)/H(N)N) and R(NH(N)/H(N)C(alpha)). The rates were interpreted using the axially symmetric Gaussian axial fluctuation model (GAF). The oscillation amplitudes as well as the positions of H(N) atoms with respect to peptide planes in ubiquitin were determined. Most N-H(N) bonds were found not to lie exactly along the bisector of the N-C' and N-C(alpha) bonds but to be slightly tilted toward the carbon-terminal side of the peptide.     

A mini-review and perspective on multicyclic peptide mimics of antibodies

This review gave a brief introduction on recent development in monocyclic and multicyclic peptide mimics of antibodies and provides a perspective on screening and design of multicyclic peptide mimics of antibodies in the future.     

Stereochemistry of anionic vinyl polymerization

The stereochemistry of anionic polymerization of vinyl monomers: CH₂=C(R)C(Y)=X where X and Y are O, N or C and R = H or alkyl is discussed in terms of a: the geometry of the -CH₂C-(R)C(Y)=X intermediate existing as E- or Z-isomers; b: the interactions of cation (Li, Na, etc.) with the anion and coordinating groups on the penultimate or antepenultimate asymmetric carbon. The E/Z ratio appears to be determined directly by the s-trans/s-cis approach of the monomer. The nature of the coordination of the counter ion is considerably more complicated and is discussed in detail.     

Combining crystallographic and quantum chemical data to understand DNA-protein π-interactions in nature

Noncovalent interactions are accepted to be prevalent across biochemical systems, including governing interactions between nucleic acids and proteins. The present review summarizes work done to characterize the abundance, structure and strength of DNA–protein π interactions by combining rigorous searches of experimental X-ray crystal structures of DNA–protein complexes and quantum chemical calculations. Focus is placed on interactions that occur between the π-containing amino acids (W, H, F, Y, R, E, and D) and the canonical DNA nucleobases (A, T, G, and C) or 2′-deoxyribose moiety. These studies highlight the considerable frequency of both DNA–protein π–π and sugar–π interactions in nature, which can involve any π-containing amino acid arranged in many unique binding orientations with respect to any DNA component. When combined with the significant strength predicted for the identified DNA–protein π contacts using density functional theory, these works underscore the potential impact of these interactions on critical biological functions. This conclusion is supported by a review of examples from the recent literature that have acknowledged the role of DNA–protein π interactions in binding, specificity, and catalysis.

     

Selective enhancement of nucleases by polyvalent DNA-functionalized gold nanoparticles

We demonstrate that polyvalent DNA-functionalized gold nanoparticles (DNA-Au NPs) selectively enhance ribonuclease H (RNase H) activity while inhibiting most biologically relevant nucleases. This combination of properties is particularly interesting in the context of gene regulation, since high RNase H activity results in rapid mRNA degradation and general nuclease inhibition results in high biological stability. We have investigated the mechanism of selective RNase H activation and found that the high DNA density of DNA-Au NPs is responsible for this unusual behavior. This work adds to our understanding of polyvalent DNA-Au NPs as gene regulation agents and suggests a new model for selectively controlling protein-nanoparticle interactions.     

Reevaluation of copper(I) affinity for amyloid-β peptides by competition with ferrozine--an unusual copper(I) indicator

The association constant of ferrozine (5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine-4,4'-disulfonic acid) with Cu(I) to form the chromophoric [Cu(I)(Fz)(2)](3-) complex was determined by UV/Vis titration experiments in Hepes buffer (0.1 M, pH 7.4). An association constant close to 10(12) M(-2), which is significantly weaker than those of the well-known, water-soluble, Cu(I) chelators bicinchoninic acid and 2,9-dimethyl-4,7-diphenyl-1,10-phenantroline disulfonic acid, was found. The [Cu(I)(Fz)(2)](3-) chromophore was used in UV/Vis competition experiments to determine Cu(I) binding affinity for the amyloid-β peptide involved in Alzheimer's disease and for a series of pertinent mutants. An association constant of approximately 10(7) M(-1) was found; this is much weaker than that reported for dithiothreitol and confirms that imidazoles are harder ligands than thiolates. Each His mutation (H6A, H13A, and H14A) impacts the peptide affinity for Cu(I). The native human amyloid-β peptide was found to be a fourfold-stronger Cu(I) ligand than the murine peptide, which differs by three point mutations (R5G, Y10F, and H13R) from the human one.     

Formation of peptide radical ions through dissociative electron transfer in ternary metal-ligand-peptide complexes

The formation and fragmentation of odd-electron ions of peptides and proteins is of interest to applications in biological mass spectrometry. Gas-phase redox chemistry occurring during collision-induced dissociation of ternary metal-ligand-peptide complexes enables the formation of a variety of peptide radicals, including the canonical radical cations, M(+?), radical dications, [M+H](2+?), radical anions, [M-2H](-?) and phosphorylated radical cations. In addition, odd-electron peptide ions with well-defined initial location of the radical site are produced through side-chain losses from the radical ions. Subsequent fragmentation of these species provides information regarding the role of charge and location of the radical site on the competition between radical-induced and proton-driven fragmentation of odd-electron peptide ions. This account summarizes current understanding of the factors that control the efficiency of the intramolecular electron transfer (ET) in ternary metal-ligand-peptide complexes resulting in formation of odd-electron peptide ions. Specifically, we discuss the effect of the metal center, the ligand and the peptide structure on the competition between the ET, proton transfer (PT) and loss of neutral peptide and neutral peptide fragments from the complex. Fundamental studies of the structures, stabilities and the energetics and dynamics of fragmentation of these complexes are also important for detailed molecular-level understanding of photosynthesis and respiration in biological systems.     

Combined computational and experimental study of substituent effects on the thermodynamics of H(2), CO,arene, and alkane addition to iridium

The thermodynamics of small-molecule (H(2), arene, alkane, and CO) addition to pincer-ligated iridium complexes of several different configurations (three-coordinate d(8), four-coordinate d(8), and five-coordinate d(6)) have been investigated by computational and experimental means. The substituent para to the iridium (Y) has been varied in complexes containing the (Y-PCP)Ir unit (Y-PCP = eta(3)-1,3,5-C(6)H(2)[CH(2)PR(2)](2)Y; R = methyl for computations; R = tert-butyl for experiments); substituent effects have been studied for the addition of H(2), C-H, and CO to the complexes (Y-PCP)Ir, (Y-PCP)Ir(CO), and (Y-PCP)Ir(H)(2). Para substituents on arenes undergoing C-H bond addition to (PCP)Ir or to (PCP)Ir(CO) have also been varied computationally and experimentally. In general, increasing electron donation by the substituent Y in the 16-electron complexes, (Y-PCP)Ir(CO) or (Y-PCP)Ir(H)(2), disfavors addition of H-H or C-H bonds, in contradiction to the idea of such additions being oxidative. Addition of CO to the same 16-electron complexes is also disfavored by increased electron donation from Y. By contrast, addition of H-H and C-H bonds or CO to the three-coordinate parent species (Y-PCP)Ir is favored by increased electron donation. In general, the effects of varying Y are markedly similar for H(2), C-H, and CO addition. The trends can be fully rationalized in terms of simple molecular orbital interactions but not in terms of concepts related to oxidation, such as charge-transfer or electronegativity differences.     

Substituent effects on the stereochemistry of gas-phase intracomplex nucleophilic substitutions

The mechanism and stereochemistry of the intracomplex solvolysis of proton-bound complexes [Y...H...M]+ between M = CH3 (18)OH and Y = 1-arylethanol [(S)-1-(para-tolyl)ethanol (1S), (S)-1-(para-chlorophenyl)ethanol (2S), (S)-1-(meta-alpha,alpha,alpha-trifluoromethylphenyl)ethanol (3S), (S)-1-(para-alpha,alpha,alpha-trifluoromethylphenyl)ethanol (4S), (R)-1-(pentafluorophenyl)ethanol (5R), (R)-alpha-(trifluoromethyl)benzyl alcohol (6R), and (R)-1-phenylethanol (7R)] have been investigated in the gas phase (CH3F; 720 Torr) in the 25-140 degrees C temperature range. Gas-phase solvolysis of [Y...H...M]+ (Y=2S, 3S, 4S, and 7R) leads to extensive racemization above a characteristic temperature t(#) (e.g. at t(#)>60 degrees C for 7R), whereas below that temperature the reaction displays a preferential retention of configuration. Predominant retention of configuration is instead observed in the intracomplex solvolysis of [Y...H...M]+ (Y=1S, 4S, 5R, and 6R) with the temperature range investigated (25 相似文献   

用扩展的Istomin-Palm模型估算双向延伸化合物R1-Y-R2生成焓

Istomin和Palm曾提出用模型Δ_fH⁰(RX)=h[R]+h[X]+φ[R]φ[X](式中h[R]和h[X]分别为烷基R 和取代基X对单取代烷烃生成焓Δ_fH⁰(RX)的贡献, φ[R]φ[X]则表示R与X之间的相互作用对Δ_fH⁰(RX)的贡献)来表示单取代烷烃生成焓Δ_fH⁰(RX). 对于双向延伸化合物R1-Y-R2, 其取代基Y位于分子链的中间, 与两个烷基(R1和R2)相连. 此类化合物分子内取代基与烷基之间的相互作用, 较单取代烷烃的相比更为复杂. 因此, Istomin-Palm模型在R1-Y-R2体系中应用必须进行修正. 本文把取代基Y、烷基R1和R2三者之间的相互作用对R1-Y-R2类化合物生成焓Δ_fH⁰(R1-Y-R2)的贡献分为三部分: R1Y与R2之间的相互作用(φ[R2]φ[R1Y]), YR2与R1之间的相互作用(φ[R1]φ[YR2]), 以及两烷基R1与R2之间的相互作用(ψ[R1]ψ[R2]). 用以上三项替换φ[R]φ[X], 扩展Istomin-Palm模型, 建立一个新的经验模型Δ_fH⁰(R1-Y-R2)=h[R1]+h[R2]+h[Y]+φ[R1]φ[YR2]+φ[R2]φ[R1Y]+ψ[R1]ψ[R2], 来表示Δ_fH⁰(R1-Y-R2)(式中h[R1]、h[R2]和h[Y]分别为烷基R1、R2和取代基Y对Δ_fH⁰(R1-Y-R2)的贡献, 后三项则表示烷基R1、R2和取代基Y两两之间相互作用对Δ_fH⁰(R1-Y-R2)的贡献). 进而, 采用本研究组最近报道的相互作用势指数IPI(X)(Wu, Y. X.; Cao, C. Z.; Yuan, H. Chin. J. Chem. Phys. 2012,25 (2), 153.)表示取代基Y对烷基的固有作用(φ[Y]), 从而建立两个定量估算生成焓的通用模型. 其中, 一个用于估算硫醚、仲胺、醚和酮类化合物生成焓, 另一个用于估算酯类化合物生成焓. 这两个模型均得到良好的结果, 与采用G3和G3MP2方法相比具有同样的精度, 还可以避免大量繁琐的计算.     

On the Rational Drug Design for Hypertension through NMR Spectroscopy

Antagonists of the AT1receptor (AT1R) are beneficial molecules that can prevent the peptide hormone angiotensin II from binding and activating the specific receptor causing hypertension in pathological states. This review article summarizes the multifaced applications of solid and liquid state high resolution nuclear magnetic resonance (NMR) spectroscopy in antihypertensive commercial drugs that act as AT1R antagonists. The 3D architecture of these compounds is explored through 2D NOESY spectroscopy and their interactions with micelles and lipid bilayers are described using solid state ¹³CP/MAS, ³¹P and ²H static solid state NMR spectroscopy. Due to their hydrophobic character, AT1R antagonists do not exert their optimum profile on the AT1R. Therefore, various vehicles are explored so as to effectively deliver these molecules to the site of action and to enhance their pharmaceutical efficacy. Cyclodextrins and polymers comprise successful examples of effective drug delivery vehicles, widely used for the delivery of hydrophobic drugs to the active site of the receptor. High resolution NMR spectroscopy provides valuable information on the physical-chemical forces that govern these drug:vehicle interactions, knowledge required to get a deeper understanding on the stability of the formed complexes and therefore the appropriateness and usefulness of the drug delivery system. In addition, it provides valuable information on the rational design towards the synthesis of more stable and efficient drug formulations.