C-C sigma complexes of rhodium

In this article, the complexes [Rh(Binor-S')(PR3)][BAr(4)(F)] (R = (i)Pr, Cy, C(5)H(9)) are described. A combination of x-ray crystallography, NMR spectroscopy, density functional theory, and "atoms in molecules" calculations unequivocally demonstrates that the complexes contain rare examples of metal...C-C agostic interactions. Moreover, they are fluxional on the NMR time scale, undergoing rapid and reversible C-C activation. Kinetic data and calculations point to a bismetallacyclobutane, Rh(V), intermediate.     

Metal ion-binding properties of (N3)-deprotonated uridine, thymidine, and related pyrimidine nucleosides in aqueous solution

The acidity constants for (N3)H of the uridine-type ligands (U) 5-fluorouridine, 5-chloro-2'-deoxyuridine, uridine, and thymidine (2'-deoxy-5-methyluridine) and the stability constants of the M(U-H)(+) complexes for M(2+) = Mg(2+), Ca(2+), Sr(2+), Ba(2+), Mn(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), and Pb(2+) were measured (potentiometric pH titrations; aqueous solution; 25 degrees C; I = 0.1 M, NaNO(3)). Plots of logK(M(U-H))(M) vs. pK(U)(H) result in straight lines that are compared with previous plots for simple pyridine-type and o-amino(methyl)pyridine-type ligands as well as with the stabilities of the corresponding M(cytidine)(2+) complexes. The results indicate monodentate coordination to (N3)(-) in M(U-H)(+) for Co(2+) and Ni(2+). For the M(U-H)(+) species of Cd(2+), Zn(2+), or Cu(2+), increased stabilities imply that semichelates form, i.e., M(2+) is (N3)(-)-bound and coordinated water molecules form hydrogen bonds to (C2)O and (C4)O; these "double" semichelates are in equilibrium with "single" semichelates involving either (C2)O or (C4)O and possibly also with four-membered chelates for which M(2+) is innersphere-coordinated to (N3)(-) and a carbonyl oxygen. For the alkaline earth ions, semichelates dominate with the M(2+) outersphere bound to (N3)(-) and innersphere to one of the carbonyl oxygens. Mn(U-H)(+) is with its properties between those of Cd(2+) (which probably also hold for Pb(2+)) and the alkaline earth ions. In nucleic acids, M(2+)-C(O) interactions are expected, if support is provided by other primary binding sites. (N3)H may possibly be acidified via carbonyl-coordinated M(2+) to become a proton donor in the physiological pH range, at which direct (N3)(-) binding of M(2+) also seems possible.     

Magnitude of the solvation pressure depends on dipole potential.

As polar surfaces in solvent are brought together, they experience a large repulsive interaction, termed the solvation pressure. The solvation pressure between rough surfaces, such as lipid bilayers, has been shown previously to decay exponentially with distance between surfaces. In this paper, we compare measured values of the solvation pressure between bilayers and the dipole potential for monolayers in equilibrium with bilayers. For a variety of polar solvents and lipid phases, we find a correlation between the measured solvation pressures and dipole potentials. Analysis of the data indicates that the magnitude of the solvation pressure is proportional to the square of the dipole potential. Our experiments also show that the oriented dipoles in the lipid head-group region, including those of both the lipid and solvent molecules, contribute to the dipole potential. We argue that (i) the field produced by these interfacial dipoles polarizes the interbilayer solvent molecules giving rise to the solvation pressure and (ii) both the solvation pressure and the dipole potential decay exponentially with distance from the bilayer surface, with a decay constant that depends on the packing density of the interbilayer solvent molecules (1-2 A in water). These results may have importance in cell adhesion, adsorption of proteins to membranes, characteristics of channel permeability, and the interpretation of electrokinetic experiments.     

A comparative serological study of antigenic glycolipids from Mycobacterium tuberculosis.

Two fractions of antigenic diacyl trehaloses (DAT1 and DAT2) were isolated from the type strain of Mycobacterium tuberculosis (H37Rv). Phenolic glycolipid (PGL) and polar glycolipid antigens (C1-C4) were isolated from an unusual smooth so-called 'Canetti' strain of M. tuberculosis. These lipids were analyzed by enzyme-linked immunosorbent assay (ELISA) using antisera against a range of mycobacteria and sera from 50 tuberculosis patients and 25 healthy blood donors. All the lipids gave strong reactions with homologous mycobacterial antisera, except the least polar 'Canetti' polar glycolipid (C4). The phenolic glycolipid (PGL) from the 'Canetti' strain gave only a very weak response with antisera against M. tuberculosis H37Rv. The diacyl trehaloses (DAT) from H37Rv gave only weak reactions with the antisera against the 2 Canetti strains of M. tuberculosis. The 3 most polar glycolipid antigens (C1-C3) from the Canetti strain gave strong responses with serum against M. tuberculosis H37Rv. None of the lipids was able to discriminate between patient and control sera at a level suitable for a serodiagnostic test. A combination of results from several lipids appears to be of greater value in this respect. Thus, PGL, DAT2 and C2 were the best combination, reacting with all but 4 of the patient sera and with only 1 of the control sera.     

Reactivity of free and coordinated radicals in biology and chemical carcinogenity. I. Coordinated phenoxy radicals generated by hydrogen transfer from hydroxy derivatives of 3,4-benzopyrene

The tautomeric keto form of 6-, 7- and 8-hydroxy-3,4-benzopyrene (BP) prevails in nonpolar solvents at laboratory temperature, in contrast with the enol form of 9-HO-BP and 3-HO-BP, as it was shown according to the ESR study of H-transfer reactions initiated by tert. butyl peroxy radicals coordinated upon the hydroxy derivative of cobalt(III)-acetylacetonate [HO-Co(acac)2]. A further hydroxylation of the keto form of 6-HO-BP, mainly in the position 3, in the thermal interval 40-60 degrees C and the presence of oxygen was observed. Because of lack of steric hindrance in the neighborhood of the position 3 or 9 the primarily formed phenoxy radical after H-abstraction remains stabilized as sigma-coordinated radical on CoIII. Such a radical complex can be destroyed after addition of polar solvents (e.g. methanol). During autooxidation of BP in aerated solutions, similarly as during enzymatic oxidation, a relatively great concentration of high-stable radicals accumulates in nonpolar solvents and in the absence of peroxides. The paramagnetic species is interpreted as a radical pair of two nondissociated semiquinones. In discussion of the carcinogenic activity of oxidative products of BP, not only the enzymatically formed, but also the randomly formed radical intermediates in the first steps of autooxidation must be taken into consideration, which reactivity to biological targets is mediated with the polarity of the biological medium.     

The mechanism of ammonia transport based on the crystal structure of AmtB of Escherichia coli

Ammonium is one of the most important nitrogen sources for bacteria, fungi, and plants, but it is toxic to animals. The ammonium transport proteins (methylamine permeases/ammonium transporters/rhesus) are present in all domains of life; however, functional studies with members of this family have yielded controversial results with respect to the chemical identity (NH(4)(+) or NH(3)) of the transported species. We have solved the structure of wild-type AmtB from Escherichia coli in two crystal forms at 1.8- and 2.1-A resolution, respectively. Substrate transport occurs through a narrow mainly hydrophobic pore located at the center of each monomer of the trimeric AmtB. At the periplasmic entry, a binding site for NH(4)(+) is observed. Two phenylalanine side chains (F107 and F215) block access into the pore from the periplasmic side. Further into the pore, the side chains of two highly conserved histidine residues (H168 and H318) bridged by a H-bond lie adjacent, with their edges pointing into the cavity. These histidine residues may facilitate the deprotonation of an ammonium ion entering the pore. Adiabatic free energy calculations support the hypothesis that an electrostatic barrier between H168 and H318 hinders the permeation of cations but not that of the uncharged NH(3.) The structural data and energetic considerations strongly indicate that the methylamine permeases/ammonium transporters/rhesus proteins are ammonia gas channels. Interestingly, at the cytoplasmic exit of the pore, two different conformational states are observed that might be related to the inactivation mechanism by its regulatory partner.     

Enzymatic mechanism and product specificity of SET-domain protein lysine methyltransferases

Molecular dynamics and hybrid quantum mechanics/molecular mechanics have been used to investigate the mechanisms of (+)AdoMet methylation of protein-Lys-NH(2) catalyzed by the lysine methyltransferase enzymes: histone lysine monomethyltransferase SET7/9, Rubisco large-subunit dimethyltransferase, viral histone lysine trimethyltransferase, and the Tyr245Phe mutation of SET7/9. At neutrality in aqueous solution, primary amines are protonated. The enzyme reacts with Lys-NH(3)(+) and (+)AdoMet species to provide an Enz.Lys-NH(3)(+).(+)AdoMet complex. The close positioning of two positive charges lowers the pK(a) of the Lys-NH(3)(+) entity, a water channel appears, and the proton escapes to the aqueous solvent; then the reaction Enz.Lys-NH(2).(+)AdoMet --> Enz.Lys-N(Me)H(2)(+).AdoHcy occurs. Repeat of the sequence provides dimethylated lysine, and another repeat yields a trimethylated lysine. The sequence is halted at monomethylation when the conformation of the Enz.Lys-N(Me)H(2)(+).(+)AdoMet has the methyl positioned to block formation of a water channel. The sequence of reactions stops at dimethylation if the conformation of Enz.Lys-N(Me)(2)H(+).(+)AdoMet has a methyl in position, which forbids the formation of the water channel.     

CD+4 CD+25调节性T细胞抑制持续性丙型肝炎病毒感染患者CD+4T细胞反应

目的探讨CD+4 CD+25调节性T细胞(CD+4 CD+25Treg细胞)在持续性HCV感染患者CD+4 T细胞下调中的意义.方法流式细胞术检测慢性丙型肝炎患者外周血中CD+4 CD+25Treg细胞的数量以及细胞内因子的合成;与正常人或患者CD+4 CD-25 T细胞共同培养,检测其抑制功能;RT-PCR检测Foxp3的mRNA表达.结果 CD+4 CD+25Treg细胞约占慢性丙型肝炎患者外周血中CD+4 T细胞的(13.5±1.8)%,高于正常对照(5.3±0.8)% (P=0.004);主要合成IL-10,高表达Foxp3;CD+4 CD+25Treg细胞显著抑制CD+4 T细胞的增殖,以及合成IFNγ,并且抑制活性较正常人增高(P=0.034),这种作用不依赖IL-10和转化生长因子β.结论持续性HCV感染患者CD+4 CD+25Treg细胞表达增加,抑制活性增强,特异性抑制Th1反应.     

Mechanism of induction of prolactin synthesis in GH cells

Prolactin-specific RNA (RNA(PRL)) in total nuclear RNA and in cytoplasmic poly(A)(+)RNA isolated from GH (rat pituitary) cells was selectively hybridized to immobilized cloned cDNA(PRL). Agarose gel electrophoresis of the nuclear RNA(PRL) sequences eluted from the nitrocellulose filters revealed several RNA species of approximately 25-30, 18-19, and 12-13 S. Only the 12-13 S RNA species could be detected in the cytoplasmic poly(A)(+)RNA fraction. Comparative analysis of total nuclear RNA of control and thyrotropin-releasing hormone (thyroliberin)-treated cells by the reverse Southern blot technique demonstrated increased levels of all the nuclear RNA(PRL) species in hormone-treated cells. Nuclear and cytoplasmic RNA(PRL) sequences in control and treated cells were quantitated by molecular hybridization to cloned cDNA(PRL). The 2- to 3-fold stimulation of PRL production by thyrotropin-releasing hormone-treated GH(4)C(1) cells could be correlated to the corresponding increase of nuclear RNA(PRL) sequences. The hybrid strain, which produces 1/5th the amount of PRL that the parent GH(4)C(1) does, had 1/5th the amounts of nuclear RNA(PRL) sequences. Thyrotropin-releasing hormone affected neither prolactin production nor nuclear RNA(PRL) level in 928-9b cells. RNA(PRL) sequences could not be detected either in nuclei or in cytoplasm of prolactin nonproducing F(1)BGH(1)2C(1) cells. However, prolactin production could be induced and RNA(PRL) sequences could be detected in the total nuclear RNA and in cytoplasmic poly(A)(+)RNA fraction after treatment of this GH cell substrain with 5-bromodeoxyuridine. These results demonstrate that differential basal prolactin production and its modulation by thyrotropin-releasing hormone and by 5-bromodeoxyuridine can be correlated to the altered levels of nuclear RNA(PRL) sequences in the three GH cell strains.     

Interstellar H(3)(+)

Protonated molecular hydrogen, H(3)(+), is the simplest polyatomic molecule. It is the most abundantly produced interstellar molecule, next only to H(2), although its steady state concentration is low because of its extremely high chemical reactivity. H(3)(+) is a strong acid (proton donor) and initiates chains of ion-molecule reactions in interstellar space thus leading to formation of complex molecules. Here, I summarize the understandings on this fundamental species in interstellar space obtained from our infrared observations since its discovery in 1996 and discuss the recent observations and analyses of H(3)(+) in the Central Molecular Zone near the Galatic center that led to a revelation of a vast amount of warm and diffuse gas existing in the region.     

CD+4CD+25 T淋巴细胞对支气管哮喘小鼠气道炎症的影响及作用机制

目的探讨CD+4 CD+25 T淋巴细胞(Treg细胞)对支气管哮喘(简称哮喘)小鼠气道炎症的影响及作用机制.方法 60只小鼠按随机数字表法分为3组,每组20只.哮喘组(A组)小鼠于第1、13天以鸡卵白蛋白(OVA)0.1 ml腹腔注射致敏,第21～29天雾化吸入2% OVA生理盐水溶液10 ml激发 30 min后建立小鼠哮喘模型.生理盐水对照组(B组)以生理盐水10 ml替代OVA处理.去除T淋巴细胞哮喘组(C组)去除小鼠体内CD+25 T淋巴细胞后再按A组方法复制小鼠哮喘模型(用药剂量和方法同A组).分离A、B、C 3组小鼠脾脏淋巴细胞,用流式细胞仪(FACS)检测Treg细胞数量,计算其占CD+4 T淋巴细胞的百分比;分离CD+4 T淋巴细胞,用逆转录-聚合酶链反应(RT-PCR)法检测白细胞介素10(IL-10)、转化生长因子β1(TGF-β1)和细胞毒性T淋巴细胞抗原4 mRNA(CTLA-4 mRNA)的表达;同时对肺组织行苏木精-伊红 (HE)染色,观察小鼠肺组织的炎症改变. 结果经过OVA反复激发,A组小鼠脾脏Treg细胞占CD+4 T淋巴细胞的百分比为(3.10±0.03)%,B组为(9.60±0.04)%,A、B两组间及C组分别与A、B组比较差异均有统计学意义(P均<0.01); IL-10、TGF-β1和CTLA-4 mRNA的表达A组分别为0.250±0.040、0.29±0.03、0.28±0.06, B组分别为0.480±0.080、0.47±0.05、0.50±0.03、C组分别为0.080±0.020、0.11±0.04、0.12±0.05,A、B两组及C组分别与A、B组比较差异均有统计学意义(P均<0.01).与B组比较,A组肺部以嗜酸粒细胞浸润为主要表现的炎症改变明显增强,C组则较A、B组显著增强.结论 Treg细胞的数量减少和(或)功能障碍可能是哮喘气道炎症发生发展的重要机制.     

Agostic interaction and intramolecular proton transfer from the protonation of dihydrogen ortho metalated ruthenium complexes

Protonation of the ortho-metalated ruthenium complexes RuH(H(2))(X)(P(i)Pr(3))(2) [X = 2-phenylpyridine (ph-py) (1), benzoquinoline (bq) (2)] and RuH(CO)(ph-py)(P(i)Pr(3))(2) (3) with [H(OEt(2))(2)](+)[BAr'(4)](-) (BAr'(4) = [(3,5-(CF(3))(2)C(6)H(3))(4)B]) under H(2) atmosphere yields the corresponding cationic hydrido dihydrogen ruthenium complexes [RuH(H(2))(H-X)(P(i)Pr(3))(2)][BAr'(4)] [X = phenylpyridine (ph-py) (1-H); benzoquinoline (bq) (2-H)] and the carbonyl complex [RuH(CO)(H-ph-py)(P(i)Pr(3))(2)][BAr'(4)] (3-H). The complexes accommodate an agostic C H interaction characterized by NMR and in the case of 1-H by x-ray diffraction. Fluxional processes involve the hydride and dihydrogen ligands in 1-H and 2-H and the rotation of the phenyl ring displaying the agostic interaction in 1-H and 3-H. NMR studies (lineshape analysis of the temperature-dependent NMR spectra) and density functional theory calculations are used to understand these processes. Under vacuum, one equivalent of dihydrogen can be removed from 1-H and 2-H leading to the formation of the corresponding cationic ortho-metalated complexes [Ru(H(2))(THF)(X)(P(i)Pr(3))(2)](+) [X = ph-py (1-THF), bq (2-THF)]. The reaction is fully reversible. Density functional theory calculations and NMR data give information about the reversible mechanism of C H activation in these ortho-metalated ruthenium complexes. Our study highlights the subtle interplay between key ligands such as hydrides, sigma-dihydrogen, and agostic bonds, in C H activation processes.     

Characterization of the subunit nature of nuclear estrogen receptors by chemical cross-linking and dense amino acid labeling

We have used chemical cross-linking and dense amino acid labeling of estrogen receptors to characterize the subunit nature and rate of turnover of nuclear 5S estrogen-receptor complexes. When MCF-7 human breast cancer cells are incubated with [3H]estradiol or [3H]antiestrogen [alpha-[4-pyrrolidinoethoxy]phenyl-4-hydroxy-alpha'-nitrostilbe ne (CI628M) or (Z)-1-[4-(2-[N-aziridinyl]ethoxy)phenyl] 1,2-diphenyl-1-butene (tamoxifen aziridine)] and nuclear estrogen-receptor complexes are extracted with 0.6 M KCl and then chemically cross-linked with the cross-linker 2-iminothiolane, the cross-linked receptor complexes sediment as a 5.4S species on 3 M urea-containing sucrose gradients, while the noncross-linked species are 4S. Sodium dodecyl sulfate-polyacrylamide gel analyses of these cross-linked nuclear receptor complexes labeled with the covalently attaching ligand [3H]tamoxifen aziridine reveal a species of about 130,000 mol wt, while the noncross-linked or the cross-linked but mercaptan-cleaved receptor is 65,000 mol wt. Both receptor species are also detectable by interaction with an immunoadsorbent column containing antireceptor monoclonal antibody. For analyses of receptor turnover rates, cells exposed for different time periods to medium containing dense (15N, 13C, and 2H) amino acids were labeled with [3H]antiestrogen [1-[4-(2-dimethylaminoethoxy)phenyl]1-[4-hydroxyphenyl] 2-phenylbut-1-(2)ene (trans-hydroxytamoxifen) or CI628M] or [3H]estradiol, and salt-extracted nuclear estrogen receptors were analyzed on sucrose gradients. The normal density 5S form shifted to a broader, more dense peak at 2 and 4 h and finally, by 8-10 h, to a more dense, sharply sedimenting species. The time course of this shift is the same as that seen for the 4S urea-dissociated nuclear receptor form (t1/2 approximately 4h), suggesting that the 5.4S nuclear receptor is composed of two species which turn over at the same rate. We conclude from these cross-linking and density shift experiments that the nuclear 5S receptor complex consists of two similarly sized units, which turn over with similar half-lives. These data provide strong evidence that the 5S nuclear receptor complex is a homodimer of two 4S, 65,000 mol wt monomers.     

Nature of hydrogen interactions with Ni(II) complexes containing cyclic phosphine ligands with pendant nitrogen bases

Studies of the role of proton relays in molecular catalysts for the electrocatalytic production and oxidation of H(2) have been carried out. The electrochemical production of hydrogen from protonated DMF solutions catalyzed by [Ni(P(2)(Ph)N(2)(Ph))(2)(CH(3)CN)](BF(4))(2), 3a (where P(2)(Ph)N(2)(Ph) is 1,3,5,7-tetraphenyl-1,5-diaza-3,7-diphosphacyclooctane), permits a limiting value of the H(2) production rate to be determined. The turnover frequency of 350 s(-1) establishes that the rate of H(2) production for the mononuclear nickel catalyst 3a is comparable to those observed for Ni-Fe hydrogenase enzymes. In the electrochemical oxidation of hydrogen catalyzed by [Ni(P(2)(Cy)N(2)(Bz))(2)](BF(4))(2), 3b (where Cy is cyclohexyl and Bz is benzyl), the initial step is the reversible addition of hydrogen to 3b (K(eq) = 190 atm(-1) at 25 degrees C). The hydrogen addition product exists as three nearly isoenergetic isomers 4A-4C, which have been identified by a combination of one- and two-dimensional (1)H, (31)P, and (15)N NMR spectroscopies as Ni(0) complexes with a protonated amine in each cyclic ligand. The nature of the isomers, together with calculations, suggests a mode of hydrogen activation that involves a symmetrical interaction of a nickel dihydrogen ligand with two amine bases in the diphosphine ligands. Single deprotonation of 4 by an external base results in a rearrangement to [HNi(P(2)(Cy)N(2)(Bz))(2)](BF(4)), 5, and this reaction is reversed by the addition of a proton to the nickel hydride complex. The small energy differences associated with significantly different distributions in electron density and protons within these molecules may contribute to their high catalytic activity.     

INAUGURAL ARTICLE by a Recently Elected Academy Member:Long-ranged contributions to solvation free energies from theory and short-ranged models

Long-standing problems associated with long-ranged electrostatic interactions have plagued theory and simulation alike. Traditional lattice sum (Ewald-like) treatments of Coulomb interactions add significant overhead to computer simulations and can produce artifacts from spurious interactions between simulation cell images. These subtle issues become particularly apparent when estimating thermodynamic quantities, such as free energies of solvation in charged and polar systems, to which long-ranged Coulomb interactions typically make a large contribution. In this paper, we develop a framework for determining very accurate solvation free energies of systems with long-ranged interactions from models that interact with purely short-ranged potentials. Our approach is generally applicable and can be combined with existing computational and theoretical techniques for estimating solvation thermodynamics. We demonstrate the utility of our approach by examining the hydration thermodynamics of hydrophobic and ionic solutes and the solvation of a large, highly charged colloid that exhibits overcharging, a complex nonlinear electrostatic phenomenon whereby counterions from the solvent effectively overscreen and locally invert the integrated charge of the solvated object.Solvation thermodynamics underlies a vast array of important processes, ranging from protein folding (1, 2) and ligand binding (3) to self-assembly at interfaces (4). Thus, understanding solvation, and driving forces rooted in solvation, has been a focus of chemistry and physics for over a century (5, 6).Quantitatively successful theories of self-solvation and solvophobic solvation in simple fluids have been developed (7–16). However, a generally useful analytic approach for solvation in complex charged and polar environments is lacking, and solvation is typically studied with computer simulations. Contributions from the long-ranged components of Coulomb interactions in periodic images of the simulation cell are typically evaluated using computationally intense Ewald and related lattice summation techniques (17). These methods generate distorted, system size-dependent interaction potentials (18) and do not scale well in massively parallel simulations (19), adding considerable computational overhead. Moreover, artifacts can arise from spurious interactions between the periodic images of solutes, as observed for proteins in water (20).The local molecular field (LMF) theory of nonuniform fluids is a promising avenue for substantially improving free energy calculations by removing many of the computational and conceptual burdens associated with long-ranged interactions (14, 21). LMF theory prescribes a way to accurately determine the structure of a full system with long-ranged intermolecular interactions in a general single particle field by studying a simpler mimic system wherein particles interact with short-ranged intermolecular interactions only. An effective field in the mimic system accounts for the averaged effects of the long-ranged “far-field” interactions in the full system.This approach is especially powerful for studying solvation in charged and polar solvents, where in the simplest case the effective field can represent the interactions between a fixed solute and the solvent. In this paper, we show that when the effective field and induced density around the solute are accurately determined by LMF theory it is very easy to integrate over the solvent structure and accurately compute the far-field contributions to the solvation free energy as well, using quantities determined solely in the short-ranged mimic system, where simulations scale linearly with system size.LMF theory presents a general conceptual framework that gives qualitative as well as quantitative insight into many other problems. Its treatment of long- and short-ranged forces makes suggestive connections to other well-established theoretical methods, such as perturbation theory for uniform simple fluids (6, 7), classical density functional theory (DFT) of nonuniform fluids (11), and the successful quasichemical approach for solvation (16). Although our focus in this paper is on the quantitative determination of the solvation free energy, many of these connections will be touched upon in our discussion here and in Supporting Information. The treatment of solvation free energies we present here can be readily generalized to determine more complex free energies, including alchemical transformations and potentials of mean force (3), and extended to more general charged and polar mixtures (21) with mobile solutes.The conceptual development of the LMF approach to solvation thermodynamics is introduced in the next section, with derivations and other technical details given in Materials and Methods, Derivation of the Far-Field Solvation Free Energy and Supporting Information. We first focus on the solvophobic solvation of a repulsive, spherical solute in a Lennard-Jones (LJ) fluid, where most of the ideas can be understood in their simplest form and the basic physics is well understood. We then turn to more challenging and experimentally relevant problems involving the length-scale transition in hydrophobic solvation of an apolar solute in water and its effect on the solvation free energies; the hydration of single ions is discussed in Supporting Information. Finally we discuss the solvation and “overcharging” of a large, highly charged colloid in an ionic fluid, a highly nontrivial process involving ion correlations (22) that is completely missed in classic mean field treatments of ionic solutions (23).     

Intrinsic backbone preferences are fully present in blocked amino acids

The preferences of amino acid residues for ,psi backbone angles vary strikingly among the amino acids, as shown by the backbone angle found from the (3)J(H(alpha),H(N)) coupling constant for short peptides in water. New data for the (3)J(H(alpha),H(N)) values of blocked amino acids (dipeptides) are given here. Dipeptides exhibit the full range of coupling constants shown by longer peptides such as GGXGG and dipeptides present the simplest system for analyzing backbone preferences. The dipeptide coupling constants are surprisingly close to values computed from the coil library (conformations of residues not in helices and not in sheets). Published coupling constants for GGXGG peptides agree closely with dipeptide values for all nonpolar residues and for some polar residues but not for X = D, N, T, and Y, which are probably affected by polar side chain-backbone interactions in GGXGG peptides. Thus, intrinsic backbone preferences are already determined at the dipeptide level and remain almost unchanged in GGXGG peptides and are strikingly similar in the coil library of conformations from protein structures. The simplest explanation for the backbone preferences is that backbone conformations are strongly affected by electrostatic dipole-dipole interactions in the peptide backbone and by screening of these interactions with water, which depends on nearby side chains. Strong backbone electrostatic interactions occur in dipeptides. This is shown by calculations both of backbone electrostatic energy for different conformers of the alanine dipeptide in the gas phase and by electrostatic solvation free energies of amino acid dipeptides.     

Contribution of T cell receptor affinity to overall avidity for virus-specific CD8+ T cell responses

Prior analysis has characterized the clonal characteristics of effector CD8(+) T cells specific for the prominent influenza A virus nucleoprotein (NP) and acid polymerase (PA) peptides presented by H2D(b). Using a single-cell approach and determination of CDR3beta profiles, a limited, predominantly "public" repertoire was found for CD8(+)D(b)NP(366)(+)Vbeta8.3+ cells, whereas diverse and "private" T cell antigen receptor (TCR)beta clonotypes were typical of the CD8(+)D(b)PA(224)(+)Vbeta7+ response. This single-cell approach has now been used to relate the contributions of particular clonotypes (or affinities) to high-avidity TCRs, as defined by binding under conditions of limiting tetramer availability. At least by the measure of CDR3beta usage, no difference could be found between total and high-avidity populations in the spectrum of TCR-pMHC affinities throughout the limited, and relatively public, CD8(+)D(b)NP(366)(+)Vbeta8.3+ populations. Conversely, the more even (by clone size), diverse, and private CD8(+)D(b)PA(224)(+)Vbeta7+ response was characterized by the clear partitioning of the largest T cell clones in the high-avidity compartment. These results suggest that the relatively constrained CD8(+)D(b)NP(366)(+)Vbeta8.3+ set utilizes a relatively narrow range of affinities, whereas the broader CD8(+)D(b)PA(224)(+)Vbeta7+ response is induced at a range of TCR-pMHC affinities. Thus, whereas TCR sequence (or affinity) appears to contribute substantially to the avidity profile of diverse virus-specific CD8+ populations, other mechanisms may be prominent where the TCR spectrum is more limited.