Controlling Dissociation Channels of Gas-Phase Protein Complexes Using Charge Manipulation

Coarse-grained simulations with charge hopping were performed for a positively charged tetrameric transthyretin (TTR) protein complex with a total charge of +20. Charges were allowed to move among basic amino acid sites as well as N-termini. Charge distributions and radii of gyration were calculated for complexes simulated at two temperatures, 300 and 600 K, under different scenarios. One scenario treated the complex in its normal state allowing charge to move to any basic site. Another scenario blocked protonation of all the N-termini except one. A final scenario used the complex in its normal state but added a basic-site containing tether (charge tag) near the N-terminus of one chain. The differences in monomer unfolding and charging were monitored in all three scenarios and compared. The simulation results show the importance of the N-terminus in leading the unfolding of the monomer units; a process that follows a zipper-like mechanism. Overall, experimentally modifying the complex by adding a tether or blocking the protonation of N-termini may give the potential for controlling the unraveling and subsequent dissociation of protein complexes.

Cation-Induced Stabilization of Protein Complexes in the Gas Phase: Mechanistic Insights From Hemoglobin Dissociation Studies

Collision-induced dissociation (CID) of electrosprayed protein complexes usually involves asymmetric charge partitioning, where a single unfolded chain gets ejected that carries a disproportionately large fraction of charge. Using hemoglobin (Hb) tetramers as model system, we confirm earlier reports that bound metal ions can stabilize protein complexes under CID conditions. We examine the mechanism underlying this effect. Nonvolatile salts cause extensive adduct formation. Significant stabilization was observed for Mg²⁺ and Ca²⁺, whereas K⁺, Rb⁺, and Cs⁺ had no effect. Precursor ion selection was used to examine Hb subpopulations with well-defined metal binding levels. K⁺, Rb⁺, and Cs⁺-adducted tetramers eject monomers that carry roughly one-quarter of the metal ions that were bound to the precursor. This demonstrates that charge migration during CID is exclusively due to proton transfer, not metal ion transfer. Also, replacement of highly mobile charge carriers (protons) with less mobile species (metal ions) does not exert a stabilizing influence under the conditions used here. Interestingly, Hb carrying stabilizing ions (Mg²⁺ and Ca²⁺) generates monomeric CID products that are metal depleted. This effect is attributed to a combination of two factors: (1) Me²⁺ binding stabilizes Hb via formation of chelation bridges (e.g., R-COO^– Me^{2+ –}OOC-R); the more Me²⁺ a subunit contains the more stable it is. (2) More than ~90 % of the tetramers contain at least one subunit with a below-average number of Me²⁺. The prevalence of monomeric CID products with depleted Me²⁺ levels is caused by the tendency of these low metal-containing subunits to undergo preferential unfolding/ejection.

Mechanism of the Formation of Molybdenum Metallocarbene Complexes in the Gas Phase

The reactions of Mo⁺ ions and Mo _x O _y ⁺ oxygen-containing molybdenum cluster ions (x = 1-3; y = 1-9) with methane, ethylene oxide, and cyclopropane were studied using ion cyclotron resonance. The formation of a number of organometallic ions, including the metallocarbene MoCH₂ ⁺ , as well as molybdenum oxometallocarbenes Mo _x O _y CH₂ ⁺ (x = 1-3; y = 2, 4, 5, or 8) and Mo _x O _y (CH₄)⁺ ions (x = 1-3; y = 2, 5, or 8), was detected. The upper and lower limits of bond energies in oxometallocarbene complexes were evaluated: 111 > D ⁰ (Mo _x O _y ⁺-CH₂) > 82 kcal/mol (x = 1-3; y = 2, 5, 8).     

碱金属离子对甘氨酸五肽气相解离过程的影响

为了获得更多的多肽结构信息,采用结构简单的甘氨酸五肽(简写为GGGGG或G5)作为模型,研究了碱金属离子(Li+、Na+、K+、Rb+)对甘氨酸五肽GGGGG气相解离过程的影响.将一定化学计量比的甘氨酸五肽分别和四种碱金属盐溶液混合后,静置10h,使反应达到平衡.电喷雾质谱结果表明,四种碱金属离子均可以在溶液中与甘氨酸五肽形成非共价复合物,其中主要组分为碱金属离子与G5配合比为1:1和2:1的非共价复合物.质谱碰撞诱导解离(CID)时的碰撞能量为25eV.气相碰撞诱导解离实验结果表明,在配合比为1:1的复合物中,其碎片化程度按照Li+、Na+、K+、Rb+的次序依次减小,Rb+的复合物碎裂过程中生成了不常见的c、z离子;在配合比为2:1的复合物中,其碎片化程度按照Li+、Na+、K+、Rb+的次序依次增大.与1:1的非共价复合物相比,Na+、K+、Rb+的2:1复合物的气相解离显得更加容易.除Li+外,两个碱金属离子对G5的活化能力明显较单个碱金属离子强,它们可以诱导多肽在更多位点断裂,生成更多类型的碎片离子.     

Ab initio Studies on the Fe-S Protein Model Complexes

In this paper, ab initio calculations of the iron-sulfur protein model complexes have been completed on Fe_2S_2(SH)_2~(n-) and Fe_4S_4(SH)_4~(n-)(n=2, 3). The results indicate that the occupied terminal sulfur characteristic orbitals are found in the front orbital site and the energy levels of the occupied Fe 3d-like orbitals appear internally below the S-H bonding orbitals in the valence band. Although the energy sequence is different from what was reported in literature, our results are in agreement with the relevant experimental facts. We have discussed the reason that variations of the active sites are produced by various oxidation levels. The action mechanism of the Fe-S proteins as electron carriers in the biological processes is also explored preliminarily.     

Charge Site Mass Spectra: Conformation-Sensitive Components of the Electron Capture Dissociation Spectrum of a Protein

A conventional electron capture dissociation (ECD) spectrum of a protein is uniquely characteristic of the first dimension of its linear structure. This sequence information is indicated by summing the primary c ^m+ and z ^m+? products of cleavage at each of its molecular ion’s inter-residue bonds. For example, the ECD spectra of ubiquitin (M?+?nH)ⁿ⁺ ions, n?=?7–13, provide sequence characterization of 72 of its 75 cleavage sites from 1843 ions in seven c ^(1–7)+ and eight z ^(1–8)+? spectra and their respective complements. Now we find that each of these c/z spectra is itself composed of “charge site (CS)” spectra, the c ^m+ or z ^m+? products of electron capture at a specific protonated basic residue. This charge site has been H-bonded to multiple other residues, producing multiple precursor ion forms; ECD at these residues yields the multiple products of that CS spectrum. Closely similar CS spectra are often formed from a range of charge states of ubiquitin and KIX ions; this indicates a common secondary conformation, but not the conventional α-helicity postulated previously. CS spectra should provide new capabilities for comparing regional conformations of gaseous protein ions and delineating ECD fragmentation pathways.

吡咯-HCN体系在气相及溶液中相互作用的理论研究

用量子化学B3LYP方法在6-311G(d, p)水平上优化了吡咯-HCN氢键复合物，通过振动频率分析确定了两个吡咯-HCN体系稳定构型.为了得到更加精确的氢键作用能，采用相关一致基组aug-cc-pVDZ以及Boys 和Bernardi的CP(counterpoise)校正方法消除基组重叠误差后得到C－H…π和N－H…N型复合物的氢键相互作用能.为了确定B3LYP方法计算的相互作用能的可靠性，在MP2/aug-cc-pVDZ水平计算了复合物的氢键相互作用能，结果分别为－25.10和－19.30 kJ·mol－1.采用自然键轨道(NBO)分析考察了吡咯与HCN分子间轨道相互作用.以自洽场理论(SCRF)中的Onsager模型研究了不同极性溶剂对吡咯-氰化氢体系N－H…N型氢键几何构型，频率位移，电荷分布以及相对能量的影响.研究发现，当溶液的介电常数在1.5～30.0范围时，溶液作用十分显著，而当介电常数超过30.0以后，溶液作用已经达到了极限.     

Infrared Multiphoton Dissociation Enables Top-Down Characterization of Membrane Protein Complexes and G Protein-Coupled Receptors

Membrane proteins are challenging to analyze by native mass spectrometry (MS) as their hydrophobic nature typically requires stabilization in detergent micelles that are removed prior to analysis via collisional activation. There is however a practical limit to the amount of energy which can be applied, which often precludes subsequent characterization by top-down MS. To overcome this barrier, we have applied a modified Orbitrap Eclipse Tribrid mass spectrometer coupled to an infrared laser within a high-pressure linear ion trap. We show how tuning the intensity and time of incident photons enables liberation of membrane proteins from detergent micelles. Specifically, we relate the ease of micelle removal to the infrared absorption of detergents in both condensed and gas phases. Top-down MS via infrared multiphoton dissociation (IRMPD), results in good sequence coverage enabling unambiguous identification of membrane proteins and their complexes. By contrasting and comparing the fragmentation patterns of the ammonia channel with two class A GPCRs, we identify successive cleavage of adjacent amino acids within transmembrane domains. Using gas-phase molecular dynamics simulations, we show that areas prone to fragmentation maintain aspects of protein structure at increasing temperatures. Altogether, we propose a rationale to explain why and where in the protein fragment ions are generated.     

Intact Four‐atom Organic Tetracation Stabilized by Charge Localization in the Gas Phase

Several features distinguish intact multiply charged molecular cations (MMCs) from other species such as monocations and polycations: high potential energy, high electron affinity, a high density of electronic states with various spin multiplicities, and charge‐dependent reactions. However, repulsive Coulombic interactions make MMCs quite unstable, and hence small organic MMCs are currently not readily available. Herein, we report that the isolated four‐atom molecule diiodoacetylene survives after the removal of four electrons via tunneling. We show that the tetracation remains metastable towards dissociation because of the localization (91–95 %) of the positive charges on the terminal iodine atoms, ensuring minimum Coulomb repulsion between adjacent atoms as well as maximum charge‐induced attractive dipole interactions between iodine and carbon. Our approach making use of iodines as the positively charged sites enables small organic MMCs to remain intact.     

Delivering Transmembrane Peptide Complexes to the Gas Phase Using Nanodiscs and Electrospray Ionization

The gas-phase conformations of dimers of the channel-forming membrane peptide gramicidin A (GA), produced from isobutanol or aqueous solutions of GA-containing nanodiscs (NDs), are investigated using electrospray ionization-ion mobility separation-mass spectrometry (ESI-IMS-MS) and molecular dynamics (MD) simulations. The IMS arrival times measured for (2GA + 2Na)²⁺ ions from isobutanol reveal three different conformations, with collision cross-sections (Ω) of 683 Å² (conformation 1, C1), 708 Å² (C2), and 737 Å² (C3). The addition of NH₄CH₃CO₂ produced (2GA + 2Na)²⁺ and (2GA + H + Na)²⁺ ions, with Ω similar to those of C1, C2, and C3, as well as (2GA + 2H)²⁺, (2GA + 2NH₄)²⁺, and (2GA + H + NH₄)²⁺ ions, which adopt a single conformation with a Ω similar to that of C2. These results suggest that the nature of the charging agents, imparted by the ESI process, can influence dimer conformation in the gas phase. Notably, the POPC NDs produced exclusively (2GA + 2NH₄)²⁺ dimer ions; the DMPC NDs produced both (2GA + 2H)²⁺ and (2GA + 2NH₄)²⁺ dimer ions. While the Ω of (2GA + 2H)²⁺ is similar to that of C2, the (2GA + 2NH₄)²⁺ ions from NDs adopt a more compact structure, with a Ω of 656 Å². It is proposed that this compact structure corresponds to the ion conducting single stranded head-to-head helical GA dimer. These findings highlight the potential of NDs, combined with ESI, for transferring transmembrane peptide complexes directly from lipid bilayers to the gas phase.

Open image in new window

Graphical Abstract ?

     

针对蛋白质复合物Other类型的打分函数

在不同类型复合物结合界面的物理化学特征不同的基础上, 针对较难预测的Other 类型复合物设计出特异性打分函数, 用于在对接过程中挑选出有效结构. 该函数由原子接触能(EACE)、范德华和静电相互作用能组成,通过多元线性回归方法获得各项的权重系数. 对来自CAPRI benchmark1 中17 个Other 类复合物例子进行打分测试. 结果表明,组合打分能够刻画出Other 类型复合物单体间相互作用的特征, 反映出复合物形成前后的能量变化, 具备一定的从众多样本中筛选出有效结构的能力. 相对于残基成对势(RP), 该组合打分获得了更高的打分成功率. 对CAPRI 第八轮竞赛中两个结构预测模型进行打分排序, 该组合打分也体现出强于RP 的鉴别有效结合模式潜力.     

Microhydration of Alanine in Gas Phase Studied by Quantum Chemical Method and ABEEMσπ/MM Fluctuating Charge Model

A fluctuating charge interaction potential function for alanine-water was constructed in the spirit of newly developed ABEEMσπ/MM(atom-bond electronegativity equalization method at the σπ level fused into molecular mechanics). The properties of gaseous neutral alanine-(H₂O)_n(n=1-7) clusters were systematically investigated by quantum mechanics(QM) and the constructed ABEEMσπ/MM potential, such as conformations, hydrogen bonds (H-bonds), interaction energies, charge distributions, and so on. The results of ABEEMσπ/MM model are in fair agreement with those of QM and available experimental data. For isolated alanine, compared with those of experimental structure, the average absolute deviations(AAD) of bond length and bond angle are 0.002 nm and 1.4°, respectively. For alanine-water clusters, the AAD of interaction energies and H-bond lengths are only 3.77 kJ/mol and 0.012 nm, respectively, compared to the results of MP2/aug-cc-pVDZ//MP2/6-311+G^** method. The ABEEMσπ charges fluctuate with the changing conformation of the system, and can accurately and reasonably reflect the interpolarization between water and alanine. The presented alanine-water potential function may provide a basis for further simulations on related aqueous solutions of biomolecules.     

Tetraphosphacubane: An Unexpectedly Strong Base in the Gas Phase

The experimental determination of physical properties of tetra-tert-butylphosphocubane (TtBuPC) is of paramount importance for understanding the reactivity of this fascinating molecule.The gas-phase basicity of TtBuPC measured by FT-ICR spectroscopy (GB = 221.8 kcal mol(-)(1), PA = 230.5 kcal mol(-)(1)) is surprisingly high although protonation in solution is only achieved under drastic conditions. A molecular orbital treatment, including electron correlation effects, predicts the unsubstituted parent compound phosphacubane (PC) to be a carbon base. Carbon protonation implies a P-C bond fission which alleviates the strain of the system. A similar behavior is also predicted for the tetramethyl derivative. However, TtBuPC is found to be a phosphorus base, because the strong repulsive interactions which appear between the tert-butyl substituents destabilize significantly the C-protonated form. These effects decrease dramatically when just one tert-butyl group is removed and both P- and C-protonated species become almost degenerate. As for other strained systems, the PAs of PC and TtBuPC are only adequately reproduced when G2-type [6-311+G(3df,2p)] basis sets are used.     

An Electrostatic Bond Energy Model for Enthalpies of Formation of Chloroalkanes in Gaseous States

An electrostatic bond energy model is formulated to fit the enthalpies of formation and dipole moments of the alkanes and chloroalkanes. In this model, the charge distributions are calculated by an electrostatic approach similar to the "MSE" method, and the enthalpy of formation of a molecule is the sum of the bond energy terms plus the electrostatic energy of the interactions between the charges on all atoms. All parameters of this model are obtained by parameterization. The calculated dipole moments for 13 chloroalkanes and enthalpies of formation for 19 alkanes and non-geminal chloroalkanes agree with the determined values very well. To calculate the enthalpies of formation of geminal chloroalkanes, a correction mainly attributed to the van der Waals interactions in the geminal substituted group, about 24 kJ/mol per pair of geminal chlorine atoms, is introduced.     

An Exchange Charge Model for Covalent Bonds in Simple Homonuclear Diatomic Molecules

The point charge in Parr's simple bond charge model is replaced by the exchange charge, which can be evaluated according to a simple ab initio method. The calculated exchange charge correlate well with the experimental values of force constants and dissociation energies for homonuclear diatomic molecules H₂, Li₂, F₂, Na₂ and Cl₂.     

正负离子表面活性剂与高聚物混合双水相体系的相行为及蛋白质的分配

报道了由正负离子表面活性剂与高聚物混合溶液形成的一种可用于蛋白质的分离及分析的新型双水相萃取体系.研究了正负离子表面活性剂(溴化十二烷基三乙铵/十二烷基硫酸钠)分别与葡聚糖和聚乙二醇混合双水相体系的形成规律、相行为及牛血清蛋白和溶菌酶在双水相体系中的分配.通过在高聚物分子中接上亲和配基,研究蛋白质在双水相体系中的亲和分配.结果表明,在该体系中,表面活性剂与高聚物分别富集于不同相中.升高温度及加入无机盐均可促进双水相体系的形成,不同蛋白质可分配于不同的相中.亲和配基的引入极大地增强了蛋白质分配的选择性.