Mapping Protein–Ligand Interactions in the Gas Phase Using a Functional Group Replacement Strategy. Comparison of CID and BIRD Activation Methods

Intermolecular interactions in the gaseous ions of two protein–ligand complexes, a single chain antibody (scFv) and its trisaccharide ligand (α-D-Galp-(1→2)-[α-D-Abep-(1→3)]-α-Manp-OCH_3, L1) and streptavidin homotetramer (S₄) and biotin (B), were investigated using a collision-induced dissociation (CID)-functional group replacement (FGR) strategy. CID was performed on protonated ions of a series of structurally related complexes based on the (scFv + L1) and (S₄?+?4B) complexes, at the +10 and +13 charge states, respectively. Intermolecular interactions were identified from decreases in the collision energy required to dissociate 50 % of the reactant ion (Ec₅₀) upon modification of protein residues or ligand functional groups. For the (scFv + L1)¹⁰⁺ ion, it was found that deoxygenation of L1 (at Gal C3 and C6 and Man C4 and C6) or mutation of His101 (to Ala) resulted in a decrease in Ec₅₀ values. These results suggest that the four hydroxyl groups and His101 participate in intermolecular H-bonds. These findings agree with those obtained using the blackbody infrared radiative dissociation (BIRD)-FGR method. However, the CID-FGR method failed to reveal the relative strengths of the intermolecular interactions or establish Man C4 OH and His101 as an H-bond donor/acceptor pair. The CID-FGR method correctly identified Tyr43, but not Ser27, Trp79, and Trp120, as a stabilizing contact in the (S₄?+?4B)¹³⁺ ion. In fact, mutation of Trp79 and Trp120 led to an increase in the Ec₅₀ value. Taken together, these results suggest that the CID-FGR method, as implemented here, does not represent a reliable approach for identifying interactions in the gaseous protein–ligand complexes.      

Thermal dissociation of protein-oligosaccharide complexes in the gas phase: mapping the intrinsic intermolecular interactions

Blackbody infrared radiative dissociation (BIRD) and functional group replacement are used to map the location and strength of hydrogen bonds between an antibody single chain fragment (scFv) and its natural trisaccharide receptor, alpha-D-Galp (1-->2)[alpha-D-Abep (1-->3)]alpha-D-Manp1-->OMe (1), in the gaseous, multiply protonated complex. Arrhenius activation parameters (E(a) and A) are reported for the loss of 1 and a series of monodeoxy trisaccharide congeners (5-8 identical with tri) from the (scFv + tri + 10H)(+10) complex. The energetic contribution of the specific oligosaccharide OH groups to the stability of the (scFv + 1 + 10H)(+10) complex is determined from the differences in E(a) measured for the trisaccharide analogues and 1 (55.2 kcal/mol). A decrease of 6 to 11 kcal/mol in E(a), measured for the monodeoxy trisaccharides, indicates that the deleted OH groups interact strongly with the scFv and that they account for a majority of the stabilizing intermolecular interactions. A partial map of the hydrogen bond donor/acceptor groups of 1 and the strength of the interactions is presented for the protonated +10 complex. A comparison of the gas-phase map with the crystal structure indicates that significant structural differences exist. The hydroxyl groups located outside of the binding pocket, and exposed to solvent in solution, participate in new protein-oligosaccharide hydrogen bonds in the gas phase. The decrease in kinetic and energetic stability of the (scFv + 2 + nH)(n)()(+) complex with increasing charge-state is attributed to conformational differences in the binding region induced by electrostatic repulsion. The similarity in the Arrhenius parameters for the +9 and +10 charge states suggests that repulsion effects on the structure of the binding region are negligible below +11.     

Influence of H-bond strength on chelate cooperativity

Intermolecular complexes formed between metalloporphyrins and pyridine ligands equipped with multiple H-bond donors and acceptors have been used to measure the free energy contributions due to intramolecular ether-phenol H-bonding in the 24 different supramolecular architectures using chemical double mutant cycles in toluene. The ether-phenol interactions are relatively weak, and there are significant populations of partially bound states where between zero and four intramolecular H-bonds are made in addition to the porphyrin-ligand coordination interaction. The complexes were analyzed as ensembles of partially bound states to determine the effective molarities for the intramolecular interactions by comparison with the corresponding intermolecular ether-phenol H-bonds. The properties of the ether-phenol interactions were compared with phosphonate diester-phenol interactions in a closely related ligand system, which has more powerful H-bond acceptor oxygens positioned at the same location on the ligand framework. This provides a comparison of the properties of weak and strong H-bonds embedded in the same 24 supramolecular architectures. When the product of the intermolecular association constant and the effective molarity KEM > 1, there is a linear increase in the free energy contribution due to H-bonding with log EM, because the intramolecular interactions contribute fully to the stability of the complex. When KEM < 1, the H-bonded state is not significantly populated, and there is no impact on the overall stability of the complex. Intermolecular phosphonate diester-phenol H-bonds are 2 orders of magnitude stronger than ether-phenol H-bonds in toluene, so for the phosphonate diester ligand system, 23 of the 24 supramolecular architectures make intramolecular H-bonds. However, only 8 of these architectures lead to detectable H-bonding in the ether ligand system. The other 15 complexes have a suitable geometry for formation of H-bonds, but the ether-phenol interaction is not strong enough to overcome the reorganization costs associated with making intramolecular contacts, i.e., KEM < 1 for the ether ligands, and KEM > 1 for the phosphonate diester ligands. The values of EM measured for two different types of H-bond acceptor are linearly correlated, which suggests that EM is a property of the supramolecular acrchitecture. However, the absolute value of EM for an intramolecular phosphonate diester H-bond is about 4 times lower than the corresponding value for an intramolecular ether-phenol interaction embedded in the same supramolecular framework, which suggests that there may be some interplay of K and EM.     

Energetics of Intermolecular Hydrogen Bonds in a Hydrophobic Protein Cavity

This work explores the energetics of intermolecular H-bonds inside a hydrophobic protein cavity. Kinetic measurements were performed on the gaseous deprotonated ions (at the ?7 charge state) of complexes of bovine β-lactoglobulin (Lg) and three monohydroxylated analogs of palmitic acid (PA): 3-hydroxypalmitic acid (3-OHPA), 7-hydroxypalmitic acid (7-OHPA), and 16-hydroxypalmitic acid (16-OHPA). From the increase in the activation energy for the dissociation of the (Lg + X-OHPA)^7– ions, compared with that of the (Lg + PA)^7– ion, it is concluded that the –OH groups of the X-OHPA ligands participate in strong (5 – 11 kcal mol^–1) intermolecular H-bonds in the hydrophobic cavity of Lg. The results of molecular dynamics (MD) simulations suggest that the –OH groups of 3-OHPA and 16-OHPA act as H-bond donors and interact with backbone carbonyl oxygens, whereas the –OH group of 7-OHPA acts as both H-bond donor and acceptor with nearby side chains. The capacity for intermolecular H-bonds within the Lg cavity, as suggested by the gas-phase measurements, does not necessarily lead to enhanced binding in aqueous solution. The association constant (K_a) measured for 7-OHPA [(2.3 ± 0.2) × 10⁵ M^–1] is similar to the value for the PA [(3.8 ± 0.1) × 10⁵ M^–1]; K_a for 3-OHPA [(1.1 ± 0.3) × 10⁶ M^–1] is approximately three-times larger, whereas K_a for 16-OHPA [(2.3 ± 0.2) × 10⁴ M^–1] is an order of magnitude smaller. Taken together, the results of this study suggest that the energetic penalty to desolvating the ligand –OH groups, which is necessary for complex formation, is similar in magnitude to the energetic contribution of the intermolecular H-bonds.

Rational design of peptide ligand for affinity chromatography of tissue-type plasminogen activator by the combination of docking and molecular dynamics simulations

Combined docking and molecular dynamics (MD) simulations are carried out for the rational design of affinity peptide ligand of tissue-type plasminogen activator (t-PA). Ten amino acids that have high affinity to three different regions of t-PA are identified by the amino acids location method on the basis of candidate pocket structure of t-PA. Then, 14 tetrapeptides are built and docked into the candidate pocket of t-PA. The absolute value of the D(score) calculated from the docking simulation is used to assess the affinity of a peptide for t-PA. Consequently, six tetrapeptides that have high D(score) values are selected and linked to a spacer arm of [NH(CH(2))(6)NH(2)] that is present on EAH Sepharose gel. The linked compounds are further evaluated by docking into the candidate pocket of t-PA. As a result, the tetrapeptide QDES with the highest D(score) value is selected. Molecular surface analysis with the MOLCAD program reveals that electrostatic interactions and hydrogen bonds (H-bonds) contribute to the affinity interactions between the tetrapeptide and t-PA. MD simulations indicate that QDES-t-PA complex keeps stable, and the distances between the carboxyl groups of Asp189, Gln192 and Asp194 and the charged amino group of glutamine change little. Moreover, all the nine H-bonds found in the docking simulation are confirmed by the MD simulations. It is also found that three water molecules act as bridges between the ligand and the protein pocket by hydrogen bonding. Finally, high binding affinity and specificity of the peptide ligand are confirmed by the purification of t-PA from crude porcine heart extract using the immobilized-ligand column for affinity chromatography.     

The binding domain of the HMGB1 inhibitor carbenoxolone: Theory and experiment

We present a combined computational and experimental study of the interaction of the Box A of the HMGB1 protein and carbenoxolone, an inhibitor of its pro-inflammatory activity. The computational approach consists of classical molecular dynamics (MD) simulations based on the GROMOS force field with quantum-refined (QRFF) atomic charges for the ligand. Experimental data consist of fluorescence intensities, chemical shift displacements, saturation transfer differences and intermolecular Nuclear Overhauser Enhancement signals. Good agreement is found between observations and the conformation of the ligand–protein complex resulting from QRFF–MD. In contrast, simple docking procedures and MD based on the unrefined force field provide models inconsistent with experiment. The ligand–protein binding is dominated by non-directional interactions.     

Dissociation of heme-globin complexes by blackbody infrared radiative dissociation: Molecular specificity in the gas phase?

The temperature dependence of the unimolecular kinetics for dissociation of the heme group from holo-myoglobin (Mb) and holo-hemoglobin alpha-chain (Hb-alpha) was investigated with blackbody infrared radiative dissociation (BIRD). The rate constant for dissociation of the 9 + charge state of Mb formed by electrospray ionization from a "pseudo-native" solution is 60% lower than that of Hb-alpha at each of the temperatures investigated. In solutions of pH 5.5-8.0, the thermal dissociation rate for Mb is also lower than that of HB-alpha (Hargrove, M. S. et al. J. Biol. Chem.1994, 269, 4207-4214). Thus, Mb is thermally more stable with respect to heme loss than Hb-alpha both in the gas phase and in solution. The Arrhenius activation parameters for both dissociation processes are indistinguishable within the current experimental error (activation energy 0.9 eV and pre-exponential factor of 10(8-10) s(-1)). The 9+ to 12+ charge states of Mb have similar Arrhenius parameters when these ions are formed from pseudo-native solutions. In contrast, the activation energies and pre-exponential factors decrease from 0.8 to 0.3 eV and 10(7) to 10(2) s(-1), respectively, for the 9 + to 12 + charge states formed from acidified solutions in which at least 50% of the secondary structure is lost. These results demonstrate that gas-phase Mb ions retain clear memory of the composition of the solution from which they are formed and that these differences can be probed by BIRD.     

Evidence for the Preservation of Native Inter- and Intra-Molecular Hydrogen Bonds in the Desolvated FK-Binding Protein·FK506 Complex Produced by Electrospray Ionization

It is now well established that electrospray ionization (ESI) is capable of introducing noncovalent protein assemblies into a desolvated environment, thereby allowing their analysis by mass spectrometry. The degree to which native interactions from the solution phase are preserved in this environment is less clear. Site-directed mutagenesis of FK506-binding protein (FKBP) has been employed to probe specific intra- and inter-molecular interactions within the complex between FKBP and its ligand FK506. Collisional activation of wild-type and mutant-FKBP?FK506 ions, generated by ESI, demonstrated that removal of native protein-ligand interactions formed between residues Asp37, Tyr82, and FK506 significantly destabilized the complex. Mutation of Arg42 to Ala42, or Tyr26 to Phe26 also resulted in lower energy dissociation of the FKBP·FK506 complex. Although these residues do not form direct H-bonds to FK506, they interact with Asp37, ensuring its correct orientation to associate with the ligand. Comparison with solution-based affinity measurements of these mutants has been discussed, including the stabilization afforded by ordered water molecules. Ion mobility spectrometry (IMS) has been employed to provide gas-phase structural information on the unfolding of the complexes. The [M + 6H](6+) complexes of the wild-type and mutants have been shown to resist unfolding and retain compact conformations. However, removal of the basic Arg42 residue was found to induce significant structural weakening of the [M + 7H](7+) complex when raised to dissociation-level energies. Overall, destabilization of the FKBP·FK506 complex, resulting from targeted removal of specific H-bonds, provides evidence for the preservation of these interactions in the desolvated wild-type complex.     

Hydroxamate类抑制剂与MMP-2的分子对接研究

通过分子动力学模拟研究了MMP-2和hydroxamate抑制剂之间的作用模式。在分子动力学模拟中,对于催化区的锌离子和其共价结合的配体(包括抑制剂和组氨酸)采用了键合的模型。从模拟的结果可以看到,R^1取代基和MMP-2的S1疏水口袋中的部分残基能形成很好的几何匹配,从而可以产生很强的范德华和疏水相互作用。模拟结果也表明,两个抑制剂和MMP-2之间分别能形成5个和8个氢键,抑制剂B比A活性更高的原因就是能够形成更加有利氢键作用模式。在整个模拟过程中,催化锌都能保持好的五配位形式,配位键的长度也处于稳定的状态,预测得到的MMP-2和其抑制剂的相互作用模式对于全新抑制剂的设计提供了非常重要的结构信息。     

A molecular dynamics investigation of CDK8/CycC and ligand binding: conformational flexibility and implication in drug discovery

Abnormal activity of cyclin-dependent kinase 8 (CDK8) along with its partner protein cyclin C (CycC) is a common feature of many diseases including colorectal cancer. Using molecular dynamics (MD) simulations, this study determined the dynamics of the CDK8-CycC system and we obtained detailed breakdowns of binding energy contributions for four type-I and five type-II CDK8 inhibitors. We revealed system motions and conformational changes that will affect ligand binding, confirmed the essentialness of CycC for inclusion in future computational studies, and provide guidance in development of CDK8 binders. We employed unbiased all-atom MD simulations for 500 ns on twelve CDK8-CycC systems, including apoproteins and protein–ligand complexes, then performed principal component analysis (PCA) and measured the RMSF of key regions to identify protein dynamics. Binding pocket volume analysis identified conformational changes that accompany ligand binding. Next, H-bond analysis, residue-wise interaction calculations, and MM/PBSA were performed to characterize protein–ligand interactions and find the binding energy. We discovered that CycC is vital for maintaining a proper conformation of CDK8 to facilitate ligand binding and that the system exhibits motion that should be carefully considered in future computational work. Surprisingly, we found that motion of the activation loop did not affect ligand binding. Type-I and type-II ligand binding is driven by van der Waals interactions, but electrostatic energy and entropic penalties affect type-II binding as well. Binding of both ligand types affects protein flexibility. Based on this we provide suggestions for development of tighter-binding CDK8 inhibitors and offer insight that can aid future computational studies.     

Quantitative determination of intermolecular interactions with fluorinated aromatic rings

The chemical double mutant cycle approach has been used to investigate substituent effects on intermolecular interactions between aromatic rings and pentafluorophenyl pi-systems. The complexes have been characterised using 1H and 19F NMR titrations, X-ray crystal structures of model compounds and molecular mechanics calculations. In the molecular zipper system used for these experiments, H-bonds and the geometries of the interacting surfaces favour the approach of the edge of the aromatic ring with the face of the pentafluorophenyl pi-system. The interactions are generally repulsive and this repulsion increases with more electron-withdrawing substituents up to a limit of +2.2 kJ mol(-1), when the complex distorts to minimise the unfavourable interaction. Strongly electron-donating groups cause a change in the geometry of the aromatic interaction and attractive stacking interactions are found (-1.6 kJ mol(-1) for NMe2). These results are generally consistent with an electrostatic model: the polarisation of the pentafluorophenyl ring leads to a partial positive charge located at the centre and this leads to repulsive interactions with the positive charges on the protons on the edge of the aromatic ring; when the aromatic ring has a high pi-electron density there is a large electrostatic driving force in favour of the stacked geometry which places this pi-electron density over the centre of the positive charge on the pentafluorophenyl group.     

Synthesis and Crystal Structure of [Pb(trz)(tfpb)(H2O)]: a Lead(II) Complex Containing 2,4,6‐Tris(2‐pyridyl)‐1,3,5‐triazine and 4,4,4‐Trifluoro‐1‐phenyl‐1,3‐butandionate

[Pb(trz)(tfpb)(H₂O)] ( 1 ) (trz and tfpb are the abbreviations of 2,4,6‐tris(2‐pyridyl)‐1,3,5‐triazine and 4,4,4‐trifluoro‐1‐phenyl‐1,3‐butandionate, respectively) have been synthesized and characterized by elemental analysis and IR, ¹H NMR, spectroscopy. The single‐crystal structure of 1 shows the coordination number of the Pb²⁺ ions is eight with three N‐donor atoms from a “trz” ligand and four O‐donors from the dionate ligand and one molecule of water. The supramolecular features in this complex are guided by lone pair activity and control of strong hydrogen bonds, weak directional intermolecular interactions and aromatic π‐π stacking interactions.     

Blackbody infrared radiative dissociation of nonspecific protein-carbohydrate complexes produced by nanoelectrospray ionization: The nature of the noncovalent interactions

Gas-phase thermal dissociation experiments, implemented with blackbody infrared radiative dissociation (BIRD) and Fourier transform ion cyclotron resonance mass spectrometry, have been performed on a series of protonated and deprotonated 1:1 and protonated 1:2 protein-carbohydrate complexes formed by nonspecific interactions during the nanoflow electrospray (nanoES) ionization process. Nonspecific interactions between the proteins bovine carbonic anhydrase II (CA), bovine ubiquitin (Ubq), and bovine pancreatic trypsin inhibitor and several carbohydrates, ranging in size from mono- to tetrasaccharides, have been investigated. Over the range of temperatures studied (60-190 degrees C), BIRD of the protonated and deprotonated complexes proceeds exclusively by the loss of the carbohydrate in its neutral form. The rates of dissociation of the 1:1 complexes containing a mono- or disaccharide decrease with reaction time, suggesting the presence of two or more kinetically distinct structures produced during nanoES or by gas-phase processes. In contrast, the 1:1 complexes of the tri- and tetrasaccharides exhibit simple first-order dissociation kinetics, a result that, on its own, is suggestive of a single preferred carbohydrate binding site or multiple equivalent sites in the gas phase. A comparative analysis of the dissociation kinetics measured for protonated 1:1 and 1:2 complexes of Ubq with alphaTal[alphaAbe]alphaMan further supports the presence of a single preferred binding site. However, a similar analysis performed on the complexes of CA and alphaTal[alphaAbe]alphaMan suggests that equivalent but dependent carbohydrate binding sites exist in the gas phase. Analysis of the Arrhenius activation parameters (E(a) and A) determined for the dissociation of 1:1 complexes of CA with structurally related trisaccharides provides evidence that neutral intermolecular hydrogen bonds contribute, at least in part, to the stability of the gaseous complexes. Surprisingly, the E(a) values for the complexes of the same charge state are not sensitive to the structure (primary or higher order) of the protein, suggesting that the carbohydrates are able to form energetically equivalent interactions with the various functional groups presented by the protein. For a given protein-carbohydrate complex, the dissociation E(a) is sensitive to charge state, initially increasing and then decreasing with increasing charge. It is proposed that both ionic and neutral hydrogen bonds stabilize the nonspecific protein-carbohydrate complexes in the gas phase and that the relative contribution of the neutral and ionic interactions is strongly influenced by the charge state of the complex, with neutral interactions dominating at low charge states and ionic interactions dominating at high charge states.     

Computational studies of the structure and cation-anion interactions in 1-ethyl-3-methylimidazolium lactate ionic liquid

Quantum chemical calculations of the structures and cation-anion interaction of 1-ethyl-3-methylimidazolium lactate ([Emim][LAC]) ion pair at the B3LYP/6-31++G** theoretical level were performed. The relevant geometrical characteristics, energy properties, intermolecular H-bonds (H-bonds), and calculated IR vibrations with respect to isolated ions were systematically discussed. The natural bond orbital (NBO) and atoms in molecule (AIM) analyses were also employed to understand the nature of the interactions between cation and anion. The five most stable geometries were verified by analyzing the relative energies and interaction energies. It was found that the most of the C-H···O intermolecular H-bonds interactions in five stable conformers have some covalent character in nature. The elongation and red shift in IR spectrum of C-H bonds which involve in H-bonds is proved by electron transfers from the lone pairs of the carbonyl O atom of [LAC] to the C-H antibonding orbital of the [Emim]+. The interaction modes are more favorable when the carbonyl O atoms of [LAC] interact with the C2-H of the imidazolium ring and the C-H of the ethyl group through the formation of triple H-bonds.     

A gadolinium(III) complex: synthesis,structure, photophysical profile and its role in the degradation of nitroaromatics

The synthesis and structural characterization of a gadolinium(III) complex with phenanthroline and thiocyanate ligands have been accomplished. The X-ray crystal structure reveals that Gd(III) in a slightly distorted square anti-prism coordinated with four thiocyanate ions and two phenanthroline molecules; one phenanthroline is protonated which compensates the charge of Gd(III) center. The crystal structure shows chemically significant non-covalent interactions like hydrogen bonding involving the thiocyanate ligand and π–π interactions between uncoordinated phenanthrolinium and coordinated phen. Investigation on the intermolecular interactions and crystal packing via Hirshfeld surface analysis reveals that close contacts are mainly associated with weak interactions. The fingerprint plots demonstrate that these weak interactions are important for crystal packing. The Gd(III) complex shows photophysical activity. The compound is capable of degrading toxic pollutants like nitroaromatics and may have far reaching consequences for cleaning these toxic pollutants from industrial effluents.     

On the characterization of host-guest complexes: surface tension, calorimetry, and molecular dynamics of cyclodextrins with a non-ionic surfactant

Three host-guest systems have been characterized using surface tension (sigma), calorimetry, and molecular dynamics simulations (MD). The hosts were three native cyclodextrins (CD) and the guest the non-ionic carbohydrate surfactant octyl-beta-d-glucopyranoside. It is shown that, for any host-guest system, a rough screening of the most probable complex stoichiometries can be obtained in a model free form, using only calorimetric data. The sigma data were analyzed using a model that includes a newly proposed adsorption isotherm. The equilibrium constants for several stoichiometries were simultaneously obtained through fitting the sigma data. For alpha- and beta-CD, the predominant species is 1:1 and to a lesser extent 2:1, disregarding the existence of the 1:2. For gamma-CD, the 1:2 species dominates, the other two being also present. In an attempt to confirm these results, 10 ns MD simulations for each CD were performed using seven different starting conformations. The MD stable conformations agree with the results found from the experimental data. In one case, the spontaneous dissociation-formation of a complex was observed. Analysis of the trajectories indicates that hydrophobic interactions are primarily responsible for the formation and stability of the inclusion complexes. For the 2:1 species, intermolecular H-bonds between CD molecules result in a tight packed structure where their original truncated cone shape is lost in favor of a cylindrical geometry. Together, the results clearly demonstrate that the often used assumption of considering only a 1:1 species is inappropriate.     

Molecular interactions between glycopeptide vancomycin and bacterial cell wall peptide analogues

The molecular interactions of the glycopeptide antibiotic vancomycin (Van) with bacterial cell wall analogues N,N'-diacetyl-L-Lys-D-Ala-D-Ala (Ac(2) KdAdA) and N,N'-diacetyl-L-Lys-D-Ala-D-Lac (Ac(2) KdAdL) were investigated in neat water, phosphate buffer and HEPES buffer by using fluorescence correlation spectroscopy (FCS) and molecular dynamics (MD) simulations. The FCS determined dissociation constants (k(d)) show that the intrinsic binding affinity between Van and the drug-sensitive peptide ligand Ac(2)KdAdA remains invariant when the solvent is changed from neat water to either PBS or HEPES buffer; this demonstrates that there are no obvious solvent effects on the association between Van and Ac(2)KdAdA due to the strong intermolecular interaction between the two moieties. When compared to Ac(2)KdAdA, a significantly larger k(d) value was observed for the binding between the drug-resistant peptide ligand Ac(2)KdAdL and Van. Furthermore, the k(d) increased by about 8- to 11-times when the solvent was changed from neat water to 10 mM phosphate/HEPES buffer. The stability of the Ac(2)KdAdL-Van complex was dependent on the concentration of the buffer and k(d) increases as the concentration of either phosphate ions or HEPES increased until an equilibrium was attained. Both FCS and MD simulation studies clearly showed that the components constituting the buffer solution (e.g., phosphate ions and HEPES) are involved in molecular interactions with the binding pocket of Van and they profoundly affect the intrinsic stability of the complex formed between the low-affinity Ac(2)KdAdL and Van. These results could help us to better understand the detailed structure and activity of glycopeptide antibiotic derivatives toward bacterial cell wall peptide analogues, and can further facilitate the development of new drug candidates against drug-resistant bacterial strains.     

Crystal and molecular structure and vibrational spectra of 2,6-bis(diphenylphosphorylmethyl)-4-methylphenol and its complex with cerium(III) nitrate

The structure of 2,6-bis(diphenylphosphorylmethyl)-4-methylphenol 2,6-[Ph₂P(O)CH₂]₂-4-MeC₆H₂OH(L¹) and its 1: 1 complex with cerium(III) nitrate were studied by X-ray diffraction. A rather strong intramolecular hydrogen bond P=O…H-O (O…O, 2.646(1) Å) exists in the L¹ molecules. In the crystal, the molecules are combined into centrosymmetric dimers through the stacking interaction between the central phenol rings; the distance between the ring planes is 3.39 Å. In the complex molecule, [Ce(L¹)(NO₃)₃ · Me₂C(O)], the neutral ligand L¹ is tridentate and the three nitrate ions are bidentate, and the tenth coordination site is occupied by acetone oxygen. No intramolecular H-bonds are present. In the crystal, the complex molecules are combined into centrosymmetric dimers through intermolecular hydrogen bonds O-H…O-NO₂ (O…O, 2.713(8) Å). The vibrational (IR, Raman) spectra of the ligand and the complex were studied and the principal bands were assigned. According to IR spectroscopy, the P=O…H-O intramolecular hydrogen bond is retained in both the ligand and the complex molecules.     

Prediction of protein–protein complexes using replica exchange with repulsive scaling

The realistic prediction of protein–protein complex structures is import to ultimately model the interaction of all proteins in a cell and for the design of new protein–protein interactions. In principle, molecular dynamics (MD) simulations allow one to follow the association process under realistic conditions including full partner flexibility and surrounding solvent. However, due to the many local binding energy minima at the surface of protein partners, MD simulations are frequently trapped for long times in transient association states. We have designed a replica-exchange based scheme employing different levels of a repulsive biasing between partners in each replica simulation. The bias acts only on intermolecular interactions based on an increase in effective pairwise van der Waals radii (repulsive scaling (RS)-REMD) without affecting interactions within each protein or with the solvent. For a set of five protein test cases (out of six) the RS-REMD technique allowed the sampling of near-native complex structures even when starting from the opposide site with respect to the native binding site for one partner. Using the same start structures and same computational demand regular MD simulations sampled near native complex structures only for one case. The method showed also improved results for the refinement of docked structures in the vicinity of the native binding geometry compared to regular MD refinement.     

Isomorphic coordination polymers of cobalt(II), zinc(II) with a flexible ligand of cis,cis,cis-1,2,3,4-cyclopentanetetracarboxylic acid and their molecular alloys: crystal structures, thermal decomposition mechanisms and magnetic properties

Three new isomorphic coordination polymers of Co(2+), Zn(2+) ions with flexible multicarboxylic acid ligand of the cis,cis,cis-1,2,3,4-cyclopentanetetracarboxylic acid (H(4)L), [Co(4)L(2)(H(2)O)(8)]·3H(2)O (1), [Zn(4)L(2)(H(2)O)(8)]·3H(2)O (2) and [Co(0.8)Zn(3.2)L(2)(H(2)O)(8)]·3H(2)O (3), have been synthesized under hydrothermal conditions and by means of controlling the pH of the reaction mixtures (with an initial pH of 6.0 for 1, 4.0 for 2, and 5.0 for 3, respectively). In the crystal of 1, two crystallographically different Co(2+) ions (Co1 and Co2) form a negatively-charged coordination polymeric chain, which contains a centrosymmetric, linear, trinuclear Co(2+) cluster (Co(3)L(2)) subunit; another crystallographically independent Co(2+) ion (Co3) coordinated to six water molecules acts as a counter ions to link the neighboring coordination polymeric chains via intermolecular H-bond interactions. The Co(2+) ions in 1 were completely and partially replaced by Zn(2+) ions to give 2 and 3, respectively. Complex 3 shows a novel molecular alloy nature, due to the random distributions of the Co(2+) and Zn(2+) ions. Three isomorphic complexes exhibit distinct thermal decomposition mechanisms. The deprotonated cis,cis,cis-1,2,3,4-cyclopentanetetracarboxylic acid ligands decompose at 420-750 °C to give the residue CoO in 1, ZnO + C in 2 and CoO + ZnO in 3. Complex 1 shows a complicated magnetic behavior with co-existence of antiferromagnetic exchange interactions between neighboring Co(2+) ions as well as strong spin-orbital coupling interactions for each Co(2+) ion; complex 3 exhibits a magnetically isolated high-spin Co(2+) ion behavior with strong spin-orbital coupling interactions.