The open-close mechanism of M2 channel protein in influenza A virus:A computational study on the hydrogen bonds and cation-π interactions among His37 and Trp41

The M2 protein from influenza A virus is a tetrameric ion channel. It was reported that the permeation of the ion channel is correlated with the hydrogen bond network among His37 residues and the cation-π interactions between His37 and Trp41. In the present study,the hydrogen bonding network of 4-methyl-imidazoles was built to mimic the hydrogen bonds between His37 residues,and the cation-π interactions between 4-methyl-imidazolium and indole systems were selected to represent the interac-tions between His37 and Trp41. Then,quantum chemistry calculations at the MP2/6-311G level were carried out to explore the properties of the hydrogen bonds and the cation-π interactions. The calcula-tion results indicate that the binding strength of the N-H···N hydrogen bond between imidazole rings is up to -6.22 kcal·mol-1,and the binding strength of the strongest cation-π interaction is up to -18.8 kcal·mol-1(T-shaped interaction) or -12.3 kcal·mol-1(parallel stacking interaction). Thus,the calcu-lated binding energies indicate that it is possible to control the permeation of the M2 ion channel through the hydrogen bond network and the cation-π interactions by altering the pH values.     

Computational Characterization of Reactive Intermediates of Carbon Monoxide Dehydrogenase

The catalytic oxidation of CO to CO2 by carbon monoxide dehydrogenases has been explored theoretically, and a large C-cluster model including the metal core [Ni-4Fe-4S] and surrounding residues and crystal water molecules was used in density functional calculations. The key species involved in the oxidation of CO at the C-cluster, Cred1, Cred2 and Cint, have been elucidated. On the basis of computational results, the plausible enzymatic mechanism for the CO oxidation was proposed. In the catalytic reaction, the first proton abstraction from the Fe（1）-bound water leads to a precursor to accommodate CO binding and the subsequently consecutive proton transfers from the metal-bound carboxylate to the amino acid residues facilitate the release of CO2. The hydrogen-bond network around the C-cluster formed by conserved residues His93, His96, Glu299, Lys563, and four water molecules in the active domain plays an important role in proton transfer and intermediate stabilization. Predicted geometries of key species show good agreement with the reported crystal structures.     

Molecular Dynamics and Combined QM/MM Studies on the Deactivation of anti-Tubercular Drug Isoniazid by Arylamine N-Acetyltransferases

Both a molecule dynamic study and a combined quantum mechanics and mole-cule mechanics(QM/MM) study on the acetylating deactivation mechanism of isoniazid were presented.This type of reaction was catalyzed by arylamine N-acetyltransferases(NATs) and the results strongly support a direct acetyl group transfer process rather than a stepwise one.The isoniazid was strictly restrained in proper relative position to accept the acetyl group by a Hydrogen-bond network formed by the residues at the active center.The residues,His110 and Cys70,would be functioned as 'general base' rather than 'general acid'.If all the residues(including H2O molecules) were removed from the system,the activation energy will be increased from 145.1 to 243.3 kJ/mol.The calculations met the experimental data with good agreement.     

THE PRIMARY STRUCTURE OF THE LACTATE DEHYDROGENASE ISOZYME M. FROM GIANT PANDA

The amino acid sequences of tryptic, chymotryptic and cyanogen bromide cleavage peptides of the lac-tate dehydrogenase isozyme M4 from giant panda have been determined. Based on the overlapping peptidesand by a comparison with the known sequence of porcine lactate dehydrogenase isozyme M subunit, thecomplete primary structure of the giant panda lactate dehydrogenase isozyme M subunit has been estab-lished. The polypeptide chain of giant panda lactate dehydrogenase isozyme M subunit consists of 331amino acid residues. There is a variance of 17 amino acid residues between the porcine and the giantpanda lactate dehydrogenase isozyme M subunits. Most of the variable residues are substitutions bychemically similar amino acids and take place at residues not related to the active center of the enzyme.     

THE DISTRIBUTION FUNCTION OF RESIDUE-RESIDUE CONTACTS IN PROTEIN MOLECULES

In protein molecules each residue has a different ability to form contacts.In this paper,we calculated the number of contacts per residue and investigated the distribution of residue-residue contacts from 495 globular protein molecules using Contacts of Structural Units(CSU)software.It was found that the probability P(n)of amino acid residues having n pairs of contacts in all contacts fits Gaussian distribution very well.The distribution function of residue-residue contacts can be expressed as:P(n)=P_0+aexp[-b(n-n_c)~2].In our calculation,P_0=-0.06,α=11.4,b=-0.04 and n_c=9.0.According to distribution function,we found that those hydrophobic(H)residues including Leu,Val,Ile,Met,Phe,Tyr,Cys,and Trp residues have large values of the most probable number of contact n_c,and hydrophilic(P)residues including Ala,Gly,Thr, His,Glu,Gln,Asp,Asn,Lys,Ser,Arg,and Pro residues have the small ones.We also compare with Fauchere-Pliska hydrophobicity scale(FPH)and the most probable number of contact n_c for 20 amino acid residues,and find that there exists a linear relationship between Fauchere-Pliska hydrophobicity scale(FPH)and the most probable number of contact n_c, and it is expressed as:n_c=a+b×FPH,here α=8.87,and b=1.15.It is important to further explain protein folding and its stability from residue-residue contacts.     

Molecular path for ligand search

A ligand is a small molecule bind to several residues of a receptor.We adapt the concept of molecular path for effective ligand search with its contacting residues.Additionally,we allow wild type definitions on atoms and bonds of molecular paths for fuzzy algorithms on structural match.We choose hydrogen bond interactions to characterize the binding mode of a ligand by several proper molecular paths and use them to query the deposited ligands in PDBe that interact with their residues in the same way. Expression of molecular path and format of database entries are described with examples.Our molecular path provides a new approach to explore the ligand-receptor interactions and to provide structural framework reference on new ligand design.     

STATISTICAL PROPERTIES OF LONG-RANGE CONTACTS IN GLOBULAR PROTEINS

The analysis of residue-residue contacts in protein structures can shed some light on our understanding of the folding and stability of proteins. In this paper, we study the statistical properties of long-range and short-range residue-residue contacts of 91 globular proteins using CSU software and analyze the importance of long-range contacts in globular protein structure. There are many short-range and long-range contacts in globular proteins, and it is found that the average number of long-range contacts per residue is 5.63 and the percentage of residue-residue contacts which are involved in long-range ones is 59.4%. In more detail, the distribution of long-range contacts in different residue intervals is investigated and it is found that the residues occurring in the interval range of 4-10 residues apart in the sequence contribute more long-range contacts to the stability of globular protein. The number of long-range contacts per residue, which is a measure of ability toform residue-residue contacts, is also calculated for 20 different amino acid residues. It is shown that hydrophobic residues (including Leu, Val, Ile, Met, Phe, Tyr, Cys and Trp) having a large number of long-range contacts easily form long-range contacts, while the hydrophilic amino acids (including Ala, Gly, Thr, His, Glu, Gln, Asp, Asn, Lys, Ser, Arg, and Pro) form long-range contacts with more difficulty. The relationship between the Fauchere-Pliska hydrophobicity scale (FPH) and the number of short-range and long-range contacts per residue for 20 amino acid residues is also studied. An approximately linear relationship between the Fauchere-Pliska hydrophobicity scale (FPH) and the number of long-range contacts per residue CL is found and can be expressed as     

PHYLETIC RELATIONSHIP OF PROTEIN STRUCTURES BASED ON SPATIAL PREFERENCE OF RESIDUES

A distance measure that infers to indicate the evolutionary relationship of protein structures has been developed based on spatial preference factors of residues. The spatial preference factor is a reflection of the environment of residues in tertiary structure. Compared with the phyletic relationships derived from sequence homologies and three-dimensional structures, we find that the two lines of evolution are similar in general. This approach is applied to a group of glins here.     

MOLECULAR POLARITY IN DNA-PROTEIN RECOGNITION——THE CASE OF λ-REPRESSOR-OPERATOR SYSTEM

The charge distribution of λ-repressor suggests that the molecular electrostatic polarity may accelerate the non-specific binding of the protein to the DNA molecule. The repressor molecule has a patch of positive charge within the first 26 residues which may contribute a non-specific binding surface. In addition, electrostatics may play an important role and account for why proteins form and use dimers in many specific DNA-protein recognition processes.     

~1H NMR INVESTIGATION OF THE BINDING OF METHYL-β-D-GALACTOSES WITH SIALIC ACID RESIDUES ON HEPATIC BINDING PROTEIN——THE EFFECT OF DIVALENT CALCIUM ION

The present study is a proton NMR investigation of the influence of Ca~(2+) on the interaction between the intact sialic acid residues on HBP (Hepatic Binding Protein) and methyl-β-D-galactoses. The proton NMR spectra of HBP and methyl-β-D-galactose mixing solution at different Ca~(2+) concentratiou have been measured. The analysis of the experimental results indicates that Ca~(2+) participates in the binding of sialic acid residues on HBP with methyl-β-D-galactoses and this enables the galactose molecules to, be in stable bound state. The proton NMR spectra of the samples containing EDTA have confirmed this conclusion.     

Mapping the Binding Site of P53 on UBC9 by NMR Spectroscopy

Human UBCP9 is a member of the E2 family of proteins.However,instead of conjugating to ubiquitin,it conjugates to a ubiquitin bomologue SUMO-1(also known as UBL1,GMP1,SMTP3,PICT-1 and sentrin).The SUMO-1 conjugation pathway is very similar to that of ubiquin with regard to the primary sequences of the ubiquitin activating enzymes(E1),the three-dimensional structures of the ubiquitin conjugating enzymes(E2),and the chemistry of the overall conjugation pathway.The interactiov of p53 and UBC9,the E2 of the SUMO-1 pathway,has heen studied by nuclear magnetic resonance spectroscopy.A peptide corresponding to the nuclear localization domain of p53 specifically interacts with UBC9 and this interaction is likely to be important for conjugation of p53 with SUMO-1.The largest chemical shift changes on UBC9 occur at residues94 and 129-135.This region is adjacent to the active site and has slgniflcant dynamic behavior on the μs-ms and ps-ns timescales.Correlation of chemical shift changes and mobility of these residues further suggest the importance of these residues in substrate recognition.     

Theoretical studies on the influence of molecular interactions on the mechanism of electron transfer in photosynthetic reaction center of Rps.viridis

Based on the QM/MM optimized X-ray crystal structure of the photosynthetic reaction center (PRC) of purple bacteria Rhodopseudomonas (Rps.) viridis, quantum chemistry density functional method (DFT, B3LYP/6-31G) has been performed to study the interactions between the pigment molecules and either the surrounded amino acid residues or water molecules that are either axially coordinated or hydrogen bonded with the pigment molecules, leading to an explanation of the mechanism of the primary electron-transfer (ET) reactions in the PRC. Results show that the axial coordination of amino acid residues greatly raises the ELUMO of pigment molecules and it is important for the possibility of ET to take place. Different hydrogen bonds between amino acid residues, water molecules and pigment molecules decrease the ELUMO of the pigment molecules to different extents. It is crucial for the ET taking place from excited P along L branch and sustains that the ET is a one-step reaction without through accessory bacterioc     

Substituent Effect on Proton Affinity of Imidazole in Cu,Zn-Superoxide Dismutase

To investigate whether the proton-accepting ability of imidazole in Cu,Zn-superoxide dismutase （SOD） was possibly modulated by Zn（Ⅱ） or not, the proton affinity （Ap） of N^3 in imidazole group was calculated by density functional theory （DFT） with B3LYP functional. It was found that Zn（Ⅱ） attenuates the Ap, because of its electron-withdrawing effect, while the three ligands connected with Zn（Ⅱ） （residues of two His and one Asp） exert an opposite effect, owing to their electron-donating ability. This finding suggested that the three ligands should play a role in the normal function of Cu,Zn-SOD and should be taken into consideration in the future study.     

Reliable folding of hybrid tetrapeptides into short β-hairpins

Five hybrid tetrapeptides, each consisting a central dipeptide segment of α-amino acid residues flanked by two aromatic γ-amino acid residues, are found to fold into well-defined β-hairpin conformations as shown by NMR, computational study, and X-ray structures. The turn loop of this β-hairpin motif accommodates different two-residue α-amino acid sequences from the highly flexible Gly-Gly, to the more restricted D-Pro-Gly. The presence of α-amino acid side chains enhances the stabilities of the ...     

Influence of Catalyst Residues on Thermo-oxidative Aging and Thermal Stability of Poly（butene-1）

Isotactic poly（butene-1） （iPB） with spherical morphology was synthesized successfully with bulk precipitation polymerization without post-treatment of the products. The bulk precipitation polymerization process made it possible for iPB to be used as general plastic due to the acceptable decreased cost compared with the solution polymerization process. The influence of catalyst residues on the aging and thermal stability of iPB synthesized by bulk precipitation polymerization method was investigated by gel permeation chromatography, mechanical performance testing, thermogravimetric analysis and infrared spectroscopic analysis. Commercial iPB and the lab-made iPB with varied catalyst residue contents were studied. The results demonstrated that the catalyst residues played an important role in the aging process of the iPB. A possible mechanism of aging promotion by catalyst residues was proposed.     

Structure determination of glycopeptide of β-momorcharin

The structure of the N-linked oligosaccharide chain of β-momorcharin, a ribosome-inactivating protein from the seeds of Momordica charantia Linn (Cucurbitaceae), was determined. A glycopeptide liberated by pronase digestion of the glycoprotein was subjected to amino acid and neutral carbohydrate analysis to establish the composition of amino acid and sugar residues. The sequences and glycosylation hnkages of the sugar and amino acid residues in the glycopeptide were determined as Manαl-6(XyIβ1-2)-Manβ1-4GlcNAcβ1-4(Fucαl-3)-GlcNAc-Asn-Leu by 2D-NMR spectroscopy and FAB-MS data.     

Rapid detection of pesticide residues in Chinese herbal medicines by molecularly imprinted membrane electrospray ionization mass spectrometry

Chinese herbal medicines(CHMs) play an increasingly important role in the field of medicine and affects public health in the world.Although more and more strict has been employed to ensure the quality and safety of CHMs,pesticide residues in CHMs remain a serious issue and are the bottleneck for the global development of CHMs.In this work,we applied molecularly imprinted membrane electrospray mass spectrometry(MIM-ESI MS) for rapid detecting 4 classes of pesticide residues in CHMs,including organophosphorus(OPP),carbamates,pyrethroids and neonicotinoids in CHMs.Compared with our previous ambient ionization method MESI,MIM-ESI is capable of achieving a ～50-fold increase in the detection limit of conventional analytical methods owing to the specificity recognition and unique enrichment of MIM.The optimal experimental conditions were determined,and the method was further validated for its sensitivity and specificity.Our data showed that MIM-ESI MS is applicable for the direct quantitation of pesticide residues in CHMs.This detection technology may help to ensure the quality of CHMs in the future.     

Molecular Modeling and Docking of Mannose-binding Lectin from Lycoris radiata

Lycoris radiata mannose-binding lectin（LRL） is a protein which binds mannose residues specifically. The maturation peptide and three mannose-binding domains（residues 49-57, 80-88 and 113--121） of LRL were identified by sequence analysis. The 3D structure of LRL constructed by homology modeling shaped a flstular triangular prism. Three flanks of the prism are mainly composed of β-sheets and each flank has a mannose-binding domain. According to the docking and dynamics simulation, the bindings of residues 49--57 and 80--88 with mannose are more stable than that of residues 113--121 with it. The key residues for binding mannose are Gin80, Asp82, Ash84 and Tyr88. The study preliminarily analyzed the interaction sites and mechanism of LRL with mannoses, which could be useful for the study on insect-resistance and related drug discovery of LRL.     

In-situ monitoring of nitrile-bearing pesticide residues by background-free surface-enhanced Raman spectroscopy

In-situ monitoring of pesticide residues during crop growth or/and in related products is of great significance in avoiding the abuse of pesticides but remains challenging thus far. In this report, we proposed a background-free surface-enhanced Raman spectroscopy（bf-SERS） platform to non-destructively track the nitrile-bearing pesticide residues in soybean leaves with high sensitivity and selectivity. The outstanding feature of the assay stems from the dramatic Raman enhancement effect of the 50...     

THE UNIFORMITY OF DISTRIBUTION OF SUBSTITUENTS ALONG THE CHAIN OF CARBOXYMETHYL CELLULOSE SYNTHESIZED IN TWO-PHASE MEDIUM C_6H_6——C_2H_5OH

Based on the property that carboxymethylcellulose (CMC ) can be de-graded to anhydroglucose residues by cellulase, the rate constant (K) of enzymatic degra-dation of CMC synthesized in the benzene-ethanol medium has been determined. Further-morel experimental equation K = 2.71× 10~(-2)(DS)~(-1.2) reflecting the relationship betweenK and the degree of substitution (DS) is correlated and used to describe chemical mi-crostructure uniformity of the distribution of substituents along chains effectively. Chainstructure parameters of enzymatic degradation products of CMC-the number of chainbreaks and the percentage of glucose released have been also measured. Average length ofsubstituted and unsubstituted chain segments are calculated simultaneously. Through thestudy of static and dynamic procedures of enzymatic degradation, the method to charac-terize the distribution of substituents of CMC along the chain has been improved.