Mechanism of G-protein activation by rhodopsin

Rhodopsin is a member of the family of G-protein-coupled receptors (GPCRs), and is an excellent molecular switch for converting light signals into electrical response of the rod photoreceptor cells. Light initiates cis-trans isomerization of the retinal chromophore of rhodopsin and leads to the formation of several thermolabile intermediates during the bleaching process. Recent investigations have identified spectrally distinguishable two intermediate states that can interact with the retinal G-protein, transducin, and have elucidated the functional sharing of these intermediates. The initial contact with GDP-bound G-protein occurs in the meta-Ib intermediate state, which has a protonated Schiff base as its chromophore. The meta-Ib intermediate in the complex with the G-protein converts to the meta-II intermediate with releasing GDP from the alpha-subunit of the G protein. Meta-II has a de-protonated Schiff base chromophore and induces binding of GTP to the alpha-subunit of the G-protein. Thus, the GDP-GTP exchange reaction, namely G-protein activation, by rhodopsin proceeds through at least two steps, with conformational changes in both rhodopsin and the G-protein.     

Recent bioorganic studies on rhodopsin and visual transduction

Rhodopsin, the pigment responsible for vision in animals, insect and fish is a typical G protein (guanyl-nucleotide binding protein) consisting of seven transmembrane alpha helices and their interconnecting extramembrane loops. In the case of bovine rhodopsin, the best studied of the visual pigments, the chromophore is 11-cis retinal attached to the terminal amino group of Lys296 through a protonated Schiff base linkage. Photoaffinity labeling with a 3-diazo-4-oxo-retinoid shows that C-3 of the ionone ring moiety is close to Trp265 in helix F (VI) in dark inactivated rhodopsin. Irradiation causes a cis to trans isomerization of the 11-cis double bond giving rise to the highly strained intermediate bathorhodopsin. This undergoes a series of thermal relaxation through lumi-, meta-I and meta-II intermediates after which the retinal chromophore is expelled from the opsin binding pocket. Photoaffinity labeling performed with 3-diazo-4-oxoretinal at -196 degrees C for batho-, -80 degrees C for lumi-, -40 degrees C for meta-I, and 0 degrees C for meta-II rhodopsin showed that in bathorhodopsin the ring is still close to Trp265. However, in lumi-, meta-I and meta-II intermediates crosslinking occurs unexpectedly at A169 in helix D (IV). This shows that large movements in the helical arrangements and a flip over of the ring moiety accompanies the transduction (or bleaching) process. These changes in retinal/opsin interactions are necessarily accompanied by movements of the extramembrane loops, which in turn lead to activation of the G protein residing in the cytoplasmic side. Of the numerous G protein coupled receptors, this is the first time that the outline of transduction pathway has been clarified.     

基于定点突变的抗克百威单链抗体的亲和力成熟

为获得亲和力更高的抗克百威(CBF)单链抗体(scFv), 从抗CBF scFv氨基酸序列出发, 通过同源模建获得抗体模型, 找出抗体中的活性口袋区域, 进而将小分子药物与抗体进行分子对接, 发现疏水作用和氢键对于抗体亲和力具有重要作用. 进一步对口袋内亲水氨基酸残基HArg40和LHis38进行模拟替换, 再进行分子对接分析, 发现当以亮氨酸为突变氨基酸时, 对接评分最高. 在此基础上, 通过构建突变scFv基因及可溶性表达, 采用ELISA法对进化后的单链抗体(evoscFv)进行了鉴定. 结果表明, evoscFv对CBF的IC₅₀值为18.11 μg/L, 低于野生型抗体的27.25 μg/L, 亲和解离常数K_d为4.06×10^-8 mol/L, 相对亲和力比野生型scFv提高了2.23倍, 说明通过分子对接分析及对抗体活性口袋中氨基酸残基进行替换, 获得了一个亲和力更高的突变体抗体.     

Proximity‐Triggered Covalent Stabilization of Low‐Affinity Protein Complexes In Vitro and In Vivo

The characterization of low‐affinity protein complexes is challenging due to their dynamic nature. Here, we present a method to stabilize transient protein complexes in vivo by generating a covalent and conformationally flexible bridge between the interaction partners. A highly active pyrrolysyl tRNA synthetase mutant directs the incorporation of unnatural amino acids bearing bromoalkyl moieties (BrCnK) into proteins. We demonstrate for the first time that low‐affinity protein complexes between BrCnK‐containing proteins and their binding partners can be stabilized in vivo in bacterial and mammalian cells. Using this approach, we determined the crystal structure of a transient GDP‐bound complex between a small G‐protein and its nucleotide exchange factor. We envision that this approach will prove valuable as a general tool for validating and characterizing protein–protein interactions in vitro and in vivo.     

Novel Antimicrobial Peptides from a Cecropin-Like Region of Heteroscorpine-1 from Heterometrus laoticus Venom with Membrane Disruption Activity

The increasing antimicrobial-resistant prevalence has become a severe health problem. It has led to the invention of a new antimicrobial agent such as antimicrobial peptides. Heteroscorpine-1 is an antimicrobial peptide that has the ability to kill many bacterial strains. It consists of 76 amino acid residues with a cecropin-like region in N-terminal and a defensin-like region in the C-terminal. The cecropin-like region from heteroscorpine-1 (CeHS-1) is similar to cecropin B, but it lost its glycine-proline hinge region. The bioinformatics prediction was used to help the designing of mutant peptides. The addition of glycine-proline hinge and positively charged amino acids, the deletion of negatively charged amino acids, and the optimization of the hydrophobicity of the peptide resulted in two mutant peptides, namely, CeHS-1 GP and CeHS-1 GPK. The new mutant peptide showed higher antimicrobial activity than the native peptide without increasing toxicity. The interaction of the peptides with the membrane showed that the peptides were capable of disrupting both the inner and outer bacterial cell membrane. Furthermore, the SEM analysis showed that the peptides created the pore in the bacterial cell membrane resulted in cell membrane disruption. In conclusion, the mutants of CeHS-1 had the potential to develop as novel antimicrobial peptides.     

Metal ion affinity purification of proteins by genetically incorporating metal-chelating amino acids

Affinity tags are efficient tools for protein purification. They allow simple one-step purification of proteins to high purity. However, in some cases the tags cause structural and functional changes in a protein, and need to be removed. Therefore, affinity tags that are readily introduced into proteins with minimal perturbation and have specific affinity for purification are desired. Herein, two metal-chelating amino acids derived from 2,2′-bipyridine and 8-hydroxyquinoline were genetically incorporated into glutathione S-transferase (GST) and the mutant proteins were purified by using the metal ion affinity of the unnatural amino acids. The purification of the GST mutants containing 2-amino-3-(8-hydroxyquinolin-3-yl)propanoic acid (HQA) showed that the proteins could be efficiently enriched in Ni–NTA by the metal ion affinity of the unnatural amino acid and purified to excellent purity. This method should be very useful for general protein affinity purification, especially for proteins whose structure or function is affected by affinity tags fused to N- or C-terminals.     

Correlations between the quantum-chemical parameters of amino acids and regioselectivity of isotope exchange with the spillover hydrogen

The effective charges and the proton affinity of carbon atoms of α-amino acids were calculated by quantum-chemical methods. The relative reactivity of the C−H bonds of amino acids under conditions of high-temperature solid-state catalytic isotope exchange (HSCIE) was studied. Correlations between the electron structure of amino acids and the regioselectivity of the solid-state isotope exchange were established. The reactivity of the carbon atoms with high proton affinity increases under HSCIE conditions. An assumption was made that the interaction of a solid organic compound with the spillover hydrogen can be described as the electrophilic substitution at the saturated and aromatic carbon atoms. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1611–1617, September, 1997.     

Site-Directed Mutagenesis and Analysis of Second-Site Revertants Indicates a Requirement for C-Terminal Amino Acids of PsaB for Stable Assembly of the Photosystem I Reaction Center Complex in Chlamydomonas reinhardtii

The PsaA and PsaB polypeptides form the reaction center core heterodimer of photosystem I (PSI). Both PsaA and PsaB are predicted to have 11 hydrophobic domains, although it is unclear how both polypeptides fold within the thylakoid membrane. If all 11 hydrophobic regions form membrane-spanning domains, the N- and C-terminus must be located on opposite sides of the membrane. The C-terminus of PsaB is very conserved in a wide range of organisms and may be important for PSI assembly or function. Using chloroplast transformation in Chlamydomonas reinhardtii we have generated a series of C-terminal extension and deletion mutants of the PsaB polypeptide. Analysis of these mutants and spontaneous revertants indicates that the C-terminus may be extended by at least 14 amino acids without impairing PSI assembly. Deletion of amino acids 732–736 also has no impact on PSI, whereas deletion of amino acids 727–736 results in no accumulation of the complex. The site of truncation in the 727–736 deletion coincides with the end of the hydrophobic domain XI supporting a location of the C-terminus of PsaB on the lumenal side of PSI.     

A quantum chemical study of the interaction of monomethyl mercury cation with G,H, S,and Y amino acids

Within DFT(B3LYP) methods, the potential interaction surface of a monomethyl mercury cation with G, H, S, and Y amino acids entering into the composition of the active cavity of acetylcholinesterase is studied. The preference for different centeres of amino acids for the interaction with the metal atom is investigated. The principal possibility of C_α-deprotonation of amino acid as a result of the interaction with the electronegative carbon center of methylmercury is analyzed. The effect of deprotonation is shown to cause demethylation of methylmercury. Iterative action is assumed to occur in Hg(II) and MeHg⁺ biochemical objects, which explains the high toxicity of microconcentrations of these compounds.     

Purification of recombinant proteins by chemical removal of the affinity tag

The efficient removal of a N-or C-terminal purification tag from a fusion protein is necessary to obtain a protein in a pure and active form, ready for use in human or animal medicine. Current techniques based on enzymatic cleavage are expensive and result in the presence of additional amino acids at either end of the proteins, as well as contaminating proteases in the preparation. Here we evaluate an alternative method to the one-step affinity/protease purification process for large-scale purification. It is based upon the cyanogen bromide (CNBr) cleavage at a single methionine placed in between a histidine tag and aPlasmodium falciparum antigen. The C-terminal segment of the circumsporozoite polypeptide was expressed as a fusion protein with a histidine tag inEscherichia coli purified by Ni-NAT agarose column chromatography and subsequently cleaved by CNBr to obtain a polypeptide without any extraneous amino acids derived from the cleavage site or from the affinity purification tag. Thus, a recombinant protein is produced without the need for further purification, demonstrating that CNBr cleavage is a precise, efficient, and low-cost alternative to enzymatic digestion, and can be applied to large-scale preparations of recombinant proteins.     

The basic amino acids in the coiled-coil domain of CIN85 regulate its interaction with c-Cbl and phosphatidic acid during epidermal growth factor receptor (EGFR) endocytosis

Background

During EGFR internalization CIN85 bridges EGFR-Cbl complex, endocytic machinery and fusible membrane through the interactions of CIN85 with c-Cbl, endophilins and phosphatidic acid. These protein-protein and protein-lipid interactions are mediated or regulated by the positively charged C-terminal coiled-coil domain of CIN85. However, the details of CIN85-lipid interaction remain unknown. The present study suggested a possible electric interaction between the negative charge of phosphatidic acid and the positive charge of basic amino acids in coiled-coil domain.

Results

Mutations of the basic amino acids in the coiled-coil domain, especially K645, K646, R648 and R650, into neutral amino acid alanine completely blocked the interaction of CIN85 with c-Cbl or phosphatidic acid. However, they did not affect CIN85-endophilin interaction. In addition, CIN85 was found to associate with the internalized EGFR endosomes. It interacted with several ESCRT (Endosomal Sorting Complex Required for Transport) component proteins for ESCRT assembly on endosomal membrane. Mutations in the coiled-coil domain (deletion of the coiled-coil domain or point mutations of the basic amino acids) dissociated CIN85 from endosomes. These mutants bound the ESCRT components in cytoplasm to prevent them from assembly on endosomal membrane and inhibited EGFR sorting for degradation.

Conclusions

As an adaptor protein, CIN85 interacts with variety of partners through several domains. The positive charges of basic amino acids in the coiled-coil domain are not only involved in the interaction with phosphatidic acid, but also regulate the interaction of CIN85 with c-Cbl. CIN85 also interacts with ESCRT components for protein sorting in endosomes. These CIN85-protein and CIN85-lipid interactions enable CIN85 to link EGFR-Cbl endocytic complex with fusible membrane during EGFR endocytosis and subsequently to facilitate ESCRT formation on endosomal membrane for EGFR sorting and degradation.

     

Applications of gas-liquid chromatography in protein chemistry. Determination of C-terminal sequences on nanomolar amounts of proteins.

A method for the determination of C-terminal amino acids and C-terminal amino acid sequences in nanomolar amounts of proteins is described, based on carboxypeptidase A digestion of the protein, followed by removal of the partially digested protein and quantitative gas-liquid chromatographic determination of the amino acids released after known time intervals. Sequences deduced from the kinetics of release of specific amino acids are compared with the known C-terminal sequences of well-characterized proteins.     

Acceleration of carbon-13 spin-lattice relaxation times in amino acids by electrolytes

A series of amino acids and carboxylic acids were determined by 13C NMR spectroscopy.The results showed that addition of 3M MgCl2 led to the 13C NMR integral area of samples being well proportional to number of carbon atoms that produce the particular signal with reliability over 95%. Measurements of 13C spin-lattice relaxation times (T1's) are reported for a number of amino acids. T1's of all the carbons in amino acids generally tend to decrease with the increase of the concentration of electrolytes, and the presence of magnesium slats is of significant. Carboxylic carbons in amino acids are the most sensitive "acceptor" of the 13C spin-lattice relaxation accelerating effects in electrolytes, and the 13C spin-lattice relaxation accelerating ability of electrolytes is Mg(ClO4)2 ＞MgCl2 ＞CaCl2 ＞NaCl ＞KCl ＞LiClO4 ＞NaOH. In general, T1's of C1 carbons in nonpolar a-amino acids are higher than those in polar and basic a-amino acids both in aqueous and 3M MgCl2 medium. In aliphatic straight-chain amino acids, a-, a-, a-, ai- and a- amino acids, T1's of C1 carbons tend to reduce with the increase of inserted carbon numbers between amino and carboxylic groups compared with Gly. T1's can be decreased even more when amino acids are mixed in 3M MgCl2, but T1's of carbons in amino acids decrease slightly with increase of the concentration of amino acids in 3M MgCl2. The mechanisms of the observed phenomena are discussed in terms of intermolecular interaction and paramagnetic impurity in electrolytes, large contributions of intermolecular interaction which is enhanced in electrolytes concentrate on the incoming "unsaturation" of the primary solvation shell of cations with the increase of electrolytes concentration and complexes formation of amino acids with metal ions. In electrolytes, amino acids are "anchored" to cations and molecule tumbling is slowed down, molecular rigidity is increased and molecular size is "enlarged", all of these are helpful to accelerate the 13C spin-lattice relaxation. Atlast, MgCl2 is proposed as an efficient relaxation agent for analysis of amino acids and some carboxylic acids.Samples were dissolved with the aid of supersonic which has the effect of degassing, and they were degassed again with supersonic for 30 seconds right before determination. All of the 13C NMR was obtained with a Bruker DPX-300 NMR instrument, using NOE-suppressed inverse gated decoupling with a recycle delay 8.00s and a sweep width 30120.48Hz, experiment temperature is integral of the carbon with the smallest chemical shift is calibrated as 10.00. Spin-lattice relaxation times (T1's) were determined by using inversion recovery according to Bruker avance user's guide.The pulse sequence is (T-90.°-T-180°-o-90t°) n.     

Dependence of the reactivity of five-membered aromatic heterocycles on their structure. 4. Proton affinity of N-aminoazoles

Proton affinity of the amino groups of 10 N-aminoazoles is calculated using the STO-3G basis set. The nature of the heterocyclic effect on proton affinity of the amino groups depends on its conformation which in turn is determined by the number of nitrogen atoms in the -position. The accuracy of the proton affinity calculation can be raised considerably by taking into account the interaction of heteroatoms in the ring.For Communication 3, see [1].Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1221–1223, September, 1989.     

Structural and molecular properties of dipeptides containing N-terminal selenomethionine: a theoretical study

Although the genetic code encodes only 22 amino acids during protein bio-synthesis, there are more than 140 natural amino acids whose incorporation into the protein structures is vital for proper functioning of the chemical and bio-chemical machineries associated with living beings. Among these, selenium-containing amino acids are of special interest for amino acid biochemistry. During the last few decades, the structure–function relationships of proteins are being best pursued by considering amino acids, dipeptides as well as their analogs as model systems. By performing this theoretical study it is intended to investigate the influence of functional group/groups present in side chain moieties of the varying C-terminal residues on the molecular and structural features of a set of seven dipeptides, constructed by conserving selenomethionine at their N-terminal positions while the C-terminal ends are varied with one of the following amino acid residues—Val, Trp, Glu, Cys, Tyr, Arg, and Sec. Geometry optimization and vibrational frequency calculations were carried out in gas and aqueous phase using B3LYP/6-311++G(d,p) level of theory. The results furnished by this DFT study provide a good account of the role of the C-terminal residue’s identity in determining the structural features of the amide planes, values of the ψ and ф dihedrals, geometry about the α-carbon atoms, theoretical IR spectra and the number and type of intramolecular H-bond interactions existing in the dipeptides. In aqueous phase, the dipeptide geometries exhibit larger values of total dipole moments, greater HOMO–LUMO energy gaps and enhanced thermodynamic stability than those in gas phase.     

First cytoplasmic loop of glucagon-like peptide-1 receptor can function at the third cytoplasmic loop position of rhodopsin

G protein-coupled receptors (GPCRs) are classified into several families based on their amino acid sequences. In family 1, GPCRs such as rhodopsin and adrenergic receptor, the structure-function relationship has been extensively investigated to demonstrate that exposure of the third cytoplasmic loop is essential for selective G protein activation. In contrast, much less is known about other families. Here we prepared chimeric mutants between Gt-coupled rhodopsin and Gi/Go- and Gs-coupled glucagon-like peptide-1 (GLP-1) receptor of family 2 and tried to identify the loop region that functions at the third cytoplasmic loop position of rhodopsin. We succeeded in expressing a mutant having the first cytoplasmic loop of GLP-1 receptor and found that this mutant activated Gi and Go efficiently but did not activate Gt. Moreover, the rhodopsin mutant having the first loop of Gs-coupled secretin receptor of family 2 decreased the Gi and Go activation efficiencies. Therefore, the first loop of GLP-1 receptor would share a similar role to the third loop of rhodopsin in G protein activation. This result strongly suggested that different families of GPCRs have maintained molecular architectures of their ancestral types to generate a common mechanism, namely exposure of the cytoplasmic loop, to activate peripheral G protein.     

PIGMENT COMPLEXES OF LIGHT-HARVESTING CHLOROPHYLL a/b BINDING PROTEIN ARE STABILIZED BY A SEGMENT IN THE CARBOXYTERMINAL HYDROPHILIC DOMAIN OF THE PROTEIN*

In order to identify segments of light-harvesting chlorophyll a/6-binding protein (LHCP) that are important for pigment binding, we have tested various LHCP mutants regarding their ability to form stable pigment-protein complexes in an in vitro reconstitution assay. Deletion of 10 C-terminal amino acids in the LHCP precursor, pLHCP, did not significantly affect pigment binding, whereas deletion of one additional amino acid, a tryptophan, completely abolished the formation of stable pigment-protein complexes. This tryptophan, however, can be exchanged with other amino acids in full-length pLHCP without noticeably altering the stability or spectroscopic properties of pigment complexes made with these mutants. Thus, the tryptophan residue is not likely to be involved in a highly specific interaction stabilizing the complex. A double mutant of LHCP lacking 66 N-terminal and 6 C-terminal amino acids still forms pigmented complexes that are virtually identical to those formed with the full-length protein concerning their pigment composition and spectroscopic properties. We conclude that about 30% of the polypeptide chain in LHCP is not involved in pigment binding.     

The amino terminus of cGMP-dependent protein kinase Iβ increases the dynamics of the protein's cGMP-binding pockets

The type I cGMP-dependent protein kinases play critical roles in regulating vascular tone, platelet activation and synaptic plasticity. PKG I α and PKG Iβ differ in their first ~100 amino acids giving each isoform unique dimerization and autoinhibitory domains with identical cGMP-binding pockets and catalytic domains. The N-terminal leucine zipper and autoinhibitory domains have been shown to mediate isoform specific affinity for cGMP. PKG Iα has a >10 fold higher affinity for cGMP than PKG Iβ, and PKG Iβ that is missing its leucine zipper has a three-fold decreased affinity for cGMP. The exact mechanism through which the N-terminus of PKG alters cGMP-affinity is unknown. In the present study, we have used deuterium exchange mass spectrometry to study how PKG Iβ's N-terminus affects the conformation and dynamics of its cGMP-binding pockets. We found that the N-terminus increases the rate of deuterium exchange throughout the cGMP-binding domain. Our results suggest that the N-terminus shifts the conformational dynamics of the binding pockets, leading to an "open" conformation that has an increased affinity for cGMP.     

Essential amino acids interacting with flavonoids: A theoretical approach

The interaction of two flavonoid species (resorcinolic and fluoroglucinolic) with the 20 essential amino acids was studied by the multiple minima hypersurface (MMH) procedures, through the AM1 and PM3 semiempirical methods. Remarkable thermodynamic data related to the properties of the molecular association of these compounds were obtained, which will be of great utility for future investigations concerning the interaction of flavonoids with proteins. These results are compared with experimental and classical force field results reported in the available literature, and new evidences and criteria are shown. The hydrophilic amino acids demonstrated high affinity in the interaction with flavonoid molecules; the complexes with lysine are especially extremely stable. An affinity order for the interaction of both flavonoid species with the essential amino acids is suggested. Our theoretical results are compared with experimental evidence on flavonoid interactions with proteins of biomedical interest. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Interactions between several <Emphasis Type="SmallCaps">l</Emphasis>-α-amino acids and potassium chloride in aqueous solutions at 298.15 K

The enthalpies of solution of l-α-aminobutyric acid, l-α-valine, l-α-leucine, l-α-isoleucine, and l-α-cysteine have been measured in aqueous potassium chloride solutions at 298.15 K. From the obtained experimental results the standard dissolution enthalpies of amino acids in aqueous KCl solutions have been determined. These data were used to calculate the heterogeneous enthalpic pair interaction coefficients based on McMillan–Mayer’s theory. These values were interpreted in the terms of the hydrophobic or hydrophilic effects of the side chains of amino acids on their interactions with dissociated potassium chloride in water.