Structural analysis of desheptapeptide(B24-B30) insulin by molecular replacement

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Molecular replacement studies on crystal structure of DesB1-B2 Despentapeptide (B26-B30) insulin

Using the crystal structure of Despentapeptide (B26-B30) insulin (DPI as the search model, the crystal structure of DesB1-B2 Despentapeptide (B26-B30) insulin (DesB1-2 DPI) has been studied by the molecular replacement method. There is one DesB1-2 DPI molecule in each crystallographic asymmetric unit. The cross rotation function search and the translation function search show apparent peaks and thus determine the orientation and position of DesB1-2 DPI molecule in the cell respectively. The subsequent three-dimensional structural rebuilding and refinement of DesB1-2 DPI molecule confirm the results by molecular replacement method.     

[B10,22-Asp,B25-Tyr-NH2]-去β链C端五肽胰岛素的合成和性质

本文报道了[B10,22-Asp,B25-Tyr-NH2]-去B链羧端五肽胰岛素的制备及其生物活性。结果表明,这一类似物的生物活力比去五肽胰岛素(DPI)的活力高一倍,但却比Gerald所报道的[B10-Asp,B25-Tyr-NH_2]-DPI的活力低很多,说明后者的高活性可能依赖于分子中B22-Arg的存在。     

Molecular replacement study on form-B monoclinic crystal of insulin

The form-B monodinic insulin crystal was obtained from the sodium citrate buffer with 1% zinc chloride, keeping phenolic content between 0.76% and 1.25%. Its space group is P21, cell constants are: a = 4.924nm, b=6.094nm, c=4.818nm, β=95.8°. There are 6 insulin molecules which form a hexamer. The initial phase was obtained by using rotation function program of X-PLOR program package and molecular packing program of our laboratory. The molecular model was chosen from 4 zinc bovine insulin hexamer. After the preliminary refinement by using the rnacromolecular rigid body refinement technique, the molecular model was further refined and adjusted by using the energy-minimizing stereochemically restrained least-squared refinement on the difference Fourier maps. The finial R-factor is 214% at 0.3nm resolution, the r.m.s. deviations from standard bond length and bond angle are 0.0022nm and 4.7°, respectively.     

Molecular replacement studies on crystal structure of allophycocyanin from red algaePorphyra yezoensis

Using the crystal structure of allophycocyanin from cyanobacterium Spirulina platensis (APC-SP) as a search model, the crystal structure of allophycocyanin from red algae Porphyra yezoensis (APC-PY) has been studied by molecular replacement methods. The APC-PY crystals (Form 3) belong to the space group of R32, cell dimensions a = b = 10.53 nm, c = 18.94 nm, α =β = 90°, γ= 120°; there is one αβ monomer in each crystallographic asymmetric unit in the cell. The translation function search gave a unique peak with a correlation coefficient (Cc) of 67.0% and an R-factor of 36.1 % for reflection data from 1.0 to 0.4 nm. Using the results by molecular replacement, the initial model of APC-PY was built, and the coincidence of the chromophore in APC-PY initial model with its 2Fo-FC OMIT map further confirms the results by molecular replacement.     

Molecular replacement studies on crystal structure of allophycocyanin from red algae Porphyra yezoensis

Using the crystal structure of allophycocyanin from cyanobacterium Spirulina platensis (APC-SP) as a search model,the crystal structure of allophycocyanin from red algae Porphyra yezoensis (APC-PY) has been studied by molecular replacement methods.The APC-PY crystals (Form 3) belong to the space group of R32,cell dimensions a=b= 10.53 nm,c=18.94 nm,α= β= 90°,γ=120°;there is one αβ monomer in each crystallographic asymmetric unit in the cell.The translation function search gave a unique peak with a correlation coefficient (Cc) of 67.0% and an R-factor of 36.1% for reflection data from 1.0 to 0.4 nm.Using the results by molecular replacement,the initial model of APC-PY was built,and the coincidence of the chromophore in APC-PY initial model with its 2Fo-Fc OMIT map further confirms the results by molecular replacement.     

Structure of desheptapeptide (B24-B30) insulin in a new crystal form

The structure of desheptapeptide (B24-B30) insulin (DHPI) in a new crystal form (form B) has been determined and refined to 0.2 nm resolution. The crystals were obtained under the same crystallization condition as previously reported crystal form (form A). The overall structures of the two crystal forms are similar but obvious differences can be observed in crystal packing and local conformation. The crystal structures of the two forms show that the two independent molecules in an asymmetric unit from a DHPI dimer, and the dimer formation buries more than 18.20 and 16.95 nm~2 of solvent accessible surfaces for form A and form B DHPI, respectively, the largest among insulin and insulin analogs ever reported. Close examination at crystal packing shows that the dimer-forming surface of DHPI, namely Surface Ⅱ, is normally present in the association of insulin and insulin analogs in their crystal structures. The results demonstrate that Surface Ⅱ is crucially important for the formation of two crystal form     

Crystal structure of (L-Arg)-BO bovine insulin at 0.21 nm resolution

The crystal structure of (L-Arg)-B0 bovine insulin has been determined, using data to 0.21 nm and atomic parameters of 2Zn porcine insulin as a starting model, by the difference Fourier method, the restrained least square method and X-PLOR package, interspersed with careful review of the electron density, to a final R-factor of 0.182 and r.m.s. deviation of 0.002 2nm for the bond lengths and 4.3° for the bond angles. The electron densities of additional (L-Arg)-B0 residues to B-chain N-terminus of two monomers in each asymmetric unit are very dear. The crystallographic micro-environment of the N-terminus of the B-chain is different from that of rhombohedral 2-zinc insulin.     

去B链羧端七肽人胰岛素的分离纯化及性质研究

在大肠杆菌温度诱导体系中以非融合方式进行去Ｂ链羧端七肽人胰岛素原基因的表达,获得去Ｂ链羧端七肽人胰岛素原,表达产物占细胞总蛋白量的１３％,表达产物经ＳｅｐｈａｄｅｘＧ－５０柱层析分离及胰蛋白酶和羧肽酶Ｂ的酶促转化等步骤,可得到纯度达９４％以上的去Ｂ链羧端七肽人胰岛素,其氨基酸组成与预期值相符,受体活性是标准猪胰岛素的１％．     

A new procedure for enzymatic semisynthesis of human insulin by hydrolysis of single-chain des-(b-30)-lnsulin precursor with lysyl endopeptidase

It has been shown that the single-chain des-(B-30)-insulin precursor (SCI) can be converted into human insulin ester by transpeptidation using trypsin in the presence of a threonine derivative. The present study demonstrates that Achromobacter lyticus protease 1 (lysyl endopeptidase) can catalyze the transpeptidation reaction more efficiently than can trypsin. It is also shown that des-(B-30)-insulin (DAI) can be produced by hydrolysis of SCI with the lysyl endopeptidase. Since it is well known that SCI can be produced by gene technology, the following method is recommended for industrial production of human insulin ester: hydrolysis of SCI with lysyl endopeptidase followed by coupling of the resulting DAI with a threonine derivative using trypsin or lysyl endopeptidase.     

X-ray studies of water structure in 2 Zn insulin crystal

The water structure of rhombohedral 2 Zn insulin crystal which contains about 280 water molecules and 0.55-0.60 mol citrate molecules per dimer has been studied by X-ray crystallographic refinement with 1.1 A resolution data. Atomic parameters of 83 fully occupied and 258 partially occupied water molecules and 0.3 mol of citrate were obtained. Full matrix least-squares method with isotropic temperature factor was used for the refinement of partially occupied water molecules. The water molecules in this crystal exist in one of the three states: fully occupied water, partially occupied water and water continuum, and a schematic model of water structure in protein crystal was proposed. The flexibility of water molecules is described.     

NMR structure of biosynthetic engineered human insulin monomer B31(Lys)-B32(Arg) in water/acetonitrile solution. Comparison with the solution structure of native human insulin monomer

A solution NMR-derived structure of a new long -acting, B31(Lys)-B32(Arg) (LysArg), engineered human insulin monomer, in H(2)O/CD(3)CN, 65/35 vol %, pH 3.6, is presented and compared with the available X-ray structure of a monomer that forms part of a hexamer (Smith, et al., Acta Crystallogr D 2003, 59, 474) and with NMR structure of human insulin in the same solvent (Bocian, et al., J Biomol NMR 2008, 40, 55-64). Detailed analysis using PFGSE NMR (Pulsed Field Gradient Spin Echo NMR) in dilution experiments and CSI analysis prove that the structure is monomeric in the concentration range 0.1-3 mM. The presence of long-range interstrand NOEs in a studied structure, relevant to the distances found in the crystal structure of the monomer, provides the evidence for conservation of the tertiary structure. Therefore the results suggest that this solvent system is a suitable medium for studying the native conformation of the protein, especially in situations (as found for insulins) in which extensive aggregation renders structure elucidations in water difficult or impossible. Starting from the structures calculated by the program CYANA, two different molecular dynamics (MD) simulated annealing refinement protocols were applied, either using the program AMBER in vacuum (AMBER_VC), or including a generalized Born solvent model (AMBER_GB). Here we present another independent evidence to the one presented recently by us (Bocian et al., J Biomol NMR 2008, 40, 55-64), that in water/acetonitrile solvent detailed structural and dynamic information can be obtained for important proteins that are naturally present as oligomers under native conditions. (c) 2008 Wiley Periodicals, Inc. Biopolymers 89: 820-830, 2008.This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com.     

Crystal structure determination of basic phospholipase A_2 from venom of Agkistrodon halys pallas by molecular replacement method

Basic phospholipase A2 (BPLA2) from the venom of Agkistrodon halys pallas has a strong ability to hemolyze erythrocytes. The asymmetrical unit of P212121 crystal of BPLA2 contains two molecules. Self-rotation function was used to study the orientation relationship of these two molecules. Cross-rotation and translation functions were then used to determine the orientations and positions of the two molecules in the unit cell. The model building and preliminary structure refinement were carried out. The result shows that the two molecules in the asymmetrical unit of orthorhombic crystal are related by a non-crystallographic 2-fold symmetry axis.     

猪B_0L-丙氨酰胰岛素和猪B_1L-亮氨酰胰岛素的制备及性质研究

 猪胰岛素经与MSC·ONsu选择性反应,得到[MSC]A_(21)B_(29)胰岛素,再与BOC-L-Ala·TTT缩合,去保护后得到[L-Ala]B_0胰岛素,将得到的[MSC]A_(21)B_(29)胰岛素经Edman降解,再与BOC-L-Leu·TTT缩合、去保护后得到[L-Leu]B_1胰岛素。样品经N-末端分析,醋酸纤维素薄膜电泳、氨基酸组成分析和紫外吸收光谱鉴定,确定它们分别为均一的[L-Ala]B_0胰岛素和[L-Leu]B_1胰岛素。放射免疫法分析[L-Al_a]B_0肽岛素和[L-Leu]B_1胰岛素的免疫活性分别相当于天然胰岛素的30％和47％,小鼠惊厥法分析表明[L-Ala]B_6胰岛素与[L-Leu]B_1胰岛素的生物活力为19.7国际单位/mg和19.1国际单位/mg,相当于天然胰岛素的76％和73％。     

CK-18降解片段M30和MMP-2在慢性乙型肝炎纤维化严重程度预测中的作用

目的:探讨血清细胞角蛋白-18裂解片段M30(CK-18 M30)和基质金属蛋白酶(MMP-2)水平对乙型肝炎e抗原(HBe Ag)阴性慢性乙型肝炎纤维化严重程度预测的作用。方法:选取我院156例HBe Ag阴性的慢性乙型肝炎(CHB)患者和51例对照组。肝组织病理学分级依据Scheuer标准。常规收集临床资料,ELISA法检测血清CK-18 M30和MMP-2水平。结果:本研究CHB组男性为106人(67.9%),女性为50人(32.1%);对照组男性为33人(63.5%),女性为19人(36.5%),两组间性别、年龄无统计学差异;CHB组CK-18 M30和MMP-2显著高于对照组(P0.001)。CK-18 M30预测是否有显著性肝纤维化的AUC为0.863(P0.001);而MMP-2预测是否有显著性肝纤维化的AUC为0.587,差异无统计学意义(P=0.064)。结论:血清CK-18 M30和MMP-2水平在CHB组显著升高,CK-18 M30可能可预测HBe Ag阴性的慢性乙型肝炎纤维化严重程度,可能具有较好的临床应用前景。     

A model of insulin fibrils derived from the x-ray crystal structure of a monomeric insulin (despentapeptide insulin)

The crystal structure of despentapeptide insulin, a monomeric insulin, has been refined at 1.3 Å spacing and subsequently used to predict and model the organization in the insulin fibril. The model makes use of the contacts in the densely packed despentapeptide insulin crystal, and takes into account other experimental evidence, including binding studies with Congo red. The dimensions of this model fibril correspond well with those measured experimentally, and the monomer–monomer contacts within the fibril are in accordance with the known physical chemistry of insulin fibrils. Using this model, it may be possible to predict mutations in insulin that might alleviate problems associated with fibril formation during insulin therapy. © 1997 Wiley-Liss Inc.     

Two-dimensional NMR studies of Des-(B26-B30)-insulin: sequence-specific resonance assignments and effects of solvent composition.

Des-pentapeptide-insulin (DPI), a monomeric analogue which lacks the C-terminal five residues of the B-chain, provides a tractable model for 2D-NMR studies of insulin under a variety of solvent conditions. In this paper we present the sequential assignment of DPI at pH 1.8 and 25 degrees C in 10% deuterated DMSO/90% H2O; the chemical shifts are in general similar to those recently described in the absence of an organic cosolvent [1], in 20% acetic acid [2] and (for intact insulin) in 35% acetonitrile [3]. Under each of these solvent conditions qualitative analysis of the 2D-NMR data indicates that the major elements of secondary structure observed in the crystal state (three alpha-helices and B-chain beta-turn) are retained in solution. However, there is disagreement in the literature regarding the stability of the insulin fold, as monitored by amide-proton exchange rates and long-range nuclear Overhauser enhancements [1-3]. In contrast to a previous study [1], we observe slowly exchanging amide resonances (in freshly prepared D2O solutions) and nonlocal NOEs under each of the solvent conditions described, implying the existence of a stably folded secondary structure and hydrophobic core. The slowly-exchanging resonances are assigned to the central alpha-helix of the B-chain, the ends of the adjoining beta-turn, and the two A-chain alpha-helices. Qualitative analysis of long-range NOEs indicates that the major features of the crystal state are retained under these solvent conditions.     

High resolution 1H-NMR studies of Des-(B26-B30)-insulin; assignment of resonances and properties of aromatic residues

The assignments of 1H resonances of the eight aromatic residues of Des-(B26-B30)-insulin are reported, based on pH titration, selective spin decoupling and its 500 MHz 1H two-dimensional (2D)-COSY spectrum. The pK values of the three tyrosines A14, A19 and B16 are 10.84, 11.27 and 10.40, respectively. Tyrosine A19 is buried in a hydrophobic environment, while Tyrosine B16 is exposed in a relatively hydrophilic state. Among the three phenylalanines, the ring proton resonances of Phe-B25 undergo abnormal upfield shifts, probably due to the ring currents of the nearby Phe-B24 and Tyr-B16. From this study of the low-field region of 1H-NMR spectrum of Des-(B26-B30)-insulin, we conclude that this molecule probably maintains the major structural features of insulin in aqueous solution, but there are some readjustments of the peptide conformation.     

Molecular docking, 3D-QSAR,molecular dynamics,synthesis and anticancer activity of tyrosine kinase 2 (TYK 2) inhibitors

Abstract

A therapeutic rationale is proposed by selectively targeting tyrosine kinase 2 (TYK 2) to obtain potent TYK 2 inhibitors by molecular modeling studies. In the present study, we have taken tyrosine kinase (TYK 2) inhibitors and carried out molecular docking, 3?D quantitative structure–activity relationship (3D-QSAR) analysis and molecular dynamics (MD). Based on the 3D-QSAR results thirteen new compounds (R-1 to R-13) were designed and synthesized in good yields. The synthesized molecules were evaluated for their in vitro anticancer activity against LnCap and A549 cell lines. The molecules R-1, R-3, R-5, R-7, and R-10 exhibited considerable anti cancer activity.     

Modification of histidine (B10) is the causative agent for a superactive form of insulin.

The site of modification that is responsible for the formation of superactive insulin (ILM) was determined. The insulin derivative was prepared by treatment of insulin-Sepharose with ammonium bicarbonate. It was found that the insulin was bound to the resin through histidine B10, His (B10), and its ammonium bicarbonate-mediated release resulted in an insulin analog in which His (B10) was modified on the imidazole ring. This modification was reversible upon storage, resulting in normal levels of insulin activity. Amino acid analysis of a peptide containing this modified histidine revealed some aspartic acid. Since Asp (B10) insulin is also superactive, the observed superactivity may thus stem from either modification of the histidine or its conversion to aspartic acid.