Upregulation of lncRNA MEG3 promotes hepatic insulin resistance via increasing FoxO1 expression.

Upregulation of lncRNA MEG3promotes hepatic insulin resistance via increasing FoxO1expression

Xiang Zhu a ,1,Yuan-Bo Wu b ,1,Jian Zhou a ,Dong-Mei Kang a ,*

a Department of Gerontology,Af ?liated Anhui Provincial Hospital,Anhui Medical University,Hefei,230001,China b

Department of Neurology,Af ?liated Anhui Provincial Hospital,Anhui Medical University,Hefei,230001,China

a r t i c l e i n f o

Article history:

Received 4November 2015Accepted 10November 2015Available online xxx Keywords:lncRNA MEG3

Hepatic insulin resistance FoxO1

Primary hepatocytes

a b s t r a c t

Background:Hepatic insulin resistance is a major characteristic of type 2diabetes mellitus.LncRNA MEG3has been shown to correlate to hepatic glucose production;however,the underlying mechanism remains unclear.This study aims to investigate the role of MEG3in hepatic insulin resistance.

Methods:High-fat diet mice,ob/ob mice and mice primary hepatocytes were used in this study.Expression of MEG3,FoxO1,G6pc and Pepck were determined by real-time PCR.FoxO1,G6pc,Pepck,HDAC1and HDAC3protein levels were analyzed by western blotting.Hepatic gluconeogenesis,glycogen accumulation,triglyceride and glycogen contents were measured by corresponding assay or kit,and body weight was monitored after an overnight fast.

Results:Gene expression of MEG3was upregulated in high-fat diet and ob/ob mice and increased by palmitate,oleate or linoleate.MEG3overexpression signi ?cantly increased FoxO1,G6pc,Pepck mRNA expressions and hepatic gluconeogenesis and suppressed insulin-stimulated glycogen synthesis in pri-mary hepatocytes,whereas palmitate-induced increase of FoxO1,G6pc and Pepck protein expressions could be reversed by MEG3interference.In addition,high fat enhanced expression of lncRNA MEG3in hepatocytes through histone acetylation.Furthermore,MEG3interference could reverse the up-regulation of triglyceride as well as impaired glucose tolerance and down-regulation of glucogen con-tent in high-fat diet mice or ob/ob mice.

Conclusion:Upregulation of lncRNA MEG3enhances hepatic insulin resistance via increasing fox-O1expression,suggesting that MEG3may be a potential target and therapeutic strategy for diabetes.

?2015Elsevier Inc.All rights reserved.

1.Introduction

Type 2diabetes mellitus (T2DM)is a globally complex disease characterized by hepatic insulin resistance,dysregulation of blood glucose and triglycerides [1].The liver plays a central role in glucose homeostasis.Endogenous glucose production in the liver is realized mainly through gluconeogenesis or glycogenolysis.As the main features of obesity,impaired glucose metabolism and dyslipidemia are closely related to insulin resistance and a high risk of cardio-vascular disease [2,3].However,the cellular and molecular mech-anisms responsible for insulin resistance remain unknown.

Fork-head box protein O1(FoxO1),also known as FKHR,is a key transcription factor in regulation of gluconeogenic and the insulin response in the liver,which plays a potential role in glucose ho-meostasis and a well-established role in turning on the gluconeo-genic program [4,5].Aberrant function of FoxO1is associated with deleterious characteristics of T2DM,including hyperglycemia and hypertriglyceridemia [6].

In the liver,insulin suppresses hepatic gluconeogenesis by activating Akt,which phosphorylates FoxO1and leads to its rapid nuclear exclusion.Conversely,FoxO1is active in the fasted state where it is dephosphorylated at the Akt sites.Recent studies have implicated an impairment in insulin-stimulated hepatic protein kinase B (Akt)activity in high-fat-fed mice [7],which could reasonably account for decreases in phosphorylation of FoxO1.Moreover,increased FoxO1activity results in hyperglycemia by promoting transcription of two key gluconeogenic enzymes,glucose-6-phosphatase catalytic subunit (G6pc)and phospho-enolpyruvate carboxykinase (Pepck)in hepatocytes [5,8,9]and

*Corresponding author.Department of Gerontology,Af ?liated Anhui Provincial Hospital,Anhui Medical University,17,Lujiang Road,Hefei,Anhui,230001,China.

E-mail addresses:?yzhu2003@https://www.wendangku.net/doc/f75191161.html, (X.Zhu),kangdongmei2006@https://www.wendangku.net/doc/f75191161.html, (D.-M.Kang).1

These authors contributed equally to this work and should be considered co-?rst

authors.

Contents lists available at ScienceDirect

Biochemical and Biophysical Research Communications

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Biochemical and Biophysical Research Communications xxx (2015)1e 7

increased cellular production of hepatic glucose.G6pc and Pepck are the rate-limiting enzymes highly activated during fasting and suppressed in the fed state and by insulin.

Long noncoding RNAs(lncRNAs)are commonly de?ned as nonprotein-coding RNA moleculars longer than200nucleotides(nt) [10,11].LncRNAs are being increasingly recognized as functional molecules in governing fundamental biological processes through diverse mechanisms.LncRNAs has shown to be involved in liver diseases[12,13].Maternally expressed gene3(MEG3),an imprinted gene also known as gene trap locus2(GTL2),is a lncRNA tumor suppressor and encodes a lncRNA correlated with several liver dis-eases[14].However,biological functional role of MEG3genes in he-patic insulin resistance in primary hepatocytes is poorly understood.

In the present study,we hypothesized that upregulation of lncRNA MEG3in the liver would lead to elevated hepatic insulin resistance via increasing FoxO1expression.Thus,expression MEG3, FoxO1and two key gluconeogenic enzymes,hepatic gluconeo-genesis and glucose production as well as Triglyceride,glycogen content and impaired glucose tolerance were evaluated.

2.Materials and methods

2.1.Animals and chemicals

Male C57BL/6aged3e5weeks,and ob/ob or control mice aged 8weeks were purchased from Jackson Laboratory(Bar Harbor,ME). Male C57mice were fed on high-fat diet or low-fat diet from4 weeks to12weeks old,when insulin resistance was obviously stimulated.During intravenous tail-vein injection,male C57mice fed on high-fat diet or low-fat diet and8week-old ob/ob or control mice were studied over10weeks,during which time they were injected with MEG3interference fragment twice a week.At week 10,hepatic triglyceride,glucogen content,mice body weight and glucose tolerance was measured after an overnight fast and mice were sacri?ced by CO2asphyxiation.

All animals were housed at Anhui Medical University and all experimental procedures involving animals were approved by the Institutional Animal Care and Use Committees of Anhui Medical University.

Palimtate,oleate and linoleate from Sigma Biotechnology(CA, USA),Anti-FoxO1,anti-G6pc and anti-Pepck from Santa Cruz(CA, USA),and anti-HDAC1and anti-HDAC3and anti-Tubulin from Abcam(MA,USA)were used.

2.2.Isolation and culture of primary hepatocytes

Hepatocytes from male C57BL/6mice were isolated by the two-step collagenase perfusion method as described previously[15]and cultured for5days in medium199(Gibco,Invitrogen,USA)as described previously[16].For experiments in the present study, cells were serum starved for5h beforehand.For determination of palmitate,oleate and linoleate action,cells were stimulated with 0.5mM palmitate,oleate and linoleate,lysed,and frozen atà80 C. Primary hepatocytes isolated from individual animals were used in each experiment.

2.3.Real-time PCR analysis

RNA was isolated from cells using the TRIzol reagent(Invi-trogen)as recommended by the manufacturer's guidelines.For reverse transcription,cDNA was synthesized using the iScript kit (Bio-Rad,PA,USA).Real-time PCR analysis was performed using Power SYBR Green RT-PCR Reagents on an ABI thermal cycler Step-One Plus(Life Technologies,Shanghai,China).PCR reactions were performed using a TaqMan Master mix(Applied Biosystems,CA,USA).The sequences of the primers for lncRNA MEG3,FoxO1,G6pc, Pepck and18S were summarized in Table1.Data were collected and quantitatively analyzed on the ABI7500Fast Sequence Detection System and software(Applied Biosystems)using2-delta delta CT method relative to18S.

2.4.Western blot analysis

Western blot analyses were performed for the determination of protein expressions.Primary hepatocytes were washed with ice-cold PBS once and lysed with lysis buffer supplemented with pro-tease inhibitors to prepare cell lysates.Protein lysate from each sample were separated by SDS-polyacrylamide gel electrophoresis and transferred onto PVDF membranes(Bio-Rad).Subsequently, membranes were blocked in5%milk/1?TBST for1h and then probed with the corresponding primary antibodies against FoxO1, G6pc,Pepck,HDAC1,HDAC3and Tubulin obtained from Santa Cruz and Abcam,respectively.Following thorough wash,membranes were incubated with appropriate horseradish peroxidase-coupled secondary antibodies(GE Healthcare,Michigan,USA)for1h. Finally,blots were detected by ECL western blotting detection re-agent(GE Healthcare).Total protein levels were normalized to Tubulin and bands were quanti?ed with Image Guage4.0(Fuji?lm).

2.5.Hepatocyte gluconeogenesis and glycogen accumulation

Hepatocytes were seeded in24-well plates and were glucose-free medium199(Gibco,pH7.4)supplemented with2mM pyru-vate(Sigma e Aldrich).Glycogenolysis was considered as glucose production in the absence of sodium lactate(the gluconeogenic substrate).After treatment with MEG3overexpression,glucose contained in the medium was determined in a hexokinase/ Glu6PDH assay previously described[17].On the other hand,the total glucose production was de?ned as glucose production in the presence of sodium lactate.After24h of insulin stimulation, cellular glycogen was digested with amyloglucosidase(Sigma-

e Aldrich)at37 C for3h and then measured as described above.

2.6.Measurement of triglyceride(TG),glycogen contents and body weight

Homogenates of liver were prepared to determine the content of hepatic TG and glycogen contents.The Triglyceride-SL kit(Gen-zyme,MA,USA)was performed to measure TG in liver according to the manufacturer's instructions.

To measure hepatic glycogen content,protein lysates were washed in ice-cold ethanol.Then,the glycogen in the supernatants was digested with amyloglucosidase(Sigma e Aldrich)at37 C for 30min.Digested glycogen standards or samples were mixed with the reaction buffer(100mM Tris,pH7.4,1mM MgCl2,0.2U/ml horse radish peroxidase,0.2U/ml glucose oxidase and0.05mM

Table1

Primer sequences of real-time PCR.

Genes Primers Sequences(50-30)

MEG3Forward50-CTGCCCATCTACACCTCACG-30

Reverse50-CTCTCCGCCGTCTGCGCTAGGGGCT-30 FoxO1Forward50-AAGAGGCTCACCCTGTCGC-30

Reverse50-GCATCCACCAAGAACTTTTCC-30

G6pc Forward50-GTGCAGCTGAACGTCTGTCTGTC-30

Reverse50-TCCGGAGGCTGGCATTGTA-30

Pepck Forward50-CTTCTCTGCCAAGGTCATCC-30

Reverse50-TTTTGGGGATGGGCAC-30

18S Forward50-AGGGTTCGATTCCGGAGAGG-30

Reverse50-CAACTTTAATATACGCTATTGG-30

X.Zhu et al./Biochemical and Biophysical Research Communications xxx(2015)1e7 2

Amplex red)for30min.Finally,glycogen levels in samples were read at an excitation wave length of530nm and an emission wave length of emission590nm using a?uorescent microplate reader from BioTek Instruments(Winooski,VT,USA).

At the end of study(week10)after MEG3interference injection, body weights of male C57mice fed on high-fat diet or low-fat diet and8week-old ob/ob or control mice were measured after an overnight fast.

2.7.Statistics

Data are expressed as mean±SEM.Two-way student's t-test was used to compare differences between two groups.A P value less than0.05denotes a statistically signi?cant difference.To analyze multiple experimental groups,one-way ANOVA was per-formed followed by Bonferroni posttests.

3.Results

3.1.Gene expression of MEG3is upregulated in high-fat diet and ob/ ob mice and increased by palmitate,oleate or linoleate Dysregulation and function of LncRNA MEG3have been pro-foundly described in development and progression of liver dis-eases.In this paper,to study effects of lncRNA MEG3on hepatic insulin resistance,we?rstly investigated gene expression of MEG3 in high-fat diet and in ob/ob mice and in primary hepatocytes treated with palmitate,oleate or linoleate.We found that high-fat diet could time-dependently elevated MEG3expression level of C57mice(Fig.1A).In addition,gene expression of MEG3of ob/ob mice was signi?cantly higher than that of control mice(Fig.1B).Furthermore,palmitate,oleate or linoleate could also strikingly increase MEG3expression level in primary hepatocytes(Fig.1C).

3.2.The effects of MEG3on FoxO1,G6pc and Pepck expressions, hepatic gluconeogenesis and insulin-stimulated glycogen synthesis in primary hepatocytes

Hepatic gluconeogenesis,a major contributor to hyperglycemia in T2DM,plays a crucial role in maintaining the blood glucose level normal during the fasting or nonfeeding phase[18].To examine whether MEG3has any effect on FoxO1,G6pc and Pepck expres-sions,hepatic gluconeogenesis and glycogen accumulation,MEG3 was overexpressed in primary hepatocytes via adenovirus-mediated gene transfer.Our data revealed that expression of MEG3was signi?cantly increased by MEG3overexpression (Fig.2A).What's more,FoxO1plays an important role in linking retinoid metabolism to hepatic gluconeogenesis.Our results showed that both FoxO1mRNA expression and protein level were also signi?cantly elevated by MEG3overexpression(Fig.2B). Because FoxO1is a key gluconeogenic transcription factor that drives G6pc and Pepck mRNA transcriptions[19],we further examined whether MEG3overexpression could regulate Pepck and G6pc transcription and gluconeogenesis by FoxO1.Results showed that enhanced both G6pc and Pepck mRNA and protein levels were markedly up-regulated in primary hepatocytes treated with Ad-MEG3(Fig.2C)resulting in increase of hepatocyte gluconeogen-esis(Fig.2D).In addition,we found that MEG3overexpression treatment very ef?ciently impaired insulin-stimulated glycogen accumulation in primary hepatocytes(Fig.2E).

Furthermore,we sought to determine whether MEG3interfer-ence has in?uence on FoxO1,G6pc and Pepck protein

expressions.

Fig.1.Gene expression of MEG3in high-fat diet and in ob/ob mice and in primary hepatocytes with palmitate,oleate or linoleate treatment.Male C57mice were fed on high-fat diet or low-fat diet from4weeks to12weeks old,when insulin resistance was obviously stimulated.(A)MEG3expression level of C57mice measured by real-time PCR at different weeks of age.All RNA values were normalized to18S mRNA expression.(B)MEG3expression level of8week-old ob/ob mice.(C)MEG3expression level in primary hepatocytes treated with palmitate,oleate or linoleate(0.5mM)for24h**P<0.01vs.Low-fat-diet or control.

X.Zhu et al./Biochemical and Biophysical Research Communications xxx(2015)1e73

The function of MEG3was disrupted by knocking down MEG3in primary hepatocytes.We found that palmitate enhanced FoxO1,G6pc and Pepck protein expressions in primary hepatocytes,which could be attenuated by MEG3interference (Fig.2F).

3.3.High fat enhances expression of lncRNA MEG3in hepatocytes through histone acetylation

We further explored the mechanisms underlying the effect of high fat in increasing MEG3expression level in hepatocytes.Our data revealed that a histone deacetylase inhibitor,Trichostatin A (TSA),elevated gene expression of MEG3in hepatocytes in a dose-dependent manner (Fig.3A).Histone deacetylases (HDACs)are a class of enzymes involved in expression of DNA,which catalyze the removal of acetyl groups from lysine residues in both histone and non-histone proteins.In this paper,western blotting analysis of HDAC1and HDAC3showed that palmitate treatment in primary hepatocytes evidently suppressed the HDAC1and HDAC3protein expressions (Fig.3B).In addition,si-HDAC3could signi ?cantly promote MEG3expression level,whereas si-HDAC1made no dif-ference to it (Fig.3C).Moreover,further treatment with RGFP966,a HDAC3inhibitor,dramatically increased gene expression of MEG3(Fig.3D).

3.4.MEG3interference recovers the up-regulation of triglyceride (TG)and down-regulation of glucogen content and attenuates glucose tolerance in high-fat diet mice and ob/ob mice

To study whether MEG3can mediate hepatic lipid accumula-tion,glucogen content and body weight of mice,mice fed on high-fat diet and ob/ob mice received intravenous tail-vein injection of MEG3interference fragment twice a week for 10weeks.Liver TG content of high-fat diet mice and ob/ob mice was signi ?cantly higher than that of low-fat diet mice and control mice,respectively (Fig.4A e B).However,MEG3interference remarkably abolished

hepatic TG accumulation of high-fat diet mice or ob/ob mice.Liver is the main storage site of glycogen and our data showed that liver glycogen content of high-fat diet mice and ob/ob mice was signif-icantly lower than that of low-fat diet mice and control mice,respectively (Fig.4A e B).Similarly,the change in liver glycogen content could be also dramatically recovered by MEG3interference.It is also interesting to note that while body weight of high-fat diet mice and ob/ob mice was signi ?cantly higher than that of low-fat diet mice and control mice,respectively (Fig.4C),the in-crease of body weight couldn't be abrogated by MEG3interference.This indicates that MEG3could mediate hepatic lipid accumulation and glucogen content in mice liver,rather than body weight of mice.

In intraperitoneal glucose tolerance test (IPGTT)mice received intravenous injections of MEG3interference fragment via tail vein as above.Fasting blood glucose levels were signi ?cantly elevated in high-fat diet and ob/ob mice compared with low-fat diet and control mice,respectively (Fig.4D e E).However,impaired glucose tolerance determined in IPGTT was more substantially compro-mised.Of particular note,treatment of high-fat diet mice and ob/ob mice with MEG3interference led to substantial improvements in both fasting blood glucose levels and impaired glucose tolerance.

4.Discussion

The liver plays a central role in energy homeostasis mainly through several insulin-mediated events.Hepatic gluconeogenesis is a major contributor to the overproduction of glucose in patients with T2DM [20].So inhibition of the gluconeogenesis pathway may be part of a strategy against the hyperglycaemia associated with T2DM [21].

While downregulation of MEG3has been gradually proved to be a primary feature of liver cancer [22],the strong upregulation of MEG3was also observed,which are abundantly expressed in fetal liver [23].Recently,numbers of studies have demonstrated that

can

Fig.2.Effects of MEG3on FoxO1,G6pc and Pepck expressions,hepatic gluconeogenesis and glycogen synthesis in primary hepatocytes.After treatment with 0.5mM palmitate,primary hepatocytes were treated with Ad-GFP and Ad-MEG3,respectively.Ad-GFP,adenovirus expressing green ?uorescent protein;Ad-MEG3,adenovirus overexpressing MEG3.(A)Transcription of MEG3in primary hepatocytes was quanti ?ed by real-time PCR.Fold change is relative to Ad-GFP.(B,C)FoxO1,G6pc and Pepck mRNA and protein levels were determined by real-time PCR and western blotting analysis,respectively.All mRNA values were normalized to 18S mRNA expression.(D)The rate of gluconeogenesis in primary hepatocytes analyzed by a hexokinase/Glu6PDH assay.(E)For insulin stimulation study,mice were given an intraperitoneal injection of insulin (0,0.01,0.05,0.25,1,10nM).Effect of MEG3overexpression on insulin-stimulated glycogen synthesis in primary hepatocytes was assessed.(F)Primary hepatocytes were treated with si-control and si-MEG3,respectively,and then treated with 0.5mM palmitate.FoxO1,G6pc and Pepck protein expressions assessed by western blotting analysis.**P <0.01vs.Ad-GFP.

X.Zhu et al./Biochemical and Biophysical Research Communications xxx (2015)1e 7

4

function as a tumor suppressor or oncogene in hepatocellular car-cinoma (HCC)and up-regulatedMEG3participated in HCC devel-opment and progression [14].Our study revealed that MEG3gene expression was upregulated in high-fat diet and ob/ob mice and increased by treatment of palmitate,oleate or linoleate in primary hepatocytes (Fig.1).Moreover,high fat enhanced expression of lncRNA MEG3in hepatocytes through histone acetylation (Fig.3).These observations were similar to previous research that in-dividuals who were prenatally exposed to famine in 1944e 1945showed increased DNA methylation of the MEG3genes [24].

As a member of the evolutionarily conserved mammalian fork-head box O class family,FoxO1has been tightly linked with hepatic gluconeogenesis [25]and is a critical regulator of hepatic glucose and lipid metabolism via its ability to regulate the expression of G6pc and Pepck in gluconeogenesis.In primary hepatocytes,enhanced level of MEG3gene expression was associated with increased expression of Akt substrate FoxO1(Ser256),which has known to play important roles in liver metabolism (Fig.2B).Moreover,MEG3interference could attenuate palmitate-induced increase of FoxO1protein expressions in primary hepatocytes (Fig.2F).

Previous studies showed that insulin reduces hepatic glucose production and increases hepatic lipid synthesis and secretion in healthy and diabetic states through FoxO1inactivation [26].While fasting blood glucose rises when FoxO1is constitutively expressed in the liver [27],extrahepatic effects of insulin are suf ?cient to maintain normal whole-body and hepatic glucose metabolism when liver FoxO1activity is disrupted [28].Additionally,liver speci ?c FoxO1knock-out mice develop fasting hypoglycemia [8].Recent studies have shown that FoxO1activity was modulated to regulate hepatic glucose production [29e 33],which potentially have therapeutic applications in T2DM.

G6pc and Pepck regulating gluconeogenesis and hepatic glucose production are known to be regulated in the liver at the tran-scriptional level by FoxO1.In fasting,the withdrawal of insulin stimulation results in gluconeogenesis through an upregulation of Pepck and G6pc [8],and induction of autophagy.This response is largely dependent on the interplay between Akt and FoxO1.FoxO1inactivation in vivo diminished the transcriptional expression of genes encoding the gluconeogenic enzymes (Pepck and G6pc)and reduced the blood glucose concentration.In this study,the effect of MEG3on FoxO1was conferred onto the key gluconeogenic en-zymes G6pc and Pepck.Firstly,the Ad-MEG3-induced activation of FoxO1led to an increase of G6pc and Pepck mRNA transcription and protein level (Fig.2C).Then increased of G6pc and Pepck protein expressions stimulated by palmitate were abrogated by MEG3interference in primary hepatocytes (Fig.2F).These results indicated that MEG3was the mediator of FoxO1,which regulated the expression of G6pc and Pepck in primary hepatocytes.

Hepatic gluconeogenesis is a concerted process that integrates transcriptional regulation with hormonal signals and an important pathway involved in the maintenance of glucose homeostasis.Hepatic gluconeogenesis has been considered to be largely responsible for hyperglycemia in T2DM [18].Our data demon-strated that the Ad-MEG3-induced activation of FoxO1also led to an increase in the rate of gluconeogenesis and an impairment of insulin-stimulated glycogen synthesis in primary hepatocytes,both of which are related to hepatic insulin resistance (Fig.2D,E).

In

Fig.3.Effects and underlying mechanisms of high fat on expression of MEG3in hepatocytes.Hepatocytes from male mice were treated with TSA (0,0.5,1.0,and 2.0m M)for 48h.(A)Gene expression of MEG3was determined by real-time RCR.(B)HDAC1and HDAC3protein expressions in primary hepatocytes treated with palmitate were analyzed by western blotting.(C)Effects of si-HDAC1and si-HDAC3on MEG3expression level.(D)MEG3expression level affected by RGFP966.**P <0.01.

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addition,hepatic insulin resistance is prominent in ob/ob mice and involves increased expression of hepatic gluconeogenic and lipo-genic enzymes [34].We also found that MEG3interference could recover the up-regulation of triglyceride and down-regulation of glucogen content in high-fat diet or in ob/ob mice (Fig.4A,B),though the increase of body weight couldn't be abrogated by MEG3interference (Fig.4C).Moreover,impaired glucose tolerance in high-fat diet and ob/ob mice was attenuated by MEG3interference (Fig.4D,E).A similar study indicated that increased DNA methyl-ation of the MEG3genes in parallel with impaired glucose tolerance [24].

5.Conclusion

In summary,this paper suggests that upregulation of lncRNA MEG3can promote hepatic insulin resistance via Increasing Fox-O1Expression,thereby provides a new insight into the molecular mechanism of hepatic insulin resistance in liver and novel targets and strategies for the treatment of T2DM.Con ?icts of interests

None.

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[1]V.T.Samuel,G.I.Shulman,Mechanisms for insulin resistance:common

threads and missing links,Cell 148(2012)852e 871.

[2] D.M.Muoio,C.B.Newgard,Mechanisms of disease:Molecular and metabolic

mechanisms of insulin resistance and beta-cell failure in type 2diabetes,Nat.Rev.Mol.Cell Biol.9(2008)193e 205.

[3] A.J.Lusis, A.D.Attie,K.Reue,Metabolic syndrome:from epidemiology to

systems biology,Nat.Rev.Genet.9(2008)819e 830.

[4]Z.Wu,P.Jiao,X.Huang,B.Feng,Y.Feng,S.Yang,et al.,MAPK phosphatase-3

promotes hepatic gluconeogenesis through dephosphorylation of forkhead box O1in mice,J.Clin.Investig.120(2010)3901e 3911.

[5]P.Puigserver,J.Rhee,J.Donovan,C.J.Walkey,J.C.Yoon,F.Oriente,et al.,In-sulin-regulated hepatic gluconeogenesis through FOXO1-PGC-1alpha inter-action,Nature 423(2003)550e 555.

[6] D.N.Gross, A.P.van den Heuvel,M.J.Birnbaum,The role of FoxO in the

regulation of metabolism,Oncogene 27(2008)2320e 2336.

[7] B.T.Bikman,S.A.Summers,Ceramides as modulators of cellular and whole-body metabolism,J.Clin.Investig.121(2011)4222e 4230.

[8]M.Matsumoto,A.Pocai,L.Rossetti,R.A.Depinho,D.Accili,Impaired regula-tion of hepatic glucose production in mice lacking the forkhead transcription factor Foxo1in liver,Cell Metab.6(2007)208e 216.

[9]W.Huang,J.Yu,X.Jia,L.Xiong,N.Li,X.Wen,Zhenqing recipe improves

glucose metabolism and insulin sensitivity by repressing hepatic FOXO1in type 2diabetic rats,Am.J.Chin.Med.40(2012)721e 733.

[10]P.J.Batista,H.Y.Chang,Long noncoding RNAs:cellular address codes in

development and disease,Cell 152(2013)1298e 1307.

[11]L.Yang,J.E.Froberg,J.T.Lee,Long noncoding RNAs:fresh perspectives into the

RNA world,Trends Biochem.Sci.39(2014)35e 43.

[12]Y.He,X.M.Meng,C.Huang,B.M.Wu,L.Zhang,X.W.Lv,et al.,Long noncoding

RNAs:novel insights into hepatocelluar carcinoma,Cancer Lett.344(2014)20e 27.

[13]J.L.Huang,L.Zheng,Y.W.Hu,Q.Wang,Characteristics of long non-coding RNA

and its relation to hepatocellular carcinoma,Carcinogenesis 35(2014)507e 514.

[14] C.Braconi,T.Kogure,N.Valeri,N.Huang,G.Nuovo,S.Costinean,et al.,

microRNA-29can regulate expression of the long non-coding RNA gene MEG3in hepatocellular cancer,Oncogene 30(2011)4750e 4756.

[15] E.M.Morris,G.M.Meers,F.W.Booth,K.L.Fritsche,C.D.Hardin,J.P.Thyfault,et

al.,PGC-1alpha overexpression results in increased hepatic fatty acid oxida-tion with reduced triacylglycerol accumulation and secretion,Am.J.Physiol.Gastrointest.Liver Physiol.303(2012)G979e G992.

[16]T.Galbo,R.J.Perry,E.Nishimura,V.T.Samuel,B.Quistorff,G.I.Shulman,PP2A

inhibition results in hepatic insulin resistance despite Akt2activation,Aging 5(2013)770e 781.

[17]T.Galbo,G.S.Olsen,B.Quistorff,E.Nishimura,Free fatty acid-induced

PP2A

Fig.4.Effects of MEG3interference on triglyceride,glucogen content,body weight,and glucose tolerance in high-fat diet mice and obese ob/ob mice.(A)Mice fed on high-fat diet or low-fat diet and ob/ob mice or control mice received intravenous injections of MEG3interference fragment via tail vein twice a week for 10weeks.Liver triglyceride contents and glycogen contents of high-fat diet and low-fat diet male mice after 10weeks of MEG3interference treatment (n ?4e 5per group).(B)Liver triglyceride contents and glycogen contents of ob/ob and control male mice after 10weeks of MEG3interference treatment (n ?4e 5per group).(C)Body weight of high-fat diet and ob/ob male mice after 10weeks of MEG3interference treatment (n ?4e 5per group).**P <0.01vs.Low-fat diet or control,##P <0.01vs.High-fat diet tsi-control or control tsi-control.(D,E)High-fat diet and ob/ob mice received intravenous tail-vein injections of MEG3interference fragment.At 10weeks,after overnight fast,glucose tolerance was tested.Group 1:Low-fat diet,Group 2:High-fat diet,Group 3:High-fat diet tsi-control,Group 4:High-fat diet tsi-MEG3;Group A:control mice,Group B:ob/ob mice,Group 3:ob/ob mice tsi-control,Group 4:ob/ob mice tsi-MEG3.**P <0.01vs.Group 1or Group A,##P <0.01vs.Group 3or Group C.

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6

hyperactivity selectively impairs hepatic insulin action on glucose meta-bolism,PloS One6(2011)e27424.

[18] D.Accili,Lilly lecture2003:the struggle for mastery in insulin action:from

triumvirate to republic,Diabetes53(2004)1633e1642.

[19] D.N.Gross,M.Wan,M.J.Birnbaum,The role of FOXO in the regulation of

metabolism,Curr.Diabet.Rep.9(2009)208e214.

[20] A.Wajngot,V.Chandramouli,W.C.Schumann,K.Ekberg,P.K.Jones,S.Efendic,

et al.,Quantitative contributions of gluconeogenesis to glucose production during fasting in type2diabetes mellitus,Metab.Clin.Exp.50(2001)47e52.

[21] A.A.Yarushkin,E.M.Kachaylo,V.O.Pustylnyak,The constitutive androstane

receptor activator4-[(4R,6R)-4,6-diphenyl-1,3-dioxan-2-yl]-N,N-dimethyla-niline inhibits the gluconeogenic genes PEPCK and G6Pase through the sup-pression of HNF4alpha and FOXO1transcriptional activity,Br.J.Pharmacol.

168(2013)1923e1932.

[22]Y.Zhou,X.Zhang,A.Klibanski,MEG3noncoding RNA:a tumor suppressor,

J.Mol.Endocrinol.48(2012)R45e R53.

[23]S.Cairo,C.Armengol,A.De Reynies,Y.Wei,E.Thomas,C.A.Renard,et al.,

Hepatic stem-like phenotype and interplay of Wnt/beta-catenin and Myc signaling in aggressive childhood liver cancer,Cancer Cell14(2008)471e484.

[24] E.W.Tobi,L.H.Lumey,R.P.Talens,D.Kremer,H.Putter,A.D.Stein,et al.,DNA

methylation differences after exposure to prenatal famine are common and timing-and sex-speci?c,Hum.Mol.Genet.18(2009)4046e4053.

[25]R.A.Haeusler,K.H.Kaestner,D.Accili,FoxOs function synergistically to pro-

mote glucose production,J.Biol.Chem.285(2010)35245e35248.

[26]K.Zhang,L.Li,Y.Qi,X.Zhu,B.Gan,R.A.DePinho,et al.,Hepatic suppression of

Foxo1and Foxo3causes hypoglycemia and hyperlipidemia in mice,Endo-crinology153(2012)631e646.

[27]M.Matsumoto,S.Han,T.Kitamura,D.Accili,Dual role of transcription factor

FoxO1in controlling hepatic insulin sensitivity and lipid metabolism,J.Clin.

Investig.116(2006)2464e2472.

[28]I.OS,W.Zhang,D.H.Wasserman,C.W.Liew,J.Liu,J.Paik,et al.,FoxO1in-

tegrates direct and indirect effects of insulin on hepatic glucose production and glucose utilization,https://www.wendangku.net/doc/f75191161.html,mun.6(2015)7079.

[29]J.A.Hall,M.Tabata,J.T.Rodgers,P.Puigserver,USP7attenuates hepatic

gluconeogenesis through modulation of FoxO1gene promoter occupancy, Mol.Endocrinol.28(2014)912e924.

[30] B.Feng,Q.He,H.Xu,FOXO1-dependent up-regulation of MAP kinase phos-

phatase3(MKP-3)mediates glucocorticoid-induced hepatic lipid accumula-tion in mice,Mol.Cell.Endocrinol.393(2014)46e55.

[31]Q.Wang,N.Wang,M.Dong,F.Chen,Z.Li,Y.Chen,GdCl3reduces hyper-

glycaemia through Akt/FoxO1-induced suppression of hepatic gluconeogen-esis in Type2diabetic mice,Clin.Sci.127(2014)91e100.

[32]U.B.Pajvani, C.J.Shawber,V.T.Samuel, A.L.Birkenfeld,G.I.Shulman,

J.Kitajewski,et al.,Inhibition of Notch signaling ameliorates insulin resistance in a FoxO1-dependent manner,Nat.Med.17(2011)961e967.

[33]H.Liu,M.M.Fergusson,J.J.Wu,II Rovira,J.Liu,O.Gavrilova,et al.,Wnt

signaling regulates hepatic metabolism,Sci.Signal.4(2011)ra6.

[34]M.P.Sajan,R.A.Ivey,M.C.Lee,R.V.Farese,Hepatic insulin resistance in ob/ob

mice involves increases in ceramide,aPKC activity,and selective impairment of Akt-dependent FoxO1phosphorylation,J.Lipid Res.56(2015)70e80.

X.Zhu et al./Biochemical and Biophysical Research Communications xxx(2015)1e77

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输出: 蛋白质的空间结构 蛋白质结构预测的可行性是有坚实依据的。因为一般而言，蛋白质的空间结构是由其一级结构确定的。生化实验表明：如果在体外无任何其他物质存在的条件下，使得蛋白质去折叠，然后复性，蛋白质将立刻重新折叠回原来的空间结构，整个过程在不到1秒种内即可完成。因此有理由认为对于大部分蛋白质而言，其空间结构信息已经完全蕴涵于氨基酸序列中。从物理学的角度讲，系统的稳定状态通常是能量最小的状态，这也是蛋白质预测工作的理论基础。 2 蛋白质结构预测方法 蛋白质结构预测的方法可以分为三种： 同源性（Homology ）方法：这类方法的理论依据是如果两个蛋白质的序列比较相似，则其结构也有很大可能比较相似。有工作表明，如果序列相似性高于75％，则可以使用这种方法进行粗略的预测。这类方法的优点是准确度高，缺点是只能处理和模板库中蛋白质序列相似性较高的情况。 从头计算（Ab initio ） 方法：这类方法的依据是热力学理论，即求蛋白质能量最小的状态。生物学家和物理学家等认为从原理上讲这是影响蛋白质结构的本质因素。然而由于巨大的计算量，这种方法并不实用，目前只能计算几个氨基酸形成的结构。IBM 开发的Blue Gene 超级计算机，就是要解决这个问题。 穿线法(Threading )方法：由于Ab Initio 方法目前只有理论上的意义，Homology 方法受限于待求蛋白质必需和已知模板库中某个蛋白质有较高的序列相似性，对于其他大部分蛋白质来说，有必要寻求新的方法。Threading 就此应运而生。 以上三种方法中，Ab Initio 方法不依赖于已知结构，其余两种则需要已知结构的协助。通常将蛋白质序列和其真实三级结构组织成模板库，待预测三级结构的蛋白质序列，则称之为查询序列(query sequence)。 3 蛋白质结构预测的Threading 方法 Threading 方法有三个代表性的工作：Eisenburg 基于环境串的工作、Xu Ying 的Prospetor 和Xu Jinbo 、Li Ming 的RAPTOR 。 Threading 的方法：首先取出一条模版和查询序列作序列比对(Alignment)，并将模版蛋白质与查询序列匹配上的残基的空间坐标赋给查询序列上相应的残基。比对的过程是在我们设计的一个能量函数指导下进行的。根据比对结果和得到的查询序列的空间坐标，通过我们设计的能量函数，得到一个能量值。将这个操作应用到所有的模版上，取能量值最低的那条模版产生的查询序列的空间坐标为我们的预测结果。 需要指出的是，此处的能量函数却不再是热力学意义上的能量函数。它实质上是概率的负对数，即 ，我们用统计意义上的能量来代替真实的分子能量，这两者有大致相同的形式。 p E log ?=如果沿着马希文教授的观点看上述工作 ，则更有意思：Eisenburg 指出如果仅仅停留在简单地使用每个原子的空间坐标(x,y,z)来形式化表示蛋白质空间结构，则难以进一步深入研究。Eisenburg 创造性地使用环境串表示结构，从而将结构预测问题转化成序列串和环境串之间的比对问题；其后，Xu Ying 作了进一步发展，将蛋白质序列表示成一系列核（core ）组成的序列，Core 和Core 之间存在相互作用。因此结构就表示成Core 的空间坐标，以及Core 之间的相互作用。在这种表示方法的基础上，Xu Ying 开发了一种求最优匹配的动态规划算法，得到了很好的结果。但是由于其较高的复杂度，在Prospetor2上不得不作了一些简化；Xu Jinbo 和Li Ming 很漂亮地解决了这个问题，将求最优匹配的过程表示成一个整数规划问题，并且证明了一些常用

蛋白质结构预测

实习 5 ：蛋白质结构预测 学号20090***** 姓名****** 专业年级生命生技**** 实验时间2012.6.21 提交报告时间2012.6.21 实验目的： 1.学会使用GOR和HNN方法预测蛋白质二级结构 2.学会使用SWISS-MODEL进行蛋白质高级结构预测 实验内容： 1.分别用GOR和HNN方法预测蛋白质序列的二级结构，并对比异同性。 2.利用SWISS-MODEL进行蛋白质的三级结构预测，并对预测结果进行解释。 作业： 1. 搜索一条你感兴趣的蛋白质序列，分别用GOR和HNN进行二级结构预测，解释预测结果，分析两个方法结果有何异同。 答：所选用蛋白质序列为>>gi|390408302|gb|AFL70986.1| gag protein, partial [Human immunodeficiency virus] （1）GOR预测结果： 图1 图1是每个氨基酸在序列中所处的状态，可以看出序列的二级结构预测结果为： 1到9位个氨基酸为无规卷曲，10到33位氨基酸为α螺旋,34到37位为β折叠，38到45位为无规卷曲，46到49位为α螺旋，50到53位为无规卷曲，54到65为α螺旋，66到72位为无规卷曲，73到95位为α螺旋，96到101位为无规卷曲，102到108为β折叠，109到115位为无规卷曲，117位为β折叠。 图2 图2为各种结构在序列中所占的比例，其中Alpha helix占53.85%，Extended strand占11.11%，Random coil占35.04%，无他二级结构。

图3 图3为各个氨基酸在序列中的状态以及二级结构在全序列中二级结构分布情况。 （2）HNN预测： 图4 图4是每个氨基酸在序列中所处的状态，可以看出序列的二级结构预测结果为： 1到6位个氨基酸为无规卷曲，7到34位氨基酸为α螺旋,35到37位为β折叠，38位为α螺旋，39到44位为无规卷曲，45到49位为α螺旋，50到55位为无规卷曲，56到65为α螺旋，66到71位为无规卷曲，72到83位为α螺旋，84到86位为无规卷曲，87到95位为α螺旋，96到102为无规卷曲，103到108位为β折叠，108到117位为无规卷曲。 图5 图5为各种结构在序列中所占的比例，其中Alpha helix占55.56%，Extended strand占7.69%，Random coil占36.75%，无他二级结构。

蛋白质结构预测网址

蛋白质结构预测网址 物理性质预测： Compute PI/MW Peptidemass TGREASE SAPS 基于组成的蛋白质识别预测 AACompIdent PROPSEARCH 二级结构和折叠类预测 nnpredict Predictprotein SSPRED 特殊结构或结构预测 COILS MacStripe 与核酸序列一样，蛋白质序列的检索往往是进行相关分析的第一步，由于数据库和网络技校术的发展，蛋白序列的检索是十分方便，将蛋白质序列数据库下载到本地检索和通过国际互联网进行检索均是可行的。 由NCBI检索蛋白质序列 可联网到：“”进行检索。 利用SRS系统从EMBL检索蛋白质序列 联网到：”，可利用EMBL的SRS系统进行蛋白质序列的检索。 通过EMAIL进行序列检索 当网络不是很畅通时或并不急于得到较多数量的蛋白质序列时，可采用EMAIL方式进行序列检索。 蛋白质基本性质分析 蛋白质序列的基本性质分析是蛋白质序列分析的基本方面，一般包括蛋白质的氨基酸组成，分子质量，等电点，亲水性，和疏水性、信号肽，跨膜区及结构功能域的分析等到。蛋白质的很多功能特征可直接由分析其序列而获得。例如，疏水性图谱可通知来预测跨膜螺旋。同时，也有很多短片段被细胞用来将目的蛋白质向特定细胞器进行转移的靶标（其中最典型的例子是在羧基端含有KDEL序列特征的蛋白质将被引向内质网。WEB中有很多此类资源用于帮助预测蛋白质的功能。 疏水性分析 位于ExPASy的ProtScale程序（）可被用来计算蛋白质的疏水性图谱。该网站充许用户计算蛋白质的50余种不同属性，并为每一种氨基酸输出相应的分值。输入的数据可为蛋白质序列或SWISSPROT数据库的序列接受号。需要调整的只是计算窗口的大小（n）该参数用于估计每种氨基酸残基的平均显示尺度。 进行蛋白质的亲/疏水性分析时，也可用一些windows下的软件如， bioedit,dnamana等。 跨膜区分析 有多种预测跨膜螺旋的方法，最简单的是直接，观察以20个氨基酸为单位的疏水性氨基酸残基的分布区域，但同时还有多种更加复杂的、精确的算法能够预测跨膜螺旋的具体位置和它们的膜向性。这些技术主要是基于对已知跨膜螺旋的研究而得到的。自然存在的跨膜螺旋Tmbase 数据库，可通过匿名FTP获得()，参见表一

蛋白质预测分析 网址集锦

蛋白质预测分析网址集锦 2007/04/06 18:31 物理性质预测： Compute PI/MW http://expaxy.hcuge.ch/ch2d/pi-tool.html Peptidemass http://expaxy.hcuge.ch/sprot/peptide-mass.html TGREASE ftp://https://www.wendangku.net/doc/f75191161.html,/pub/fasta/ SAPS http://ulrec3.unil.ch/software/SAPS_form.html 基于组成的蛋白质识别预测 AACompIdent http://expaxy.hcuge.ch/ch2d/aacompi.html AACompSim http://expaxy.hcuge.ch/ch2d/aacsim.html PROPSEARCH http://www.embl-heidelberg.de/prs.html 二级结构和折叠类预测 nnpredict https://www.wendangku.net/doc/f75191161.html,/~nomi/nnpredictPredictprotein http://www.embl-heidelberg.de/predictprotein/SOPMA http://www.ibcp.fr/predict.htmlSSPRED http://www.embl-heidelberg.de/sspred/ssprd_info.html 特殊结构或结构预测 COILS http://ulrec3.unil.ch/software/COILS_form.htmlMacStripe https://www.wendangku.net/doc/f75191161.html,/matsudaira/macstripe.html 与核酸序列一样，蛋白质序列的检索往往是进行相关分析的第一步，由于数据库和网络技校术的发展，蛋白序列的检索是十分方便，将蛋白质序列数据库下载到本地检索和通过国际互联网进行检索均是可行的。 由NCBI检索蛋白质序列 可联网到： “https://www.wendangku.net/doc/f75191161.html,:80/entrz/query.fcgi?db=protein”进行检索。 利用SRS系统从EMBL检索蛋白质序列 联网到：https://www.wendangku.net/doc/f75191161.html,/”，可利用EMBL的SRS系统进行蛋白质序列的检索。 通过EMAIL进行序列检索 当网络不是很畅通时或并不急于得到较多数量的蛋白质序列时，可采用EMAIL 方式进行序列检索。 蛋白质基本性质分析 蛋白质序列的基本性质分析是蛋白质序列分析的基本方面，一般包括蛋白质的氨基酸组成，分子质量，等电点，亲水性，和疏水性、信号肽，跨膜区及结构功能域的分析等到。蛋白质的很多功能特征可直接由分析其序列而获得。例如，疏水

蛋白质结构预测在线软件

蛋白质预测分析网址集锦 物理性质预测： Compute PI/MW SAPS 基于组成的蛋白质识别预测 AACompIdent PROPSEARCH 二级结构和折叠类预测 nnpredict Predictprotein SSPRED 特殊结构或结构预测 COILS MacStripe 与核酸序列一样，蛋白质序列的检索往往是进行相关分析的第一步，由于数据库和网络技校术的发展，蛋白序列的检索是十分方便，将蛋白质序列数据库下载到本地检索和通过国际互联网进行检索均是可行的。 由NCBI检索蛋白质序列 可联网到：“”进行检索。 利用SRS系统从EMBL检索蛋白质序列 联网到：”，可利用EMBL的SRS系统进行蛋白质序列的检索。 通过EMAIL进行序列检索 当网络不是很畅通时或并不急于得到较多数量的蛋白质序列时，可采用EMAIL方式进行序列检索。 蛋白质基本性质分析 蛋白质序列的基本性质分析是蛋白质序列分析的基本方面，一般包括蛋白质的氨基酸组成，分子质量，等电点，亲水性，和疏水性、信号肽，跨膜区及结构功能域的分析等到。蛋白质的很多功能特征可直接由分析其序列而获得。例如，疏水性图谱可通知来预测跨膜螺旋。同时，也有很多短片段被细胞用来将目的蛋白质向特定细胞器进行转移的靶标（其中最典型的例子是在羧基端含有KDEL序列特征的蛋白质将被引向内质网。WEB中有很多此类资源用于帮助预测蛋白质的功能。 疏水性分析 位于ExPASy的ProtScale程序（）可被用来计算蛋白质的疏水性图谱。该网站充许用户计算蛋白质的50余种不同属性，并为每一种氨基酸输出相应的分值。输入的数据可为蛋白质序列或SWISSPROT数据库的序列接受号。需要调整的只是计算窗口的大小（n）该参数用于估计每种氨基酸残基的平均显示尺度。 进行蛋白质的亲/疏水性分析时，也可用一些windows下的软件如，bioedit,dnamana等。 跨膜区分析 有多种预测跨膜螺旋的方法，最简单的是直接，观察以20个氨基酸为单位的疏水性氨基酸残基的分布区域，但同时还有多种更加复杂的、精确的算法能够预测跨膜螺旋的具体位置和它们的膜向性。这些技术主要是基于对已知跨膜螺旋的研究而得到的。自然存在的跨膜螺旋Tmbase 数据库，可通过匿名FTP获得(，参见表一

蛋白质结构预测在线软件

蛋白质结构预测在线软 件 Company Document number：WUUT-WUUY-WBBGB-BWYTT-1982GT

蛋白质预测分析网址集锦？ 物理性质预测：？ Compute PI/MW？ ？ SAPS？ 基于组成的蛋白质识别预测？ AACompIdentPROPSEARCH？ 二级结构和折叠类预测？ nnpredict？ Predictprotein？ SSPRED？ 特殊结构或结构预测？ COILS？ MacStripe？ 与核酸序列一样，蛋白质序列的检索往往是进行相关分析的第一步，由于数据库和网络技校术的发展，蛋白序列的检索是十分方便，将蛋白质序列数据库下载到本地检索和通过国际互联网进行检索均是可行的。？ 由NCBI检索蛋白质序列？ 可联网到：“”进行检索。？ 利用SRS系统从EMBL检索蛋白质序列？ 联网到：”，可利用EMBL的SRS系统进行蛋白质序列的检索。？ 通过EMAIL进行序列检索？

当网络不是很畅通时或并不急于得到较多数量的蛋白质序列时，可采用EMAIL方式进行序列检索。？ 蛋白质基本性质分析？ 蛋白质序列的基本性质分析是蛋白质序列分析的基本方面，一般包括蛋白质的氨基酸组成，分子质量，等电点，亲水性，和疏水性、信号肽，跨膜区及结构功能域的分析等到。蛋白质的很多功能特征可直接由分析其序列而获得。例如，疏水性图谱可通知来预测跨膜螺旋。同时，也有很多短片段被细胞用来将目的蛋白质向特定细胞器进行转移的靶标（其中最典型的例子是在羧基端含有KDEL序列特征的蛋白质将被引向内质网。WEB中有很多此类资源用于帮助预测蛋白质的功能。？ 疏水性分析？ 位于ExPASy的ProtScale程序（）可被用来计算蛋白质的疏水性图谱。该网站充许用户计算蛋白质的50余种不同属性，并为每一种氨基酸输出相应的分值。输入的数据可为蛋白质序列或SWISSPROT数据库的序列接受号。需要调整的只是计算窗口的大小（n）该参数用于估计每种氨基酸残基的平均显示尺度。？ 进行蛋白质的亲/疏水性分析时，也可用一些windows下的软件如， bioedit,dnamana等。？ 跨膜区分析？ 有多种预测跨膜螺旋的方法，最简单的是直接，观察以20个氨基酸为单位的疏水性氨基酸残基的分布区域，但同时还有多种更加复杂的、精确的算法能够预测跨膜螺旋的具体位置和它们的膜向性。这些技术主要是基于对已知跨膜螺旋的研究而得到的。自然存在的跨膜螺旋Tmbase 数据库，可通过匿名FTP获得(，参见表一？ 资源名称网址说明？

蛋白质序列分析常用网站-2018.8

蛋白质序列分析 蛋白质序列的基本性质分析是蛋白质序列分析的基本方面，一般包括蛋白质的氨基酸组成，分子质量，等电点，亲水性，和疏水性、信号肽，跨膜区及结构功能域的分析等到。蛋白质的很多功能特征可直接由分析其序列而获得。例如，疏水性图谱可通知来预测跨膜螺旋。同时，也有很多短片段被细胞用来将目的蛋白质向特定细胞器进行转移的靶标(其中最典型的例子是在羧基端含有KDEL序列特征的蛋白质将被引向内质网。WEB中有很多此类资源用于帮助预测蛋白质的功能。 基本理化性质分析：https://https://www.wendangku.net/doc/f75191161.html,/protparam/ 信号肽预测：http://www.cbs.dtu.dk/services/SignalP/ 在生物内，蛋白质的合成场所与功能场所常被一层或多层细胞膜所隔开，这样就涉及到蛋白质的转运。合成的蛋白质只有准确地定向运行才能保证生命活动的正常进行。一般来说，蛋白质的定位的信息存在于该蛋白质自身结构中，并通过与膜上特殊的受体相互作用而得以表达。在起始密码子之后，有一段编码疏水性氨基酸序列的RNA片段，这个氨基酸序列就这个氨基酸序列就是信号肽序列。含有信号肽的蛋白质一般都是分泌到细胞外，可能作为重要的细胞因子起作用，从而具有潜在的应用价值。 糖基化位点预测：http://www.cbs.dtu.dk/services/Net NGlyc/ 跨膜区分析：TMORED 蛋白质序列含有跨膜区提示它可能作为膜受体起作用，也可能是定位于膜的锚定蛋白或者离子通道蛋白等，从而，含有跨膜区的蛋白质往往和细胞的功能状态密切相关。 蛋白酶的结构功能进行预测和分析：http://smart.embl-heidelberg.de/ 同源建模分析：https://www.wendangku.net/doc/f75191161.html,//SWISS-MODEL.html 二级结构及折叠类预测：Predictprotein 特殊结构或结构预测：COILS MacStripe 疏水性分析：ExPASy的ProtScale 基于序列同源性分析的蛋白质功能预测： 至少有80个氨基酸长度范围内具有25%以上序列一致性才提示可能的显著性意义。类似于核酸序列同源性分析，用户直接将待分析的蛋白质序列输入NCBI/BLAST(https://www.wendangku.net/doc/f75191161.html,/blast)，选择程序BLASTP就可网上分析。 基于motif、结构位点、结构功能域数据库的蛋白质功能预测 蛋白质的磷酸化与糖基化对蛋白质的功能影响很大，所以对其的分析也是生物信息学的一个部分。同时，分子进化方面的研究表明，蛋白质的不同区域具有

蛋白质结构及功能预测

物理性质预测 Compute PI/MW http://expaxy.hcuge.ch/ch2d/pi-tool.html Peptidemass http://expaxy.hcuge.ch/sprot/peptide-mass.html TGREASE ftp://https://www.wendangku.net/doc/f75191161.html,/pub/fasta/ SAPS http://ulrec3.unil.ch/software/SAPS_form.html 基于组成的蛋白质识别预测 http://expaxy.hcuge.ch/ch2d/aacompi.html AACompSim http://expaxy.hcuge.ch/ch2d/aacsim.html PROPSEARCH http://www.embl-heidelberg.de/prs.html 二级结构和折叠类预测 https://www.wendangku.net/doc/f75191161.html,/~nomi/nnpredictPredictprotein http://www.embl-heidelberg.de/predictprotein/SOPMA http://www.ibcp.fr/predict.htmlSSPRED http://www.embl-heidelberg.de/sspred/ssprd_info.html 特殊结构或结构预测 http://ulrec3.unil.ch/software/COILS_form.htmlMacStripe https://www.wendangku.net/doc/f75191161.html,/matsudaira/macstripe.html 检索 由NCBI检索蛋白质序列 https://www.wendangku.net/doc/f75191161.html,:80/entrz/query.fcgi?db=protein进行检索。 利用SRS系统从EMBL检索蛋白质序列 https://www.wendangku.net/doc/f75191161.html,/可利用EMBL的SRS系统进行蛋白质序列的检索。 通过EMAIL进行序列检索 当网络不是很畅通时或并不急于得到较多数量的蛋白质序列时，可采用EMAIL方式进行序列检索。 疏水性分析 位于ExPASy的ProtScale程序https://www.wendangku.net/doc/f75191161.html,/cgi-bin/protscale.pl可被用来计算蛋白质的疏水性图谱。该网站充许用户计算蛋白质的50余种不同属性，并为每一种氨基酸输出

蛋白质结构预测原理概述

蛋白质结构预测原理概述 蛋白质结构预测技术已经有很多发展，但是基本原理未变，可以参考；基本操作也可以参考下文。 摘自：阎隆飞,孙之荣主编，蛋白质分子结构，清华大学出版社，1999. 现在计算机互联网高速发展,已经成为遍布全球的一个网络,成为科学研究的有力工具,也是进行蛋白质结构和功能研究的重要工具。国际上一些著名的分子生物学实验室都 在互联网上建立了蛋白质结构预测服务器。可以在互联网上进入这些服务器,利用这些服 务器提供的软件进行蛋白质结构预测研究。 下面以欧洲分子生物学实验室蛋白质结构预测服务器为例作一说明。 13.6.1欧洲分子生物学实验室蛋白质结构预测服务器 (1)该实验室提供的服务内容 欧洲分子生物学实验室(EuropeanMolecular BiologyLabraroty,EMBL)提供的服 务包括:①多序列联配的生成(MaxHom);②二级结构预测(PHDsec);③溶剂可及 性的预测(PHDacc);④跨膜螺旋预测(PHDhtm);⑤跨膜蛋白拓扑结构预测( PHDtopology);⑥用基于预测的Threading方法进行折叠子识别(PHDthreader);⑦ 二级结构预测结果评估(EvalSec)。 用Email或WWW方式访问该服务器,可完成以上7种功能。其Email或WWW地 址如下: WWW.embl—heidelberg.de/predictprotein/predictprotein.html 把要预测序列发往PredictProtein@EMBL-Heidelberg.DE; 如有问题可以给Predict-Help@EMBL-Heidelberg.DE发电子邮件。 (2)结构预测步骤 已知蛋白质一级序列的结构,预测步骤如下:①在序列库(SWISSPROT)中搜索同 源序列;②用MaxHom程序进行多序列联配;③把多序列联配的结果作为基于profile 的神经网络预测方法的输入,进行结构预测。 在交互验证实验中,其预测率如下:对水溶性球蛋白其三态预测率(螺旋、折叠和其他)大于72%[34,35];跨膜螺旋的两态(跨膜和非跨膜)预测率大于95%;优化后的跨膜螺旋和拓扑结构预测,螺旋预测率为89%左右,拓扑结构预测率大于86%[39]。 基于Threading预测的折叠子识别方法(prediction-basedthreading)把二级结构和可及性预测结果与PDB数据库中各蛋白联配,找出同源蛋白,从而预测未知空间结构蛋白的折叠类型。预测准确率的评估数据包括:总体三态预测准确率、相关系数、信息熵、部分片段重叠、二级结构预测内容和结构类型[40]。 下面介绍各种结构预测服务。 1)多序列联配的生成(MaxHom) MaxHom主要由两部分组成:①用一标准动力学程序把数据库中各序列与待预测 序列进行联配。每联配一个序列后就编译生成profile,然后再联配下一个序列,如此反复 联配编译,直到联配完所有同源序列。②当所有同源序列联配上去后,重新编译profile, 再次运行动力学程序,利用以上生成的profile一个一个序列地进行重新联配。

总结了一些在线蛋白质结构预测站点

总结了一些在线蛋白质结构预测站点，希望能对大家有所帮助！ WURST It takes a protein sequence, aligns it to a library of structures and mails structure predictions back to you (protein threading). http://www.zbh.uni-hamburg.de/wurst/index.php MODWEB (需要Modeller的注册码，可以在Modeller站点申请) https://www.wendangku.net/doc/f75191161.html,/modweb-cgi/main.cgi I-TASSER on-line https://www.wendangku.net/doc/f75191161.html,/I-TASSER/ VHMPT https://www.wendangku.net/doc/f75191161.html,.tw/bioinfo/vhmpt/user.htm SWISS-MODEL https://www.wendangku.net/doc/f75191161.html,/ ESyPred3D Web Server 1.0 http://www.fundp.ac.be/sciences/biologie/urbm/bioinfo/esypred/ CPHmodels 2.0 Server http://www.cbs.dtu.dk/services/CPHmodels/ TASSER-Lite https://www.wendangku.net/doc/f75191161.html,/skolnick/webservice/tasserlite/index.html Pfam 20.0 https://www.wendangku.net/doc/f75191161.html,/ 3D-JIGSAW https://www.wendangku.net/doc/f75191161.html,/servers/3djigsaw/ PredictProtein https://www.wendangku.net/doc/f75191161.html,/ SCWRL (recommend for side chain modelling，also free for academic institutions): https://www.wendangku.net/doc/f75191161.html,/SCWRL3.php HMMTOP http://www.enzim.hu/hmmtop/index.html

蛋白质功能-结构-相互作用预测网站工具合集

蛋白质功能-结构-相互作用预测网站工具合集

蛋白质组学 蛋白质是生物体的重要组成部分，参与几乎所有生理和细胞代谢过程。此外，与基因组学和转录组学比较，对一个细胞或组织中表达的所有蛋白质，及其修饰和相互作用的大规模研究称为蛋白质组学。 蛋白质组学通常被认为是在基因组学和转录组学之后，生物系统研究的下一步。然而，蛋白质组的研究远比基因组学复杂，这是由于蛋白质内在的复杂特点，如蛋白质各种各样的翻译后修饰所决定的。并且，研究基因组学的技术要比研究蛋白质组学的技术强得多，虽然在蛋白质组学研究中，质谱技术的研究已取得了一些进展。 尽管存在方法上的挑战，蛋白质组学正在迅速发展，并且对癌症的临床诊断和疾病治疗做出了重要贡献。几项研究鉴定出了一些蛋白质在乳腺癌、卵巢癌、前列腺癌和食道癌中表达变化。例如，通过蛋白质组学技术，人们可以在患者血液中明确鉴定出肿瘤标志物。表1列出了更多的蛋白质组学技术用于研究癌症的例子。 另外，高尔基体功能复杂。最新研究表明，它除了参与蛋白加工外，还能参与细胞分化及细胞间信号传导的过程，并在凋亡中扮演重要角色，其功能障碍也许和肿瘤的发生、发展有某种联系。根据人类基因组研究，约1000多种人类高尔基体蛋白质中仅有500~600种得到了鉴定，建立一条关于高尔基体蛋白质组成的技术路线将有助于其功能的深入研究。

类型所在地网站 同源搜索NCBI：美国国立生物技术信息 中心；NIH：美国国家医学研 究院 https://www.wendangku.net/doc/f75191161.html,/BLASTselect protein-protein BLAST 同源搜索 美国弗吉尼亚大学、日本京都 大学 https://www.wendangku.net/doc/f75191161.html,http://fasta.genome.jp/ 同源搜索NCBI：美国国立生物技术信息 中心；NIH：美国国家医学研 究院 https://www.wendangku.net/doc/f75191161.html,/BLASTselect “PSI PHI-BLAST” 蛋白质家族鉴定华盛顿大学https://www.wendangku.net/doc/f75191161.html, 保守结构域搜索 EMBL：欧洲分子生物学实验 室 http://smart.embl-heidelberg.de 功能模体搜索瑞士生物信息研究所https://www.wendangku.net/doc/f75191161.html,/prositehttp://motif.genome.ad.jp 真核生物功能结构域 搜索 ELM 联合体https://www.wendangku.net/doc/f75191161.html, 通过比较基因组学进行功能预测EMBL（欧洲分子生物学实验 室） http://string.embl.de 亚细胞定位预测人类基因组中心东京大学https://www.wendangku.net/doc/f75191161.html,