1、12(I)Secondary Structure：The local spatial arrangement of amino acid residues that are nearby in the sequence,that is,the relative positions of backbone atoms of a certain peptide segment.The side chains are not considered.Forms:helix,pleated sheet,turn,helix,random coil Major Bond：Hydrogen bond I.C
2、onformation of Protein3Right-handed helix3.6 amino acid residues per turn of helixThe pitch of the helix is 0.54nm,diameter is 0.23nmThe N-H of every peptide bond is hydrogen-bonded to the C=O of neighboring peptide bond located four peptide bonds away in the same chain.,including 13 atoms,so also k
3、nown as 3.613 helix.All the main chain C=O and NH are hydrogen bonded.Linus Pauling 1.-helix(1)4The alpha helix is a coiled secondary structure due to a hydrogen bond every fourth amino acid56Direction of hydrogen bonds are parallel to the vertical axis of helix.The stability of an-helix arises prim
4、arily from hydrogen bonds.The side chains are on the outside of the helix,not directly participate in the formation of helix.-helix is the most stable secondary conformation1.-helix(2)：78Adjacent peptide unit form a zigzag or pleated pattern,the intersection angle is 110。.-Sheets are stabilized by h
5、ydrogen bonding between polypeptide strands.The direction of hydrogen bonds are vertical to the peptide strands.Adjacent chains in a b sheet can run in opposite directions(antiparallel b sheet)or in the same direction(parallel b sheet).The side chains of adjacent amino acids point in opposite direct
6、ions2.-pleated sheet structure 91011Peptide chain arises a tight 180turn.A-turn involves four amino acid residues,the first residues is hydrogen bonded to the fourth.Proline is often present in-turnOften lie on the globulin surface and serve key biologic role.3.-turn1213Left-handed helix，4.4 amino a
7、cid residues per turn.Hydrogen bonds stabilize the-helix，every hydrogen bond across 18 atoms,so also named as 4.418 helix.Often found in collagen.Triple left-handed helixes twist to form right-handed super helix and turn to collagenous fibers.4.-helix1415uGeneral name of a series of unordered confor
8、mation in protein.u Important structural and functional segments of protein.5.Random Coil166.Supersecondary Structure of Cytochrome C of PCNAof plasminogen17Motif in Calcium-binding Protein Zinc Finger Side chains can disrupt or induce the formation of secondary structure Shape:Pro having a rigid ri
9、ng(helix disrupter)Size:helix and -sheet needs AAs of small side chain.Leu,Ile,Trp,and Asn,having bulky sides,hard to form helix and-sheet)Charge:Too many charged AAs in a short region of one peptide is hard to form helix.1819*Definition:The entire three-dimensional conformation of a polypeptide cha
10、in.It refers to the spatial arrangement of amino acid residues that are far apart in the sequence and to the pattern of disulfide bonds.It indicates,in three-dimensional space,how secondary structural assemble to form domains and how these domains relate spatially to one another.(II)Tertiary Structu
11、re 20uSingle or several super secondary structure units gather and fold independently into a compact,stable structure,termed domain.uDomain is the function element of protein.The different domains of a protein are often associated with different functions.uDomain is the partial folding region at the
12、 level of tertiary structure.Motif is its subunit.uEvery domain is encoded by one exon.Domain（结构域（结构域）21NADHPyruvateLactate Dehydrogenase N terminalC terminal EGF ReceptorIntracellular protein kinase domain is regulated via the binding of the peptide hormone EGF to its extracellular domain.2223*Feat
13、ures：To the single peptide protein,tertiary structure is the highest level of structure.Form hydrophilic surface and hydrophobic inner core.*Major Bond：Hydrophobic Interaction24Myoglobin(肌红蛋白肌红蛋白)25Quaternary structure defines the polypeptide composition of a protein for an oligomeric protein,and th
14、e spatial relationships between its subunits.Subunit（亚基（亚基）Each polypeptide chain in such a protein is called a subunit.Subunit is inactive when it exists alone.(III)Quaternary Structure 26Features:l Quarternary structure arises when two or more polypeptides join to form a proteinl Subunit is inacti
15、ve when it exists on its own.l Subunits are linked by secondary bonds（H-bonds,ionic interactions,and hydrophobic interactions）l If the peptide chains are linked by covalent bonds(disulfide bond)，it is not belong to quaternary structure.l Polypeptide chains can be in dimer,trimer.,as well as homo-or
16、hetero-form.For example,hemoglobin is composed of 4 polypeptide chainsLink to video27NH3 COO 2 NH3 COO 2 COO NH3 1COO NH3 1Asp HisArg Asp LysLys Asp ArgHis Asp94 146141 126 4040 126 141146 94Ionic Forces in Hemoglobin282930 Primary Structure：Peptide bond、Disulfide bond Secondary Structure：Hydrogen b
17、ond Tertiary Structure：Hydrophobic interaction Quaternary Structure：Ioni c bond (IV)Non-covalent Bonds stabilize Protein Structure31 Hydrogen bondA hydrogen atom is shared by two other atoms.H-donor:the atom to which H atom is more tightly attached,and the other is H-acceptor.32 Hydrophobic interact
18、ionNonpolar molecules tend to cluster together in water,that is,amino acids with nonpolar side chains cluster in the core of the protein,out of contact with water33 A charged group is able to attract another group of opposite charges.Ionic interaction34 The attraction between a pair of atoms increas
19、es as they come closer,until they are repelled by van der Waals contact distance.van der Waals force 35 Disulfide bridgeStrong covalent bonds between sulfur atoms in the amino acid cysteine36The folding of many proteins is protected by chaperonin proteins that shield out bad influences.Chaperon37Pos
20、t-translational Modification3839II.Structure-Function Relationship of Proteins Sequence of DNA Amino acid sequence of proteinConformation of ProteinFunction of ProteinPrimary structure is basis,Conformation is the key factor.401.The alternation of key AAs in a protein will cause the loss of its biol
21、ogical functions l Sickle cell anemia Abnormal hemoglobin,develop because of a single amino acid substitution.This is the first case of molecular disease identified in history(I)Primary Structure and Function41 HbA Val-His-Leu-Thr-Pro-Glu-Glu-LysHbS Val-His-Leu-Thr-Pro-Val-Glu-Lys4243 分子病分子病 相应蛋白质分子
22、的异常或缺失相应蛋白质分子的异常或缺失镰状细胞贫血镰状细胞贫血 血红蛋白血红蛋白家族性高胆固醇血症家族性高胆固醇血症 低密度脂蛋白受体低密度脂蛋白受体原发性痛风病原发性痛风病 磷酸核糖焦磷酸酶磷酸核糖焦磷酸酶白化病白化病 酪氨酸酶酪氨酸酶血友病血友病A与与B 凝血因子凝血因子与与重度联合免疫缺陷症重度联合免疫缺陷症(SCID)腺苷脱氨酶腺苷脱氨酶苯丙酮酸尿症苯丙酮酸尿症 苯丙氨酸羟化酶苯丙氨酸羟化酶蚕豆病蚕豆病 6-磷酸葡萄糖脱氢酶磷酸葡萄糖脱氢酶顽固性佝偻病顽固性佝偻病 25-羟维生素羟维生素D31-羟化酶羟化酶Lesch-Nyhan(自毁脸容自毁脸容)次黄嘌呤次黄嘌呤-鸟嘌呤磷酸鸟嘌呤磷酸
23、综合征综合征 核糖转移酶核糖转移酶 Molecular Disease分子病分子病Inherited diseases in which the manifestations are due to alterations in protein primary structure and function.The AA variation is due to the gene mutation.442.Proteins having similar amino acid sequences demonstrate the functional similarity.*InsulinA8A9 A1
24、0A30Human ThrSerIle ThrBovineAlaSerVal AlaSwineAlaSerIle AlaOvineAlaGlyVal Ala45ACTH(促肾上腺皮质激素促肾上腺皮质激素)and MSH(促黑激素促黑激素)have a same peptide segment,so ACTH also has the function of promoting melanogenesis.46Cytochrome C is a protein which can be found in all a e r o b i c o r g a n i s m s.Comparison
25、 of their primary structure can help t o u n d e r s t a n d t h e evolutionary relationship between different species.Organisms which are closer in the process of species evolution will have more similar primary structure of cytochrome C.47(II)Spatial structure and function Proteins will experience
26、 multiple processes to become correctly folded,that is,having a correct structure.The incorrect protein structure may lead to function alternation or diseases.A particular spatial structure of a protein is strongly correlated with its specific biological functions.481.Amphipathichelix1.Amphipathiche
27、lix492Ion ChannelHydrophobic amino acidHydrophobic amino acidHydrophilic amino acidCell Membrane2.The structural properties of silk are due to beta pleated sheets.The presence of so many hydrogen bonds makes each silk fiber stronger than steel.5051An effect that arises when the binding of an effecto
28、r molecule at the polymeric proteins allosteric site regulates protein activity as a result of conformational changes.1)Only proteins which have quaternary structure possess this property.2)Allosteric agents are small physiological molecules,such as O2、ATP3)Allosteric site is a site other than the p
29、roteins active site.4)Slightly change conformation can increase or decrease protein activity subsequently.3.Allosteric effect（变构效应（变构效应)5253The iron atom moves into the plane of the heme on oxygenation.Histidine F8 and its associated residues are pulled along with the iron atom.54The Allosteric Effe
30、ct of Hemoglobins55Schematic Diagram of Allosteric Effect of Hemoglobin56573.蛋白质构象改变可导致蛋白质构象改变可导致构象病构象病 Protein Conformational Disorders：A class of diseases in which certain proteins fail to fold into their normal conformation and lose their normal function,thereby disrupt the function of cells,tiss
31、ues and organs of the body.58 Pathogenic Mechanism：Some misfolding proteins aggregate and form anti-protease amyloidosis,and thereby cause disease.Diseases:Alzheimers disease,Parkinsons disease,prion disease,type 2 diabetes,amyloidosis59BSE is a transmissible,inheritable neurodegenerative diseases i
32、n mammals caused by prion protein(PrP,朊病毒蛋白).Normal PrP is rich in-helix，termed PrPc.PrPc is a normal constituent of brain tissue in all mammals.Abnormal PrP is rich in pleated sheet,termed PrPsc.A number of PrPsc aggregate extracellularly within the central nervous system to form plaques known as a
33、myloid,which destroy brain tissues by converting them to a spongy appearance disrupt and lead to brain damage and death.Bovine spongiform encephalopathy(BSE,疯牛病疯牛病)60 NH NH3 3+NH NH3 3+NH NH2 2 COOH COO COOH COO-COO COO-Positive IonPositive Ion ZwitterionZwitterion Negative IonNegative Ion （pHPI)pHP
34、I)P P PP P PIII.Physicochemical Properties of Protein(I)Ampholyte of protein1.+H+H+H+H+OH+OH+OH+OH612.pI of Protein：the pH at which a particular molecule carries no net electrical charge.3.The charge of protein is related to surroundings pH.pH PI negative ion pH=PI electric neutrality4.pI of most pr
35、otein is 5.0,and negatively charged in body fluid(pH7.4)pI 7.4:basic proteins:protamine,histone pI 7.4:acidic proteins:pepsin 62 Serum Protein Electrophoretogram_+2 1 63(II)Macromolecule Properties 1.Stability of Hydrophilic colloid is due to:Hydration Shell Electric Repulsion 2.Dialysis 3.Ultracent
36、rifugationMW:10,000 1,000,000Diameter:1100nm,in the range of colloid(III)UV absorption max：280nm（Tyr，Trp）64+Positive Charged ProteinPositive Charged ProteinNegative Charged ProteinNegative Charged Protein Protein in pI Protein in pIHydration ShellHydration Shell+Positive Charged ProteinPositive Char
37、ged ProteinNegative Charged ProteinNegative Charged ProteinUnstable ProteinUnstable ProteinacidacidbasebaseacidacidbasebaseacidacidbasebaseDehydrationDehydrationDehydrationDehydrationDehydrationDehydrationPrecipitation of ProteinPrecipitation of Protein65(IV)Denaturation（蛋白质的变性蛋白质的变性）1.DefinitionThe
38、 process in which a protein loses its native conformation under the treatment of denaturants.(1)Denaturants：physical:heat,ultraviolet light,violent shaking,chemical:strong acids,bases,organic solvents,detergents,(2)Nature of Denaturation：Broken of no covalent bonds Loss of spatial structure(3)Result
39、s：Change of physical and chemical properties Loss of biological activity662.Properties of denatured proteins（1）Loss of biological activity（2）Decrease of solubility（3）Change of physicochemical properties：Increase of viscosity,increase of UV absorption，easy to hydrolysis by protease3.Applications：Ster
40、ilization,preservation(low temperature)674.Renaturation复性复性Denatured proteins will regain their native structure and their biological activity if returned to conditions in which the native conformation is stable.This process is called renaturation.68Disulfide BondRenaturation of unfolded,denatured r
41、ibonucleaseair oxidation69DenaturationAllosteric EffectDenaturing agents are foreign materials,high intensity,no specificityAllosteric agents are physiological molecules,have specificityConformation is brokenConformation is slightly changedBiological activity is lostBiological activity is changedPhysicochemical properties are changed Physicochemical properties are not changedNot arise in normal cellsGeneral pattern of protein function regulation in normal cells
