分子生物学Chapter 2Protein Structure.docx

1、分子生物学Chapter 2 Protein Structure Chapter 2 Protein Structure IntroductionSizes and shapes of proteins Globlar proteins, including most enzymes, behave in solution like compact , roughly spherical particles. Fibrous proteins have a high axial ratio and are often of structural importance, for example

2、fibroin and keratin. Sizes range from a few thousand to several million Daltons. Some proteins contain bound nonprotein materials (prosthetic groups or other macromolecules), which accounts for the increased sizes and functionalities of the protein complexs.Shapes of proteinsGlobular proteins: enzym

3、esFibrous proteins: important structural proteins (silk fibroin, keratin in hair and wools )Chapter 2 Protein Structure 1. Aminp Acids R-CH(NH2)-COOHv a-carbon is chiral (asymmetric) except in glycine (R is H)v Amino acids can exit in both D- and L- stereoisomers, but only L-isomers are found in pro

4、teinsv Amino acids are dipolar ions (zwitterions) in aqueous solution and are amphoteric .v The side chains (R) differ in size, shape, charge and chemical reactivityv A few proteins contain nonstandard amino acids that are formed by post-translational modification of the parent amino acids.1.1 Amino

5、 acids with charged side chains“Basic” amino acids: containing positively charged groupsLysine (Lys, K): a second amino group attached to the e-carbon atomArginine (arg, R): a guanidino group attached to the d-carbon atom Histidine (His, H): a imidazole group has a pKa near neutrality. This group ca

6、n be reversibly protonated under physiological conditions, which contribute to the catalytic mechanism of many enzymes. 1.2. Amino acids with polar uncharged side chains (hydrophilic)-containing groups that form hydrogen bonds with waterSerine (Ser, S) & threonine (Thr, T) have hydroxyl groups. 1.3.

7、 Amino acids with nonpolar aliphatic side chains (hydrophobic )Alkyl side chains1.4. Amino acids with aromatic side chains (hydrophobic )2. Primary structure Amino acids are linked by peptide bonds between alpha-carboxyl and alpha-amino groups. The resulting polypeptide sequence has an N terminus an

8、d a C terminus. Polypeptides commonly have between 100 and 1500 amino acids linked in this wayFormation of a peptide bond (shaded in gray) in a dipeptide. v The amino acid in a peptide is also called a residue. The smallest amino acid, glycine, has a single hydrogen atom as its R group. Its small si

9、ze allows it to fit into tight spaces. Unlike any of the other common amino acids, proline has a cyclic ring that is produced by formation of a covalent bond between its R group and the amino group on C. Proline is very rigid, and its presence creates a fixed kink in a protein chain. Proline and gly

10、cine are sometimes found at points on a proteins surface where the chain loops back into the protein3. Secondary Structure v Secondary structure refers to the localized organization of parts of a polypeptide chain, which can assume several different spatial arrangements. A single polypeptide may exh

11、ibit all types of secondary structure. Without any stabilizing interactions, a polypeptide assumes a random-coil structure. 3.1 Model of the a helix. The polypeptide backbone is folded into a spiral that is held in place by hydrogen bonds (black dots) between backbone oxygen atoms and hydrogen atoms

12、. All the hydrogen bonds have the same polarity. The outer surface of the helix is covered by the side-chain R groups.a-helixevery 3.6 residues make one turn, the distance between two turns is 0.54 nm, the C=O (or N-H) of one turn is hydrogen bonded to N-H (or C=O) of the neighboring 3.2 Beta Strand

13、 and Beta Sheet v In a strand, the torsion angle of N-C-C-N in the backbone is about 120 degrees. The following figure shows the conformation of an ideal strand. Note that the sidechains of two neighboring residues project in the opposite direction from the backbone. Beta sheetv A sheet consists of

14、two or more hydrogen bonded strands. The two neighboring strands may be parallel if they are aligned in the same direction from one terminus (N or C) to the other, or anti-parallel if they are aligned in the opposite direction.b SHEETS. (a) A simple two-stranded b sheet with antiparallel b strands.

15、A sheet is stabilized by hydrogen bonds (black dots) between the b strands. The planarity of the peptide bond forces a b sheet to be pleated; hence, this structure is also called a b pleated sheet, or simply a pleated sheet. (b) Side view of a b sheet showing how the R groups protrude above and belo

16、w the plane of the sheet. (c) Model of binding site in class I MHC (major histocompatibility complex) molecules, which are involved in graft rejection. A sheet comprising eight antiparallel b strands (green) forms the bottom of the binding cleft, which is lined by a pair of a helices (blue). A disul

17、fide bond is shown as two connected yellow spheres. The MHC binding cleft is large enough to bind a peptide 8 10 residues long.3.3 Turns Composed of three or four residues, turns are compact, U-shaped secondary structures stabilized by a hydrogen bond between their end residues. They are located on

18、the surface of a protein, forming a sharp bend that redirects the polypeptide backbone back toward the interior. Glycine and proline are commonly present in turns.4. Tertiary Structurev Tertiary structure, the next-higher level of structure, refers to the overall conformation of a polypeptide chain,

19、 that is, the three-dimensional arrangement of all the amino acids residues. In contrast to secondary structure, which is stabilized by hydrogen bonds, tertiary structure is stabilized by hydrophobic interactions between the nonpolar side chains and, in some proteins, by disulfide bonds. These stabi

20、lizing forces hold the helices, strands, turns, and random coils in a compact internal scaffold The ribbon representation of the 3D structure of RNase A. v Noncovalent interaction between side chains that hold the tertiary structure together: van der Waals forces, hydrogen bonds, electrostatic salt

21、bridges, hydrophobic interactionsv Covalent interaction: disulfide bondsv Denaturation of protein by disruption of its 2o and 3o structure will lead to a random coil conformation5. Quaternary structureMany proteins are composed of two or more polypeptide chains (subunits). These subunits may be iden

22、tical or different. The same forces which stabilize tertiary structure hold these subunits together. This level of organization called quaternary structure.Prosthetic groupsv Prosthetic groups covalently or noncovalently attached to many conjugated proteins, and give the proteins chemical functional

23、ity. Many are co-factors in enzyme reactions.v Examples : heme groups in hemogobin Organization of the catabolite activator protein (CAP)6. Domains, motifs and families6.1 Protein Motifs v A motif is a characteristic domain structure consisting of two or more helices or strands. v Common examples in

24、clude coiled coil, helix-turn-helix helix-loop-helix, zinc finger, leucine zipper etc. v Many proteins contain one or more motifs built from particular combinations of secondary structures. v A motif is defined by a specific combination of secondary structures that has a particular topology and is o

25、rganized into a characteristic three-dimensional structure. Structural motifs: Groupings of secondary structural elements that frequently occur in globular proteins Often have functional significance and represent the essential parts of binding or catalytic sites conserved among a protein family Rep

26、resent the best solution to a structural-functional requirement motif6.2 Domains: Structurally independent units of many proteins, connected by sections with limited higher order structure within the same polypeptide.They can also have specific function such as substrate bindingFunctional Domains v

27、Domains sometimes are defined in functional terms based on observations that the activity of a protein is localized to a small region along its length. For instance, a particular region or regions of a protein may be responsible for its catalytic activity (e.g., a kinase domain) or binding ability (

28、e.g., a DNA-binding domain, membrane-binding domain). Modules:v The organization of tertiary structure into domains further illustrates the principle that complex molecules are built from simpler components. Like secondary-structure motifs, tertiary-structure domains are incorporated as modules into

29、 different proteins, thereby modifying their functional activities. The modular approach to protein architecture is particularly easy to recognize in large proteins, which tend to be a mosaic of different domains and thus can perform different functions simultaneously Schematic diagrams of various p

30、roteins, illustrating their modular nature. v Epidermal growth factor (EGF) is generated by proteolytic cleavage of a precursor protein containing multiple EGF domains (orange). The EGF domain also occurs in Neu protein and in tissue plasminogen activator (TPA). Other domains, or modules, in these p

31、roteins include a chymotryptic domain (purple), an immunoglobulin domain (green), a fibronectin domain (yellow), a membrane-spanning domain (pink), and a kringle domain (blue). 6.3 Protein families: Structurally and functionally related proteins from different sourcesEvolutionary tree showing how th

32、e globin protein family arose, starting from the most primitive oxygen-binding proteins, leghemoglobins, in plants. Sequence comparisons have revealed that evolution of the globin proteins parallels the evolution of vertebrates. Major junctions occurred with the divergence of myoglobin from hemoglobin and the later divergence of hemoglobin into the a and b subunits.Domains, motif