Struktur dan Fungsi Protein g

Protein Structure
Primary (10)
Sequence of amino acids

Tertiary (30)
Grouping of secondary structures
Secondary structures coil and fold into layers y H and disulfide bonds

Secondary (20)
Twisting of chains into coiled structures
helix sheet

Quaternary (40)
Several tertiary structures linked Large complex proteins

H bonding

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Secondary Structure of protein y p

The term secondary structure refers to the local co o at o of some part of polypeptide. conformation o so e pa t o a po ypept de The discussion of secondary structure most usefully focuses on common regular folding patterns of the polypeptide backbone. backbone A few types of secondary structure are particularly stable and occur widely in proteins. The most prominent are the helix and conformations Using fundamental chemical principles and a few experimental observations, Pauling and Corey p p g y predicted the existence of these secondary structures in 1951, several years before the first complete protein structure was elucidated.

-helix
Is a Common Protein Secondary Structure The simplest arrangement the polypeptide chain could assume with its rigid peptide bonds (but other single bonds free to rotate) is a helical structure which Pauling and Corey structure, called the helix an helix makes optimal use of internal hydrogen bonds. The structure is stabilized by a hydrogen bond between the hydrogen atom attached to the nitrogen atom of a peptide linkage and the carbonyl oxygen atom of the fourth amino acid on the amino-terminal side of that peptide bond Within the helix, every peptide bond (except those close to each end of the helix) participates in such hydrogen bonding.

Knowing the Right Hand from the Left

There is a simple method for determining whether a helical structure is right-handed or left handed. left-handed Make fists of your two hands with thumbs outstretched and pointing straight up. Looking at your right hand, think of a helix spiraling up y p g p your right thumb in the g direction in which the other four fingers are curled as shown (counterclockwise). The resulting helix is right-handed. Your left hand will demonstrate a lefthanded helix, which rotates in the clockwise direction as it spirals up your thumb.

Not all polypeptides can form a stable helix. Interactions between amino acid side chains can stabilize or d t bili thi structure. i id id h i t bili destabilize this t t The twist of an helix ensures that critical interactions occur between an amino acid side chain and the side chain three (and sometimes four) f ) residues away on either side of it id ith id f it.

Interactions between R groups of amino acids three residues apart in an helix. An ionic interaction between Asp100 and Arg103 in an -helical region of the protein troponin

-sheet
In the conformation, the backbone of the polypeptide chain is extended into a zigzag rather than helical structure The zigzag polypeptide chains can be arranged side by side to form a structure resembling a series of pleats, -sheet hydrogen bonds are formed between adjacent segments of y g j g polypeptide chain The individual segments that form a sheet are usually nearby on the polypeptide chain, but can also be quite distant from each other in the linear sequence of th polypeptide; th may even b segments th li f the l tid they be t in different polypeptide chains. The adjacent polypeptide chains in a -sheet can be either parallel or antiparallel (having the same or opposite amino-to-carboxyl orientations, respectively). The structures are somewhat similar, although the repeat period is p (6.5 , versus 7 for , shorter for the parallel conformation ( antiparallel) and the hydrogen bonding patterns are different.

 Some protein structures limit the kinds of amino acids that can occur in the sheet. Wh two or more sheets are layered close t When t h t l d l together th within a protein, the R groups of the amino acid residues on the touching surfaces must be relatively small. Keratins s ch as silk fibroin and the fibroin of spider -Keratins such webs have a very high content of Gly and Ala residues, the two amino acids with the smallest R groups. Indeed in silk fibroin Gly and Ala alternate over large Indeed, parts of the sequence.

 turn -turn
In globular proteins, which have a compact folded structure, nearly one-third of the amino acid residues are i turns or l hi d f h i id id in loops where the h h polypeptide chain reverses direction These are the connecting elements that link successive runs of helix or conformation Particularly common are turns that conformation. -turns connect the ends of two adjacent segments of an antiparallel sheet g , The structure is a 1800 turn involving four amino acid residues, with the carbonyl oxygen of the first residue forming a hydrogen bond with the amino-group hydrogen of the fourth. The peptide groups of the central two residues do not participate in any i t interresidue h d id hydrogen b di bonding. Gly and Pro residues often occur in turns, the former because it is small and flexible, the latter because peptide bonds involving the imino nitrogen of proline readily assume the cis configuration

Protein Tertiary and Quaternary Structures

The overall three-dimensional arrangement of all atoms in a protein is referred to as the proteins tertiary structure protein s structure. tertiary structure includes longer-range aspects of amino acid sequence. Amino id th t A i acids that are f apart in th polypeptide sequence and th t far t i the l tid d that reside in different types of secondary structure may interact within the completely folded structure of a protein Interacting segments of polypeptide chains are h ld i th i I t ti t f l tid h i held in their characteristic tertiary positions by different kinds of weak bonding interactions (and sometimes by covalent bonds such as disulfide cross-links) between the segments segments. Some proteins contain two or more separate polypeptide chains, or subunits, which may be identical or different. The arrangement of these protein subunits in three-dimensional complexes constitutes quaternary structure.

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Fibrous proteins and globular proteins

Fibrous proteins, having polypeptide chains arranged in long strands or sheets and globular proteins having polypeptide sheets, proteins, chains folded into a spherical or globular shape. The two groups are structurally distinct: fibrous proteins usually consist largely of a single type of secondary structure; globular proteins often contain several types of secondary structure. The two groups differ functionally in that the structures that provide support, shape, and external protection to vertebrates are made of fibrous proteins, whereas most enzymes and regulatory p g y proteins are g globular p proteins. Certain fibrous proteins played a key role in the development of our modern understanding of protein structure and provide p particularly clear examples of the relationship between y p p structure and function.

Globular protein structures are compact and varied. Human serum albumin (Mr 64,500) has 585 residues in a single chain. ( ) g Given here are the approximate dimensions its single polypeptide chain would have if it occurred entirely in extended conformation or as an helix. Also shown is the size of the protein in its native globular form, as determined by X-ray crystallography; the polypeptide chain must be very very compactly folded to fit into these dimensions.

Myoglobin Provided Early Clues about the Complexity of Globular Protein Structure

(a) The polypeptide backbone, (b) A mesh image emphasizes the protein surface. (c) A surface contour image, (d) A ribbon representation, (e) A space-filling model with all amino acid side chain

Protein Denaturation and Folding

Renaturation of unfolded, denatured ribonuclease.

Urea is used to denature ribonuclease, and mercaptoethanol to reduce and thus cleave the disulfide bonds to yield eight Cys residues. Renaturation involves reestablishment of the correct disulfide cross-links.

A simulated folding pathway. The folding pathway of a 36 residue segment of pathway 36-residue the protein villin (an actin-binding protein found principally in the microvilli lining the intestine) was simulated by computer.

Biological Functions of Proteins

Principal organic chemical constituents of body organs and soft tissues Enormous functional diversity
Cell membrane structure and function Enzymes Hormones and other chemical messengers g Immune factors (antibodies) Fluid balance Acid-base Acid base balance Transport Source of energy and glucose

Enzymes
Proteins that catalyze (speed up) chemical reactions without being used up or destroyed in the process Anabolic (putting things together) and catabolic (breaking things down) functions Examples Digestion g Salivary amylase yp Trypsin

Hormones
Chemical messengers that are made in one part of the body but act on cells in other parts of the body N t th t "steroid Note that " t id hormones" are not proteins! Examples Insulin Some reproductive hormones

Receptors, Receptors Carriers

Transport materials across cell membranes

Transport Proteins
Transport substances in th b t i the blood
Lipoproteins (transport lipids) Hemoglobin g (transports oxygen and carbon dioxide)

Fluid Balance
Proteins in the blood help maintain appropriate fluid levels in the vascular system Fluid is forced into tissue spaces b bl d ti by blood pressure generated by pumping action of the heart h t Fluid returns to blood because of osmotic pressure

Acid-Base Balance
Body works to keep pH of blood near 7.45 H Homeostasis IMPORTANT t i Proteins help buffer blood to keep pH acceptable

Immune Function (Antibodies)

Antibodies are proteins that attach to and inactivate bacteria and viruses that cause infection

Source of Glucose
When excess protein is fed
Some amino acids converted to glucose which is converted to fat

Source of Energy
Proteins are the last to be used for energy!
Occurs in starvation and low carbohydrate diets y