Biochemistry, 4th Edition P22 pps

The way in which separate folded monomeric protein subunits associate to form the oligomeric protein constitutes the quaternary struc-ture of that protein.. Oligomeric associations of p

6.5 How Do Protein Subunits Interact at the Quaternary

Level of Protein Structure?

Many proteins exist in nature as oligomers, complexes composed of (often

sym-metric) noncovalent assemblies of two or more monomer subunits In fact, subunit

association is a common feature of macromolecular organization in biology Most

intracellular enzymes are oligomeric and may be composed either of a single type

of monomer subunit (homomultimers) or of several different kinds of subunits

(het-eromultimers) The simplest case is a protein composed of identical subunits Liver

al-cohol dehydrogenase, shown in Figure 6.41, is such a protein Alal-cohol consumed in

a beer or mixed drink is oxidized in the liver by alcohol dehydrogenase Hormonal

signals modulate blood sugar levels by controlling the activity of glycogen

phos-phorylase, an elegantly regulated homodimeric muscle enzyme Oxygen is carried

in the blood by hemoglobin, which contains two each of two different subunits

(het-erotetramer) A counterpoint to these small clusters is made by the proteins that form

large polymeric aggregates Proteins are synthesized on large complexes of many

pro-tein units and several RNA molecules called ribosomes Muscle contraction depends

on large polymer clusters of the protein myosin sliding along filamentous polymers

of another protein, actin The way in which separate folded monomeric protein

subunits associate to form the oligomeric protein constitutes the quaternary

struc-ture of that protein Table 6.3 lists several proteins and their subunit compositions

(see also Table 4.2) Proteins with two to four subunits predominate in nature, but

many cases of higher numbers exist.

The subunits of an oligomeric protein typically fold independently and then

in-teract with other subunits The surfaces at which subunits inin-teract are similar in

na-ture to the interiors of the individual subunits—closely packed with both polar and

hydrophobic interactions Interacting surfaces must therefore possess

complemen-tary arrangements of polar and hydrophobic groups.

Oligomeric associations of protein subunits can be divided into those between

identical subunits and those between nonidentical subunits Interactions among

identical subunits can be further distinguished as either isologous or heterologous.

In isologous interactions, the interacting surfaces are identical and the resulting

structure is necessarily dimeric and closed, with a twofold axis of symmetry (Figure

6.42) If any additional interactions occur to form a trimer or tetramer, these must

use different interfaces on the protein’s surface Many proteins, such as

transthy-retin, form tetramers by means of two sets of isologous interactions (Figure 6.43).

Such structures possess three different twofold axes of symmetry In contrast,

het-erologous associations among subunits involve nonidentical interfaces These

sur-faces must be complementary, but they are generally not symmetric.

FIGURE 6.41 The quaternary structure of liver alcohol dehydrogenase Within each subunit is a six-stranded

parallel sheet Between the two subunits is a two-stranded antiparallel sheet (pdb id  1CDO).(Jane Richardson.)

Number of

Triose phosphate isomerase 2

Bacteriochlorophyll protein 3

Glyceraldehyde-3-phosphate 4 dehydrogenase

Aspartate transcarbamoylase 6 6

Coat of tomato bushy stunt 180 virus

TABLE 6.3 Aggregation Symmetries

of Globular Proteins

There Is Symmetry in Quaternary Structures

Many multimeric proteins are symmetric arrangements of asymmetric objects (the monomer subunits) All of the polypeptide’s -carbons are asymmetric, and the

polypeptide nearly always folds to form a low-symmetry structure (The long helical arrays formed by some synthetic polypeptides are an exception.) Thus, protein sub-units do not have mirror reflection planes, points, or axes of inversion The only metry operation possible for protein subunits is a rotation The most common sym-metries observed for multisubunit proteins are cyclic symmetry and dihedral

symmetry In cyclic symmetry, the subunits are arranged around a single rotation

axis, as shown in Figure 6.44 If there are two subunits, the axis is referred to as a

twofold rotation axis Rotating the quaternary structure 180° about this axis gives a

structure identical to the original one With three subunits arranged about a three-fold rotation axis, a rotation of 120° about that axis gives an identical structure

Dihedral symmetry occurs when a structure possesses at least one twofold rotation

axis perpendicular to another n-fold rotation axis This type of subunit arrangement (Figure 6.44) occurs in annexin XII (where n  3).

Quaternary Association Is Driven by Weak Forces

Weak forces stabilize quaternary structures Typical dissociation constants for simple two-subunit associations range from 108to 1016M These values correspond to free

energies of association of about 50 to 100 kJ/mol at 37°C Dimerization of subunits is accompanied by both favorable and unfavorable energy changes The favorable in-teractions include van der Waals inin-teractions, hydrogen bonds, ionic bonds, and hy-drophobic interactions However, considerable entropy loss occurs when subunits in-teract When two subunits move as one, three translational degrees of freedom are lost for one subunit because it is constrained to move with the other one In addition,

(b) Heterologous association (d) Isologous tetramer

Symmetry axis

FIGURE 6.42 Isologous and heterologous associations between protein subunits (a) An isologous interaction be-tween two subunits with a twofold axis of symmetry perpendicular to the plane of the page (b) A heterologous interaction that could lead to the formation of a long polymer (c) A heterologous interaction leading to a closed structure—a tetramer (d) A tetramer formed by two sets of isologous interactions.

Monomer A

Monomer A

Monomer B

Monomer B

Monomer A Monomer B

(a)

(b)

FIGURE 6.43 Many proteins form tetramers by means of

two sets of isologous interactions The dimeric (a) and

tetrameric (b) forms of transthyretin (also known as

prealbumin) are shown here (pdb id  1GKE).The

monomers of this protein form a dimer in a manner that

extends the large monomer -sheet.The tetramer is

formed by isologous interactions between the large

-sheets of two dimers.

B anthracis dihydrodipicolinate

synthase (pdb id = 1XL9)

Pentamer Shiga-like toxin I B (pdb id = 1CZG)

Trimer

E blattae acid phosphatase

(pdb id = 2EOI)

Dimer

ARNT PAS-B

(pdb id = 2HV1)

Bundled hexamer Uridylate kinase (pdb id = 2A1F)

Trimer of dimers Annexin XII (pdb id = 1DM5)

Cyclic hexamer

Circadian clock protein KaiC

(pdb id = 1TF7)

Octamer

Limulus polyphemus SAP-like pentraxin

(pdb id = 1QTJ)

Heptamer

M tuberculosis chaperonin-10

(pdb id = 1HX5)

Dodecamer

Lactococcus lactis MG1363 DpsB protein

(pdb id = 1ZS3)

FIGURE 6.44 Multimeric proteins are symmetric arrangements of asymmetric objects A variety of symmetries is

displayed in these multimeric structures

units must involve approximately 130 to 220 kJ/mol of favorable interactions.1Van der Waals interactions at protein interfaces are numerous, often running to several hundred for a typical monomer–monomer association This would account for about

150 to 200 kJ/mol of favorable free energy of association However, when solvent is removed from the protein surface to form the subunit–subunit contacts, nearly as many van der Waals associations are lost as are made One subunit is simply trading water molecules for peptide residues in the other subunit As a result, the energy of subunit association due to van der Waals interactions actually contributes little to the stability of the dimer Hydrophobic interactions at the subunit–subunit interface, however, are generally very favorable For many proteins, the subunit association process effectively buries as much as 20 nm2of surface area previously exposed to sol-vent, resulting in as much as 100 to 200 kJ/mol of favorable hydrophobic interactions Together with whatever polar interactions occur at the protein–protein interface, this

is sufficient to account for the observed stabilization that occurs when two protein subunits associate.

An additional and important factor contributing to the stability of subunit asso-ciations for some proteins is the formation of disulfide bonds between different sub-units All antibodies are 22-tetramers composed of two heavy chains (53 to 75 kD)

and two light chains (23 kD) In addition to intrasubunit disulfide bonds (four per heavy chain, two per light chain), two intersubunit disulfide bridges hold the two

heavy chains together and a disulfide bridge links each of the two light chains to

a heavy chain (Figure 6.45).

1For example, 130 kJ/mol of favorable interaction minus 80 kJ/mol of unfavorable interaction equals

a net free energy of association of 50 kJ/mol

S S

S S

S S

S S

S S

S S

S S

S S

N N

S S S S

SS

S

C (CH2O)n addition site

C

CH2 CH3 446

CH1

VH

VL

CL

Hinge region

N

NHeavy Light

214

Antigen binding

Antigen binding

4.5 nm

FIGURE 6.45 Schematic drawing of an immunoglobulin molecule, showing the intermolecular and intra-molecular disulfide bonds Two identical L chains are joined with two identical H chains Each L chain is held to

an H chain via an interchain disulfide bond The variable regions of the four polypeptides lie at the ends of the arms of the Y-shaped molecule These regions are responsible for the antigen recognition function of antibody molecules For purposes of illustration, some features are shown on only one or the other L chain or H chain, but all features are common to both chains

Open Quaternary Structures Can Polymerize

All of the quaternary structures we have considered to this point have been closed

structures, with a limited capacity to associate Many proteins in nature associate to

form open heterologous structures, which can polymerize more or less indefinitely,

creating structures that are both esthetically attractive and functionally important to

the cells or tissue in which they exist One such protein is tubulin, the -dimeric

protein that polymerizes into long, tubular structures that are the structural basis

of cilia, flagella, and the cytoskeletal matrix The microtubule thus formed (Figure

6.46) may be viewed as consisting of 13 parallel filaments arising from end-to-end

aggregation of the tubulin dimers Human immunodeficiency virus, HIV, the

causative agent of AIDS (also discussed in Chapter 14), is enveloped by a spherical

shell composed of hundreds of coat protein subunits, a large-scale, but closed,

qua-ternary association.

There Are Structural and Functional Advantages

to Quaternary Association

There are several important consequences when protein subunits associate in

oligomeric structures.

Stability One general benefit of subunit association is a favorable reduction of

the protein’s surface-to-volume ratio The surface-to-volume ratio becomes smaller

as the radius of any particle or object becomes larger (This is because surface area

is a function of the radius squared and volume is a function of the radius cubed.)

Because interactions within the protein usually tend to stabilize the protein

ener-getically and because the interaction of the protein surface with solvent water is

of-ten energetically unfavorable, decreased surface-to-volume ratios usually result in

more stable proteins Subunit association may also serve to shield hydrophobic

residues from solvent water Subunits that recognize either themselves or other

sub-units avoid any errors arising in genetic translation by binding mutant forms of the

subunits less tightly.

Genetic Economy and Efficiency Oligomeric association of protein monomers is

genetically economical for an organism Less DNA is required to code for a

monomer that assembles into a homomultimer than for a large polypeptide of the

same molecular mass Another way to look at this is to realize that virtually all of

the information that determines oligomer assembly and subunit–subunit

interac-tion is contained in the genetic material needed to code for the monomer For

ex-ample, HIV protease, an enzyme that is a dimer of identical subunits, performs a

catalytic function similar to homologous cellular enzymes that are single

polypep-tide chains of twice the molecular mass (see Chapter 14).

A DEEPER LOOK

Immunoglobulins—All the Features of Protein Structure Brought Together

The immunoglobulin structure in Figure 6.45 represents the

con-fluence of all the details of protein structure that have been thus

far discussed As for all proteins, the primary structure determines

other aspects of structure There are numerous elements of

sec-ondary structure, including -sheets and tight turns The tertiary

structure consists of 12 distinct domains, and the protein adopts a

heterotetrameric quaternary structure To make matters more

in-teresting, both intrasubunit and intersubunit disulfide linkages act

to stabilize the discrete domains and to stabilize the tetramer itself

One more level of sophistication awaits As discussed in

Chap-ter 28, the amino acid sequences of both light and heavy

immuno-globulin chains are not constant! Instead, the primary structure of these chains is highly variable in the N-terminal regions (first 108 residues) Heterogeneity of the amino acid sequence leads to vari-ations in the conformation of these variable regions This variation accounts for antibody diversity and the ability of antibodies to rec-ognize and bind a virtually limitless range of antigens This full po-tential of antibody⬊antigen recognition enables organisms to mount immunological responses to almost any antigen that might challenge the organism

8.0 nm

3.5- to 4.0-nm subunit

α β

FIGURE 6.46 The structure of a typical microtubule, showing the arrangement of the - and -monomers of

the tubulin dimer

Bringing Catalytic Sites Together Many enzymes (see Chapters 13 to 15) derive

at least some of their catalytic power from oligomeric associations of monomer sub-units This can happen in several ways The monomer may not constitute a com-plete enzyme active site Formation of the oligomer may bring all the necessary cat-alytic groups together to form an active enzyme For example, the active sites of bacterial glutamine synthetase are formed from pairs of adjacent subunits The dis-sociated monomers are inactive.

Oligomeric enzymes may also carry out different but related reactions on differ-ent subunits Thus, tryptophan synthase is a tetramer consisting of pairs of differdiffer-ent subunits, 22 Purified -subunits catalyze the following reaction:

Indoleglycerol phosphate34indole  glyceraldehyde-3-phosphate and the -subunits catalyze this reaction:

Indole L-serine34L-tryptophan Indole, the product of the -reaction and the reactant for the -reaction, is passed

directly from the -subunit to the -subunit and cannot be detected as a free

inter-mediate.

Cooperativity There is another, more important consequence when monomer subunits associate into oligomeric complexes Most oligomeric enzymes regulate catalytic activity by means of subunit interactions, which may give rise to coopera-tive phenomena Multisubunit proteins typically possess multiple binding sites for a given ligand If the binding of ligand at one site changes the affinity of the protein

for ligand at the other binding sites, the binding is said to be cooperative Infor-mation transfer in this manner across long distances in proteins is termed allostery,

literally “action at another site.” Increases in affinity at subsequent sites represent positive cooperativity, whereas decreases in affinity correspond to negative cooper-ativity The points of contact between protein subunits provide a mechanism for this signal transduction through the protein structure and for communication between the subunits This in turn provides a way in which the binding of ligand to one sub-unit can influence the binding behavior at the other subsub-units Such cooperative be-havior, discussed in greater depth in Chapter 15, is the underlying mechanism for regulation of many biological processes.

Insulin is a peptide hormone secreted by the pancreas that

regu-lates glucose metabolism in the body Insufficient production of

insulin or failure of insulin to stimulate target sites in liver, muscle,

and adipose tissue leads to the serious metabolic disorder known

as diabetes mellitus Diabetes afflicts millions of people worldwide.

Diabetic individuals typically exhibit high levels of glucose in the

blood, but insulin injection therapy allows these individuals to

maintain normal levels of blood glucose

Insulin is composed of two peptide chains covalently linked by

disulfide bonds (see Figure 5.8) This “monomer” of insulin is

the active form that binds to receptors in target cells However,

in solution, insulin spontaneously forms dimers, which

them-selves aggregate to form hexamers The surface of the insulin

molecule that self-associates to form hexamers is also the surface

that binds to insulin receptors in target cells Thus, hexamers of

insulin are inactive

Insulin released from the pancreas is monomeric and acts

rapidly at target tissues However, when insulin is administered (by

injection) to a diabetic patient, the insulin hexamers dissociate

slowly and the patient’s blood glucose levels typically drop slowly

(over several hours)

In 1988, G Dodson showed that insulin could be genetically engineered to prefer the monomeric (active) state Dodson and his colleagues used recombinant DNA technology (discussed in Chapter 12) to produce insulin with an aspartate residue replac-ing a proline at the contact interface between adjacent subunits The negative charge on the Asp side chain creates electrostatic repulsion between subunits and increases the dissociation con-stant for the hexamer 34 monomer equilibrium Injection of this mutant insulin into test animals produced more rapid de-creases in blood glucose than did ordinary insulin This mutant in-sulin, marketed by the Danish pharmaceutical company Novo as NovoLog in the United States and as NovoRapid in Europe, may eventually replace ordinary insulin in the treatment of diabetes NovoLog has a faster rate of absorption, a faster onset of action, and a shorter duration of action than regular human insulin It is particularly suited for mealtime dosing to control postprandial glycemia, the rise in blood sugar following consumption of food Regular human insulin acts more slowly, so patients must usually administer it 30 minutes before eating

6.1 What Noncovalent Interactions Stabilize Protein Structure?

Sev-eral different kinds of noncovalent interactions are of vital importance in

protein structure Hydrogen bonds, hydrophobic interactions,

electrosta-tic bonds, and van der Waals forces are all noncovalent in nature yet are

extremely important influences on protein conformations The

stabiliza-tion free energies afforded by each of these interacstabiliza-tions are highly

de-pendent on the local environment within the protein

Hydrogen bonds are generally made wherever possible within a

given protein structure Hydrophobic interactions form because

non-polar side chains of amino acids and other nonnon-polar solutes prefer to

cluster in a nonpolar environment rather than to intercalate in a polar

solvent such as water Electrostatic interactions include the attraction

between opposite charges and the repulsion of like charges in the

pro-tein Van der Waals interactions involve instantaneous dipoles and

in-duced dipoles that arise because of fluctuations in the electron charge

distributions of adjacent nonbonded atoms

6.2 What Role Does the Amino Acid Sequence Play in Protein

Struc-ture? All of the information necessary for folding the peptide chain

into its “native” structure is contained in the amino acid sequence of the

peptide Just how proteins recognize and interpret the information that

is stored in the polypeptide sequence is not yet well understood It may

be assumed that certain loci along the peptide chain act as nucleation

points, which initiate folding processes that eventually lead to the

cor-rect structures Regardless of how this process operates, it must take the

protein correctly to the final native structure, without getting trapped in

a local energy-minimum state, which, although stable, may be different

from the native state itself

6.3 What Are the Elements of Secondary Structure in Proteins, and

How Are They Formed? Secondary structure in proteins forms so as to

maximize hydrogen bonding and maintain the planar nature of the

peptide bond Secondary structures include -helices, -sheets, and

tight turns

6.4 How Do Polypeptides Fold into Three-Dimensional Protein Struc-tures? First, secondary structures—helices and sheets—form when-ever possible as a consequence of the formation of large numbers of hy-drogen bonds Second, -helices and -sheets often associate and pack

close together in the protein There are a few common methods for such packing to occur Third, because the peptide segments between secondary structures in the protein tend to be short and direct, the pep-tide does not execute complicated twists and knots as it moves from one region of a secondary structure to another A consequence of these three principles is that protein chains are usually folded so that the sec-ondary structures are arranged in one of a few common patterns For this reason, there are families of proteins that have similar tertiary struc-ture, with little apparent evolutionary or functional relationship among them Finally, proteins generally fold so as to form the most stable struc-tures possible The stability of most proteins arises from (1) the forma-tion of large numbers of intramolecular hydrogen bonds and (2) the re-duction in the surface area accessible to solvent that occurs upon folding

6.5 How Do Protein Subunits Interact at the Quaternary Level of Protein Structure? The subunits of an oligomeric protein typically fold into ap-parently independent globular conformations and then interact with other subunits The particular surfaces at which protein subunits interact are similar in nature to the interiors of the individual subunits These terfaces are closely packed and involve both polar and hydrophobic in-teractions Interacting surfaces must therefore possess complementary arrangements of polar and hydrophobic groups

PROBLEMS

Preparing for an exam? Create your own study path for this

chapter at www.cengage.com/login

1.The central rod domain of a keratin protein is approximately

312 residues in length What is the length (in Å) of the keratin

rod domain? If this same peptide segment were a true -helix,

how long would it be? If the same segment were a -sheet, what

would its length be?

2.A teenager can grow 4 inches in a year during a “growth spurt.”

As-suming that the increase in height is due to vertical growth of

col-lagen fibers (in bone), calculate the number of colcol-lagen helix turns

synthesized per minute

3.Discuss the potential contributions to hydrophobic and van der

Waals interactions and ionic and hydrogen bonds for the side

chains of Asp, Leu, Tyr, and His in a protein

4.Pro is the amino acid least commonly found in -helices but most

commonly found in -turns Discuss the reasons for this behavior.

5.For flavodoxin (pdb id  5NLL), identify the right-handed

cross-overs and the left-handed cross-cross-overs in the parallel -sheet.

6.Choose any three regions in the Ramachandran plot and discuss

the likelihood of observing that combination of and  in a

pep-tide or protein Defend your answer using suitable molecular

mod-els of a peptide

7.A new protein of unknown structure has been purified Gel

filtra-tion chromatography reveals that the native protein has a

molecu-lar weight of 240,000 Chromatography in the presence of 6 M

guanidine hydrochloride yields only a peak for a protein of M r

60,000 Chromatography in the presence of 6 M guanidine

hydro-chloride and 10 mM -mercaptoethanol yields peaks for proteins of

M r34,000 and 26,000 Explain what can be determined about the

structure of this protein from these data

8. Two polypeptides, A and B, have similar tertiary structures, but A normally exists as a monomer, whereas B exists as a tetramer, B4 What differences might be expected in the amino acid composition

of A versus B?

9. The hemagglutinin protein in influenza virus contains a remarkably long-helix, with 53 residues.

a How long is this -helix (in nm)?

b How many turns does this helix have?

c Each residue in an -helix is involved in two H bonds How many

H bonds are present in this helix?

10. It is often observed that Gly residues are conserved in proteins to a greater degree than other amino acids From what you have learned

in this chapter, suggest a reason for this observation

11. Which amino acids would be capable of forming H bonds with a lysine residue in a protein?

12. Poly-L-glutamate adopts an -helical structure at low pH but

becomes a random coil above pH 5 Explain this behavior

13. Imagine that the dimensions of the alpha helix were such that there were exactly 3.5 amino acids per turn, instead of 3.6 What would be the consequences for coiled-coil structures?

Preparing for the MCAT Exam

14. Consider the following peptide sequences:

EANQIDEMLYNVQCSLTTLEDTVPW LGVHLDITVPLSWTWTLYVKL QQNWGGLVVILTLVWFLM CNMKHGDSQCDERTYP YTREQSDGHIPKMNCDS AGPFGPDGPTIGPK

d The helical portions of a protein found in your hair

15. To fully appreciate the elements of secondary structure in proteins,

it is useful to have a practical sense of their structures On a piece

of paper, draw a simple but large zigzag pattern to represent a

tions along the coil and indicating the locations of the R groups in your drawing

16.The dissociation constant for a particular protein dimer is 1 micro-molar Calculate the free energy difference for the monomer to dimer transition

FURTHER READING

General

Branden, C., and Tooze, J., 1991 Introduction to Protein Structure New

York: Garland Publishing

Chothia, C., 1984 Principles that determine the structure of proteins

Annual Review of Biochemistry 53:537–572.

Fink, A., 2005 Natively unfolded proteins Current Opinion in Structural

Biology 15:35-41.

Greene, L., Lewis, T., Addou, S., et al., 2006 The CATH domain

struc-ture database: New protocols and classification levels give a more

comprehensive resource for exploring evolution Nucleic Acids

Re-search 35:D291–D297.

Hardie, D G., and Coggins, J R., eds., 1986 Multidomain Proteins:

Struc-ture and Evolution New York: Elsevier.

Harper, E., and Rose, G D., 1993 Helix stop signals in proteins and

peptides: The capping box Biochemistry 32:7605–7609.

Judson, H F., 1979 The Eighth Day of Creation New York: Simon and

Schuster

Lupas, A., 1996 Coiled coils: New structures and new functions Trends

in Biochemical Sciences 21:375–382.

Petsko, G., and Ringe, D., 2004 Protein Structure and Function London:

New Science Press

Richardson, J S., 1981 The anatomy and taxonomy of protein

struc-ture Advances in Protein Chemistry 34:167–339.

Schulze, A J., Huber, R., Bode, W., and Engh, R A., 1994 Structural

as-pects of serpin inhibition FEBS Letters 344:117–124.

Smith, T., 2000 Structural Genomics—special supplement Nature

Struc-tural Biology Volume 7, Issue 11S This entire supplemental issue is

devoted to structural genomics and contains a trove of information

about this burgeoning field

Tompa, P., 2002 Intrinsically unstructured proteins Trends in

Biochemi-cal Sciences 27:527–533.

Tompa, P., Szasz, C., and Buday, L., 2005 Structural disorder throws new

light on moonlighting Trends in Biochemical Sciences 30:484–489.

Uversky, V N., 2002 Natively unfolded proteins: A point where biology

waits for physics Protein Science 11:739–756.

Webster, D M., 2000 Protein Structure Prediction—Methods and Protocols.

New Jersey: Humana Press

Protein Folding

Aurora, R., Creamer, T., Srinivasan, R., and Rose, G D., 1997 Local

in-teractions in protein folding: Lessons from the -helix The Journal

of Biological Chemistry 272:1413–1416.

Baker, D., 2000 A surprising simplicity to protein folding Nature 405:

39–42

Creighton, T E., 1997 How important is the molten globule for correct

protein folding? Trends in Biochemical Sciences 22:6–11.

Deber, C M., and Therien, A G., 2002 Putting the -breaks on

mem-brane protein misfolding Nature Structural Biology 9:318–319.

Dill, K A., and Chan, H S., 1997 From Levinthal to pathways to

fun-nels Nature Structural Biology 4:10–19.

Dinner, A R., Sali, A., Smith, L J., Dobson, C M., and Karplus, M., 2001

Understanding protein folding via free-energy surfaces from theory

and experiment Trends in Biochemical Sciences 25:331–339.

Han, J.-H., Batey, S., Nickson, A., et al., 2007 The folding and evolution

of multidomain proteins Nature Reviews Molecular Cell Biology 8:

319–330

Kelly, J., 2005 Structural biology: Form and function instructions

Nature 437:486–487.

Mirny, L., and Shakhnovich, E., 2001 Protein folding theory: From

lat-tice to all-atom models Annual Review of Biophysics and Biomolecular

Structure 30:361–396.

Mok, K., Kuhn, L., Goez, M., et al., 2007 A pre-existing hydrophobic

collapse in the unfolded state of an ultrafast folding protein Nature

447:106–109

Murphy, K P., 2001 Protein Structure, Stability, and Folding New Jersey:

Humana Press

Myers, J K., and Oas, T G., 2002 Mechanisms of fast protein folding

Annual Review of Biochemistry 71:783–815.

Orengo, C., and Thornton, J., 2005 Protein families and their evolution—

a structural perspective Annual Review of Biochemistry 74:867–900.

Radford, S E., 2000 Protein folding: Progress made and promises

ahead Trends in Biochemical Sciences 25:611–618.

Raschke, T M., and Marqusee, S., 1997 The kinetic folding intermedi-ate of ribonuclease H resembles the acid molten globule and

par-tially unfolded molecules detected under native conditions Nature

Structural Biology 4:298–304.

Srinivasan, R., and Rose, G D., 1995 LINUS: A hierarchic procedure to

predict the fold of a protein Proteins: Structure, Function and Genetics

22:81–99

Secondary Structure

Xiong, H., Buckwalter, B., Shieh, H., and Hecht, M H., 1995 Periodic-ity of polar and nonpolar amino acids is the major determinant of

secondary structure in self-assembling oligomeric peptides

Proceed-ings of the National Academy of Sciences 92:6349–6353.

Structural Studies

Bradley, P., Misura, K., and Baker, D., 2005 Toward high-resolution de

novo structure prediction for small proteins Science 309:1868–1871.

Hadley, C., and Jones, D., 1999 A systematic comparison of protein

struc-ture classifications: SCOP, CATH, and FSSP Strucstruc-ture 7:1099–1112.

Lomas, D., Belorgey, D., Mallya, M., et al., 2005 Molecular mousetraps

and the serpinopathies Biochemical Society Transactions 33 (part 2):

321–330

Wagner, G., Hyberts, S., and Havel, T., 1992 NMR structure determina-tion in soludetermina-tion: A critique and comparison with X-ray

crystallogra-phy Annual Review of Biophysics and Biomolecular Structure 21:167–242.

Wand, A J., 2001 Dynamic activation of protein function: A view

emerg-ing from NMR spectroscopy Nature Structural Biology 8:926–931.

Diseases of Protein Folding

Bucchiantini, M., et al., 2002 Inherent toxicity of aggregates implies a

common mechanism for protein misfolding diseases Nature 416:

507–511

Sifers, R M., 1995 Defective protein folding as a cause of disease

Na-ture Structural Biology 2:355–367.

Stein, P E., and Carrell, R W., 1995 What do dysfunctional serpins tell

us about molecular mobility and disease? Nature Structural Biology

2:96–113

Thomas, P J., Qu, B-H and Pedersen, P L., 1995 Defective protein

fold-ing as a basis of human disease Trends in Biochemical Sciences 20:

456–459

© Burstein Collection/CORBIS

and the Glycoconjugates

of Cell Surfaces

Carbohydrates are the single most abundant class of organic molecules found in

na-ture Energy from the sun captured by green plants, algae, and some bacteria

dur-ing photosynthesis (see Chapter 21) converts more than 250 billion kilograms of

carbon dioxide into carbohydrates every day on earth In turn, carbohydrates are

the metabolic precursors of virtually all other biomolecules Breakdown of

carbo-hydrates provides the energy that sustains animal life In addition, carbocarbo-hydrates

are covalently linked with a variety of other molecules These glycoconjugates are

important components of cell walls and extracellular structures in plants, animals,

and bacteria In addition to the structural roles such molecules play, they also serve

in a variety of processes involving recognition between cell types or recognition of

cel-lular structures by other molecules Recognition events are important in normal cell

growth, fertilization, transformation of cells, and other processes.

All of these functions are made possible by the characteristic chemical features

of carbohydrates:

• the existence of at least one and often two or more asymmetric centers

• the ability to exist either in linear or ring structures

• the capacity to form polymeric structures via glycosidic bonds

• the potential to form multiple hydrogen bonds with water or other molecules

in their environment.

The name carbohydrate arises from the basic molecular formula (CH2O)n, where

n  3 or more (CH2O)ncan be rewritten (CH2O)nto show that these substances

are hydrates of carbon.

Carbohydrates are generally classified into three groups: monosaccharides (and

their derivatives), oligosaccharides, and polysaccharides The monosaccharides

are also called simple sugars and have the formula (CH2O)n Monosaccharides

cannot be broken down into smaller sugars under mild conditions

Oligosaccha-rides derive their name from the Greek word oligo, meaning “few,” and consist of

from two to ten simple sugar residues Disaccharides are common in nature, and

trisaccharides also occur frequently Four- to six-sugar-unit oligosaccharides are

usually bound covalently to other molecules, including glycoproteins As their

name suggests, polysaccharides are polymers of the simple sugars and their

deriv-atives They may be either linear or branched polymers and may contain hundreds

or even thousands of monosaccharide units Their molecular weights range up to

1 million or more.

“The Discovery of Honey”—Piero di Cosimo (1492)

Sugar in the gourd and honey in the horn,

I never was so happy since the hour I was born.

Turkey in the Straw, stanza 6

(classic American folk tune)

KEY QUESTIONS

7.1 How Are Carbohydrates Named?

7.2 What Is the Structure and Chemistry

of Monosaccharides?

7.3 What Is the Structure and Chemistry

of Oligosaccharides?

7.4 What Is the Structure and Chemistry

of Polysaccharides?

7.5 What Are Glycoproteins, and How Do They Function in Cells?

7.6 How Do Proteoglycans Modulate Processes

in Cells and Organisms?

7.7 Do Carbohydrates Provide a Structural Code?

ESSENTIAL QUESTION

Carbohydrates are a versatile class of molecules of the formula (CH2O)n They are a

major form of stored energy in organisms, and they are the metabolic precursors of

virtually all other biomolecules Conjugates of carbohydrates with proteins and

lipids perform a variety of functions, including recognition events that are important

in cell growth, transformation, and other processes.

What is the structure, chemistry, and biological function of carbohydrates?

Create your own study path for this chapter with tutorials, simulations, animations,

and Active Figures at www.cengage.com/ login

Monosaccharides consist typically of three to seven carbon atoms and are described

either as aldoses or ketoses, depending on whether the molecule contains an

alde-hyde function or a ketone group The simplest aldose is glyceraldealde-hyde, and the simplest ketose is dihydroxyacetone (Figure 7.1) These two simple sugars are

termed trioses because they each contain three carbon atoms The structures and

names of a family of aldoses and ketoses with three, four, five, and six carbons are

shown in Figures 7.2 and 7.3 Hexoses are the most abundant sugars in nature

Nev-ertheless, sugars from all these classes are important in metabolism.

HCOH CHO

CH2OH 2

1

3

D -Glyceraldehyde

Carbon number

HCOH

CH2OH

3 4

D -Erythrose

HCOH

CHO 2

1

HCOH

CH2OH

D -Threose

HOCH CHO

HCOH

CH2OH

4 5

D -Ribose (Rib)

HCOH 3

HCOH

CHO 2 1

HCOH

CH2OH

D -Arabinose (Ara)

HCOH HOCH CHO

HCOH

CH2OH

D -Xylose (Xyl)

HOCH HCOH CHO

HCOH

CH2OH

D -Lyxose (Lyx)

HOCH HOCH CHO

HCOH

CH2OH 5

D -Allose

HCOH 4

HCOH 3

HCOH

CHO 2 1

Carbon number

Carbon number

Carbon

number

6

HCOH

CH2OH

D -Altrose

HCOH HCOH HOCH CHO

HCOH

CH2OH

D -Glucose (Glc)

HCOH HOCH HCOH CHO

HCOH

CH2OH

D -Mannose (Man)

HCOH

HOCH CHO

HOCH

HCOH

CH2OH

D -Gulose

HOCH

HCOH CHO

HCOH

CH2OH

D -Idose

HCOH HOCH CHO

HCOH

HOCH

HCOH

CH2OH

D -Galactose (Gal)

HOCH

HCOH CHO

HCOH

CH2OH

D -Talose

HOCH CHO

HOCH

ALDOTRIOSE

ALDOTETROSES

ALDOPENTOSES

ALDOHEXOSES

FIGURE 7.2 The structure and stereochemical relationships of D-aldoses with three to six carbons The configu-ration in each case is determined by the highest numbered asymmetric carbon (shown in pink) In each row, the “new” asymmetric carbon is shown in yellow Blue highlights indicate the most common aldoses

CH2OH CH2OH

L -Isomer D -Isomer

Glyceraldehyde

CH2OH

Dihydroxy-acetone

H

HO

CHO

CH2OH

L -Glyceraldehyde

OH H

CHO

CH2OH

D -Glyceraldehyde

FIGURE 7.1 Structure of a simple aldose

(glyceralde-hyde) and a simple ketose (dihydroxyacetone)

Glyco: A generic term relating to sugars.