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Protein folding in vivo

Protein folding in vitro

Protein folding in vivo, the role of molecular chaperones

Protein folding in vitro

Protein folding in in vitro experiments can be different from that of inside the cells.

The methods, mainly used in folding experiments, can be seen in one of the previoussections. Following the in vitro folding can lead us to very important discoveries in this

field, but in the interpretation of the data we have to be very careful, as the environment

of the folding protein is very different under in vitro and in vivo circumstances. Themajor difference is, that in in vitro experiments there is only one protein, with an

unfolded structure, which cannot interact with other components of the solvent. On the

other hand, there are a lot of interactions in the cell between different proteins, during thefolding process. The viscosity of the cytoplasm is rather different from that of the

solvents, used in in vitro experiments, the molecular crowding makes the cytoplasm just

like honey. The proteins in the experiments are folded, or they can be denatured bychemical or physical methods, which may not reflect the in vivo circumstances of folding

totally. There are some proteins that need a special help in the folding process, this help is

given by molecular chaperones.

Protein folding in vivo, the role of molecular chaperones

The chaperones are major prokaryotic and eukaryotic proteins, with the function ofhelping in folding of nascent polypeptide chains, helping refolding of denatured proteins,and preventing aggregation of surface!exposed hydrophobic parts of proteins, having

problems with folding. "haperones help the proteins to fold, so they increase the speed of

folding, by stabili#ing unstable intermediates of the appropriate polypeptide chain, and

decreasing the activation!energy barriers during folding. They do not change thethermodynamics of folding, ie. the ratio of folded and unfolded polypeptides, they only

influence the kinetics of gyration. $n this sense they are often correlated with the

en#ymes. %owever, sometimes they are very similar to them, but sometimes are verydifferent, as they are not too specific for the ligands, they help to fold, the substrates are

very large, and their large!scale functions make them key!molecules of the cells. Their

unspecifity is very good, since a protein can fold incorrectly in a lot of ways, so theremay be a lot of incorrect intermediates, but the correct folding can occur only in one way

in most cases. &ostly they recogni#e hydrophobic surfaces on the proteins, and prevent

them from aggregation.

'eside this function, chaperones can play an important role in signal transduction, inthe maintenance of the organi#ed state of the cytoplasm and other intracellular

compartments, in the motions inside the cell, and some other vital functions of the cells.

(ometimes they are called stress proteins, or heat shock proteins, because their synthesis

http://www.chaperone.sote.hu/Examples.html#invitrohttp://www.chaperone.sote.hu/Examples.html#invivohttp://www.chaperone.sote.hu/Examples.html#invivohttp://www.chaperone.sote.hu/Methods.htmlhttp://www.chaperone.sote.hu/Methods.htmlhttp://www.chaperone.sote.hu/Examples.html#invitrohttp://www.chaperone.sote.hu/Examples.html#invivohttp://www.chaperone.sote.hu/Methods.htmlhttp://www.chaperone.sote.hu/Methods.html

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increases )in most of the cases* after various forms of cellular stress, such as heat, cold,

detergents, increase of ionic strength, changes in p%, toxic agents. %owever, the termini

are not e+uivalent to each other, as some of the chaperones level does not change uponstress, in these some cases they are called heat shock cognate proteins )referring to the

state, that they are homologous to heat shock proteins, but their synthesis does not depend

on stress*. The hsp abbreviation is used in the first, and the hsc in the second case. Thegrp!s )glucose regulated proteins* are chaperones, that function in the endoplasmic

reticulum. They are more or less the homologues of the cytoplasmic chaperones. There

are cold shock proteins as well, they are abbreviated as csp!s, their role is in some kinddifferent from that of the hsp!s. )-s at lower temperature the stability of hydrogen bonds

increase according to the 'olt#mann!function, the intra! and intermolecular associations

can get stronger, which is unfavourable, when the dissociation of these molecules, such

as different strands of /- is re+uired. This problem is solved by the cold shockproteins.* 0et us read some things on the major families of chaperones in prokaryotic and

eukaryotic organisms.

These are the most important chaperone families1

2bi+uitin, and the family of hsp3

4ro5( and the corresponding hsp67 family

%sp89, hsp8: and hsp;8, the small molecular chaperones

7

%sp>:, collagenin

PP$!s, the peptidil!prolil!cis!trans!isomerases

P

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during the first steps of folding and needs to be degraded in order to maintain the cellular

homeostasis.

The ubiquitin is a small, 8 kDa eight protein, ith an alpha!heli" and beta!sheet in its structure#

$ro%& and the corresponding hsp' family

This family is further described in the chapter on4ro50 and hsp?7, as they form alarge structural and functional complex together.

sp*+, hsp*, hsp-*, the small molecular chaperones

These chaperones called small molecular chaperones, as their molecular weight is in

the range between 89 and ;8 k

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Dna and hsp7

The 7 are strongly related to the function

of the : can be found in the endoplasmic reticulum of the cells in a

phosphorylated form. $t binds very strongly the type $. and $D. procollagen molecules,and possesses a serine!protease inhibitor activity. (o it prevents the procollagen extension

peptides from being degraded, which is essential in the later formation of +uaternary

structure of collagen molecules outside the cell. $t dissociates from the procollagen onlyin the 4olgi!vesicles.

The interesting structure of the hsp7, hich is a serine!proteinase inhibitor#

PP6!s, the peptidil!prolil!cis!trans!isomerases

The PP$!s are members of the large, cytosolic chaperone complex, thefoldosomesothey can be found there, as well as the1

PD6!s, the protein!disulfide!isomerases

$ro%9 and the hsp4

The 4ro50 molecule is a ?7 k

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interaction with the appropriate 4ro50 ring influences the symmetry as well, so the

4ro50!4ro5( complex has a single point group : symmetry. %owever, there are forms,

when both the two 4ro5(!binding sites of the 4ro50 molecule binds the 4ro5(!heptamer, but the function of this complex is not known (T:r:k, ;

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of the polypeptide chain, which can be good in case of reverse turn structures, but in

other cases it can hinder the protein folding. This activation free!energy barrier is very

high in normal conditions, so it could lead to considerable folding traps during folding.The PP$!s give the solution to this problem, as they can catali#e the geometrical

isomerisation of the amide bonds. This leads to an acceleration in protein folding.

The protein!disulfide!isomerases )P

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The hsp3 has three distinct domains, the A!terminal domainBs structure as resolved in '33# The figure

shos the A!terminal domain# The helices are indicated by red# There is a cleft beteen helices and the

eight!stranded beta!sheet# This cleft is capable of bindind 2TP and 2DP# The 2DP molecule is shon by a

spacefill model in the figure#

$f you are interested more on this chaperone, you can find some more, interesting detailson this site.

The =lp!families, the hsp' and ''

The hsp677 or hsp667 is an approximately 67> k