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Contents

  1. ISBN 10: 0896032302
  2. Protein Characterization
  3. Rapid characterization of secreted recombinant proteins by native mass spectrometry
  4. Natural proteins: Sources, isolation, characterization and applications

RP-HPLC, an extremely versatile technique for isolation of synthetically or biologically obtained peptides and proteins is used for both analytical and preparative applications, which involves molecules separation from the mobile phase to immobilized hydrophobic ligands attached to the stationary phase, i. For large-scale protein separation, the use of RP-HPLC is limited because acidic buffering systems and hydrophobicity of n -alkyl silica supports results into low mass yields or loss of biological activity of larger polypeptides.

Ten microliters of Milli-Q water was used as the blank. Large and polar biomolecules are not easily ionized and transferred into the gas phase; hence, electrospray ES and matrix-assisted laser desorption ionization MALDI techniques are used. Mass spectrometry in proteomics is used in three major areas. Recombinant proteins, macromolecule characterization and quality control in the field of biotechnology.

Protein identification, either in classical biochemical projects or in large-scale proteomic ones. Detection and characterization of post-translational modifications or any method like any covalent modification that alters mass of a protein using versatility of it to detect the molecular weight of the protein. Tessier et al.

Proteins are used in drug and gene delivery systems as protein-based nanocarriers. Extended applications include use in controlled delivery, as a film coater, as hydrogels, as composites, as albumin-based nanoparticles, as microparticles and as beads. Some examples are:. Whey proteins used as hydrogels, nanoparticle systems for encapsulation and controlled delivery of bioactive compounds[ 83 ]. As anti-hypertensive use, like genetically modified soybean seeds accumulating novokinin[ 84 ]. As solubility enhancer of curcumin in the food industry due to protein—micelle structure beta-casein , acting as a nano vehicle[ 85 ].

As a source of bioactive peptides, e. As a novel antifungal, e. Sugar snap pea legumes. In microencapsulation, e. As pest control: Proteinaceous cysteine proteinase inhibitor, an insecticidal protein found in pulses used to control the proteolytic activity of endogenous digestive cystein proteinase in the mid-gut of some insects.

Source of Support: Nil. Conflict of Interest: None declared. National Center for Biotechnology Information , U. Journal List Pharmacogn Rev v. Pharmacogn Rev. Jitendra Y. Nehete , Rajendra S. Bhambar , Minal R. Narkhede , 1 and Sonali R. Rajendra S. Minal R. Sonali R. Author information Article notes Copyright and License information Disclaimer. Address for correspondence: Dr. E-mail: moc. This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-Share Alike 3.

This article has been cited by other articles in PMC. Abstract Worldwide, plant protein contributes substantially as a food resource because it contains essential amino acids for meeting human physiological requirements. Keywords: Amino acid, natural proteins, SDS gel electrophoresis, salting out. Building blocks of proteins Amino acids Naturally occurring organic compounds containing amino and carboxyl groups, which are the chief constituents of protein and are necessary for human and animal growth and nutrition, are termed as essential amino acids.

Open in a separate window. Properties of proteins Solubility Protein solubility properties are summarized as: Forms colloidal solutions in water due to huge size Solubility depends on electrostatic charges; net charge depends on number, identity, location of amino acids and pH of solvent It depends upon isoelectric point range Shape Protein shape varies as globular insulin , oval albumin , fibrous or elongated fibrinogen. Color reactions of proteins Useful to identify the nature of the amino acids present in proteins as given in Table 2.

In vivo half-life This indicates the means time taken by proteins to disappear after its synthesis in cell to its initial half amount, and is predicted using three model organisms human, yeast and E. Extinction coefficient It indicates at the amount of light absorbed by a protein at a certain wavelength. Aliphatic index The aliphatic index of a protein indicates a relative volume occupied by the aliphatic side chains alanine, valine, isoleucine and leucine , which also increase the thermostability of the globular proteins with increasing value.

Protein sequencing The amino acid sequence determination, protein conformation and extent of complexation with any non-peptide molecules in a protein is called as protein sequencing. Edman degradation reaction Ordered amino acid composition of a protein can be determined by using this reaction. The reaction scheme with sequencing steps for protein is as follows: Break any disulfide bridges in protein with an oxidizing agent like performic acid or reducing agent like 2-mercaptoethanol.

Proteins containing more than one chain are separated and purified Determine the amino acid composition of each chain Determine the terminal amino acid of each chain Break each chain into fragments under 50 amino acids long Separate and purify fragments Determine the sequence of each fragment Repeat with a different pattern of cleavage Construct a sequence of the overall protein. Mass spectrometry The protein sequence can be directly determined by this technique using electro-spray ionization.

Separation Separation of amino acids from peptides is performed by eluting the mixture of peptide and buffers with increasing pH using a sulfonated polystyrene ion-exchange chromatography column. Quantitation Reactions with ninhydrin quantify the amino acids from a peptide in micrograms. Protein sources: Plant and animal Animal products, meat, milk, milk products, egg, poultry and fish are rich sources of protein containing a balanced level of amino acids.

Animal protein and plant vegetable protein are differentiated as: Animal protein is generally associated with high fat content and, because of this, when consumed in large amounts, it leads to high risks of diseases, including high blood pressure and heart diseases Animal protein has a balanced combination of all amino acids; hence, it is called complete protein. Plant proteins Vegetables, legumes and fruits are good sources of protein. Table 3 Parts of plants as source of proteins with examples. Table 4 Plants and their proteins. Soybean proteins Soy proteins are a mixture of globular proteins - conglycinin kDa with glycosylated three subunits and Glycinin kDa with six AB subunits comprised of an acidic [A] and a basic [B] polypeptide linked via disulfide bonds and are obtained from the plant species Glycine max , family Fabaceae.

Rice Proteins During processing of white rice, rice bran is obtained, which is a rich source of inexpensive high-quality proteins obtained from grain during the milling process. Sunflower Proteins Proteins are majority constituents in sunflower oil cakes. Animal proteins Protein from animal sources contains essential amino acids needed for an adult's diet. Whey protein Technically, whey proteins are those that remain in milk serum after coagulating caseins at 4.

Meat proteins Sarcoplasmic, stromal and myofibrillar are types of meat protein. Egg albumin Protein fractions: Ovalbumin Silk proteins The silkworm Bombyx mori produces silk to weave its cocoon. Isolation of proteins[ 69 ] Selective precipitation of proteins can be used as: Bulk method to recover majority of the proteins from a crude lysate Selective method to fractionate a subset of proteins from a protein solution Specific method to recover a single protein of interest from a purification step.

Selective precipitation methods Salting out Isoionic precipitation Organic co-solvent precipitation Two carbon C2 organic co-solvent precipitation of proteins C4 and C5 organic co-solvent precipitation, phase partitioning and extraction of proteins Protein exclusion and crowding agents neutral polymers and osmolytes Synthetic and semisynthetic polyelectrolyte precipitation Metallic and polyphenolic heteropolyanion precipitation Hydrophobic ion pairing HIP entanglement ligands Matrix-stacking ligand co-precipitation Di- and trivalent metal cation precipitation.

Salting out Proteins are salted out as co-precipitate by ammonium sulfate because the saturation concentration provides high molarity that causes precipitation of most proteins. Figure 1. Isoionic precipitation Column method Proteins are frequently least soluble and most precipitable when they are isoionic. Dialysis method One of the older methods of rendering proteins salt free or nearly salt free i.

Purification and separation Sodium dodecyl sulfate SDS gel electrophoresis. One-dimensional gel electrophoresis This type of electrophoresis can provide information about the molecular size and purity of the proteins as well as the number and molecular size of its subunits.

Two-dimensional gel electrophoresis This type of electrophoresis separates proteins in the first dimension by isoelectric focusing and in the second dimension by electrophoresis in the presence of SDS.

ISBN 10: 0896032302

Monitor protein accumulation during development Comparisons between differentiated organs and tissues Comparisons of genetic variability within and between species Detection of protein synthesis effected by various environmental stimuli, such as growth substances ABA, GA , abiotic stresses high temperature, low temperature, drought, anaerobiosis and salt and pathogenic attack. Protein staining Coomassie blue staining This staining requires an acidic medium for generation of an electrostatic attraction between the dye molecules and the amino groups of proteins.

Silver staining Silver staining is times more sensitive than Coomassie Blue staining. Characterization Prior purification is required to characterize proteins, which can be done by a separation mechanism or by chromatographic techniques. Table 5 Separation mechanism and technique. Reversed-phase high-performance liquid chromatography RP-HPLC RP-HPLC, an extremely versatile technique for isolation of synthetically or biologically obtained peptides and proteins is used for both analytical and preparative applications, which involves molecules separation from the mobile phase to immobilized hydrophobic ligands attached to the stationary phase, i.

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Protein Characterization

Mass spectrometry of proteins Large and polar biomolecules are not easily ionized and transferred into the gas phase; hence, electrospray ES and matrix-assisted laser desorption ionization MALDI techniques are used. Applications of proteins Proteins are used in drug and gene delivery systems as protein-based nanocarriers. Some examples are: Whey proteins used as hydrogels, nanoparticle systems for encapsulation and controlled delivery of bioactive compounds[ 83 ] As anti-hypertensive use, like genetically modified soybean seeds accumulating novokinin[ 84 ] As solubility enhancer of curcumin in the food industry due to protein—micelle structure beta-casein , acting as a nano vehicle[ 85 ] As vehicles for bioactives, like milk proteins As a source of bioactive peptides, e.

Hermann JR. Protein and the Body. Exercise physiology: Energy, Nutrition, and Human Performance. Vitamins, minerals, and water; pp.

Rapid characterization of secreted recombinant proteins by native mass spectrometry

Millward DJ. The nutritional value of plant based diets in relation to human amino acid and protein requirements. Proc Nutr Soc. Furst P, Stehle P. Satyanarayana U, Chakrapani U. Books of Biochemistry. In vivo half-life of a protein is a function of its amino-terminal residue. How to measure and predict the molar absorption coefficient of a protein. Protein Sci. Edelhoch H. Spectroscopic determination of tryptophan and tyrosine in proteins. Calculation of protein extinction coefficients from amino acid sequence data. Anal Biochem. Ikai A. Thermostability and aliphatic index of globular proteins.

J Biochem. Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol. Alterman MA, Hunziker P. Creighton TE. New York: Freeman WH; Proteins: Structures and molecular properties. Coon JJ. Collisions or Electrons? Protein Sequence Analysis in the 21 st Century.

Anal Chem. Bender W, Smith M. Population, Food and Nutrition. Popul Bull. Practical Applications in Sports Nutrition; pp. J Ethnopharmacol. Effects of different oils on the properties of soy protein isolate emulsions and gels. Food Res Int. Purification and characterization of novel ribosome, inactivating proteins, alpha- and beta-pisavins from seeds of the garden pea Pisum Sativum. Biochem Biophys Res Commun. Isolation of pisumin, a novel antifungal protein from legumes of the sugar snap pea Pisum sativum var.

Optimization and in vitro stability of legumin nanoparticles obtained by a coacervation method. Int J Pharm. Preparation of lectin—vicilin nanoparticle conjugates using the carbodiimide coupling technique. Properties of glutaraldehyde Crosslink's vicilin nano and microparticles. J Microencapsul. Ng TB. Influence of soy protein's structural modifications on their microencapsulation properties: Atocopherol microparticles preparation. If you add this item to your wish list we will let you know when it becomes available. Is the information for this product incomplete, wrong or inappropriate?

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Welcome to Loot. Checkout Your Cart Price. The question of the mechanism of protein folding has intrigued scientists for many decades. As far back as , a time when nothing was known about protein structure, Wu had analyzed the reverse of the folding process, denaturation. Shortly thereafter, Northrop in , and Anson and Mirsky in succeeded in reversing the denaturation of several proteins, such as hemoglobin, chymotrypsinogen, and trypsinogen. In , Kauzmann proposed that the hydrophobic effect is the driving force in directing the folding process.

Later, the determination of the three-dimensional structures of proteins by X-ray diffraction provided a new basis on which to study the folding process. Significant progress began to be made when Anfinsen successfully refolded denatured and reduced ribonuclease into the fully active enzyme. He stated the fundamental principle of protein folding in the folding of a protein is determined by its amino acid sequence. The evidence gathered over many years supports this principle even for folding in vivo assisted by molecular chaperones.

The fundamental questions are the following. How does the sequence code for the fold, given that the backbone of all proteins has the same composition; in other words, how do the side chains dictate the overall fold? How does a given sequence find its specific native structure in a finite time among the enormous number of possible conformations that a polypeptide chain could adopt? How is the folding process initiated and what is are the pathway s of folding? And last, are the main rules of protein folding deduced from in vitro studies valid for folding in vivo?

At the present time, protein folding is an extremely active field of research involving aspects of biology, chemistry, biochemistry, computer science and physics. The fundamental principles have practical applications in the exploitation of the recent advances in genome research, in the understanding of several pathologies and in the design of novel proteins with special functions. Although the detailed mechanisms of folding are not completely known, significant advances have been made in the understanding of this complex process through both experimental and theoretical approaches 3.

The fundamentals of protein folding from the Anfinsen postulate to the new view. The remarkable achievement of C. Anfinsen and his group in refolding denatured and reduced ribonuclease into a fully active enzyme marked the beginning of the modern era of the protein folding problem. From his results, the author concluded that "all the information necessary to achieve the native conformation of a protein in a given environment is contained in its amino acid sequence" 4.

The thermodynamic control of protein folding is a corollary to the Anfinsen postulate; it means that the native structure is at a minimum of the Gibbs free energy. This statement was discussed by Levinthal in a consideration of the short time required for the folding process in vitro as well as in vivo. Indeed, for a amino acid polypeptide chain, if we assume only two possible conformations for each residue, there are 10 30 possible conformations for the chain as a whole. If only 10 second is required to convert one conformation into another, a random search of all conformations would require 10 11 years, an irrealistic time in a biological context where the folding time is of the order of seconds or minutes.

Thus, it is clear that evolution has found an effective solution to this combinatorial problem. This is referred to as the Levinthal paradox and has dominated discussions for the last 30 years. Different mechanisms have been suggested in order to solve the Levinthal paradox. Among them is Wetlaufer's proposed model in which protein folding is under kinetic control rather than thermodynamic control. This states that the protein is trapped in an energetic minimum which is not the global minimum, a high energetic barrier preventing the protein from reaching the latter see Ref.

In order to understand how the polypeptide chain could overcome the Levinthal paradox, different folding models arising from theoretical considerations 5, and references therein , folding simulations, or experimental observations 6, and references therein have been proposed. The classical nucleation-propagation model, which applies to helix-coil transitions, involves a nucleation step followed by a rapid propagation, the limiting step being the nucleation process.

This model has been proposed to explain the folding of ribonuclease A but was forsaken after new kinetic studies of the refolding of ribonuclease were performed 6. More recently a nucleation-condensation model, different from the classical one, has been proposed by Fersht 7. This model proposes a mechanism involving a weak local nucleus which is stabilized by long range interactions.

A stepwise sequential and hierarchical folding process, in which several stretches of structure are formed and assemble at different levels following a unique route, has been supported by several authors for many years 6,8. According to this model, the first event, nucleation, is followed by the formation of secondary structures which associate to generate supersecondary structures, then domains and eventually the active monomer; the association of domains induces the last conformational refinements which generate the functional properties.

Such a hierarchy of protein folding corresponds to the hierarchy of protein structure. Similarly, the framework model assumes that the secondary structure is formed in an early step of folding, before the tertiary structure, emphasizing the role of short range interactions in directing the folding process 9. A modular model of folding was suggested on the basis of the three-dimensional structures of proteins.

This model assumes that not only domains, but also subdomains can be considered as folding units which fold independently into a native structure, forming structural modules that assemble to yield the native protein 10, The diffusion-collision model of folding was developed in by Karplus and Weaver and reconsidered in in the light of more recent experimental data In such a model, nucleation occurs simultaneously in different parts of the polypeptide chain generating microstructures which diffuse, associate and coalesce to form substructures with a native conformation.

These microstructures have a lifetime controlled by segment diffusion, so the folding of a polypeptide chain containing to amino acids can occur within a very short time, less than a second. According to this model, folding occurs through several diffusion-collision steps. The hydrophobic collapse model implies that the first event of protein folding consists of a collapse via long range hydrophobic interactions and occurs before the formation of a secondary structure The idea originates from the work of Kauzmann considering the hydrophobic effect as the driving force in protein folding and stabilization.

Later, Dill and co-workers proposed that the formation of stretches of secondary structures occurs simultaneously with the hydrophobic collapse. The jigsaw puzzle model was introduced in by Harrison and Durbin This model admits the existence of multiple folding routes to reach a single solution.

According to this hypothesis, the identification of folding intermediates represents a kinetic description rather than a structural one, each intermediate consisting of heterogeneous species in rapid equilibrium. It was the subject of controversy until recently but presents some similarities with the diffusion-collision model proposed by Karplus and Weaver. The unfolding-refolding transition under equilibrium transition has often been described as a two-state process in which only the unfolded and the native species are significantly populated.


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The intermediates are generally unstable and poorly populated under equilibrium conditions. The two-state approximation, which applies to very cooperative transitions, is frequently valid for small proteins. Such an approximation allows the determination of D G o , the free energy of denaturation. The existence of intermediates has been shown from kinetic studies for most proteins even when the two-state approximation describes the overall denaturation process.

For many proteins, monophasic unfolding kinetics and multiphasic refolding kinetics are observed. This is one of many ways in which the experimental evidence proves the occurrence of intermediates in the folding pathway. The structural characterization of such intermediates is a prerequisite to solving the folding problem. However, while kinetic studies demonstrate the existence of intermediates and their location on the folding pathway, these intermediates are often too poorly populated to obtain detailed structural information.

Two major impediments to characterizing these species are thus the high cooperativity and the rapidity of the process, especially in the early events of protein folding. In spite of these inherent difficulties, much effort has been devoted to characterizing these transient species. Kinetic trapping of intermediates during the refolding of disulfide-bridged proteins was developed for lysozyme 16 and used for bovine pancreatic trypsin inhibitor BPTI 17, In the past decade, technological advances have improved our approaches to the study of the protein folding process.

Several methods have been developed allowing some of the intermediates to be characterized, particularly stopped-flow mixing devices coupled to circular dichroism, and NMR using rapid hydrogen-deuterium exchange associated with a mixing system allowing for the pulse labeling of transient species. This method is very informative, yielding residue-specific information Protein engineering has also been successfully employed to stabilize intermediates or to probe particular regions of a protein during the folding process Another approach frequently used is the study of protein fragments 10, Transient folding species have been found to accumulate at low pH for several proteins, and especially for a -lactalbumin, permitting the study of their structural properties.

The formation of secondary structures in the early steps of protein folding has been observed for many proteins 24, Such early species with a high content of secondary structures were named "the molten globule" by Ohgushi and Wada Ptitsyn 27 has suggested that it is a general intermediate in the folding pathway of proteins.

Characterization of Therapeutic Proteins for Biological Drug Development

The literature being rather confusing concerning the structural characteristics of the molten globule state, Goldberg and colleagues 29 have introduced the term "specific molten globule", and defined its characteristics. The specific molten globule is a rather compact intermediate with a high content of native secondary structure, but a fluctuating tertiary structure.

It contains an accessible hydrophobic surface susceptible to binding a hydrophobic dye, aniline naphthalene sulfonate.

INTRODUCTION

Since the tertiary structure is not stabilized, the aromatic residues can rotate in a symmetrical environment and are accessible to the solvent, as assessed by the absence of near UV circular dichroism. However, the secondary structures observed in the early steps of the folding process are not always identical to those observed in the native structure. Even in the case of the paradigmatic molten globule of a -lactalbumin, some differences have been observed by NMR spectroscopy.

This molten globule appears as a heterogeneous species. Furthermore, the side chains of Tyr, Trp and His are packed within a hydrophobic cluster in a region that differs in structure from the native one The folding pathway of hen egg white lysozyme includes transient steps corresponding to a reorganization of secondary structures An intermediate preceding the molten globule state has been identified by Ptitsyn 27 , and Uversky and Ptitsyn This species, less compact than a molten globule, has a significant secondary structure content but smaller than that of a molten globule, and displays hydrophobic regions accessible to a solvent.

It has been called a "pre-molten globule" by Jeng and Englander The rapid formation of transient intermediates, either molten or pre-molten, or both, with a high content of secondary structure and a small amount of fluctuating tertiary structure, is supported by a great number of observations 22, However, since these transient states are formed within the dead-time of a stopped-flow device, it is possible that their formation might be preceded by an earlier event.

According to another point of view, the first event in the folding of a polypeptide chain consists of a hydrophobic collapse preceding the formation of secondary structure or occurring simultaneously, and being followed by a rearrangement of a small number of condensed states. This view emphasizes both the hydrophobic effect and the role of long range interactions in the initiation of the folding process.

Several experimental data are consistent with a hydrophobic collapse during the early stages of folding. For example, residual microstructures persisting during the denaturation process have been characterized for several proteins. These microstructures may be involved in the folding process as hydrophobic nucleation centers. They have been observed in the folding of repressor, in FK binding protein, in staphylococcal nuclease, in dihydrofolate reductase, and in a peptide from BPTI for a review, see Classical rapid mixing techniques such as stopped-flow, continuous flow and quenched-flow are limited to the millisecond time scale, preventing analysis of the events occurring within the initial burst phase of folding.

Most of the secondary structures are formed within the dead-time of a stopped-flow device. This is particularly inconvenient as a crucial part of the folding problem is the characterization of the very early intermediates. Recent technical advances to improve the resolution time of kinetic studies have been made Submillisecond mixing techniques have been developed and applied to the refolding of cytochrome c. Non-mixing techniques such as the classical T-jump, nanosecond infrared laser-induced T-jump and picosecond T-jump have been used to study the refolding of cold-denatured proteins.

Other rapid techniques such as nanosecond laser photolysis, optical electron transfer and dynamic NMR methods have been reported. They allow detection of very fast events which occur on a time scale of less than a microsecond. Moreover, the use of a laser T-jump method has allowed the detection of two very fast phases during the folding of this protein. The first one occurring in ns is a local collapse around Trp14 and consists of non-native hydrophobic contacts and helix formation. These two rapid phases are followed by a slower final phase of 0.

It appears therefore that the very fast events of protein folding consist of a hydrophobic collapse accompanied or not by the formation of secondary structures, depending on the protein. Intermediate events on the folding time scale occur after the formation of the molten globule and before the rate-limiting step of the folding process which generates the native and functional structure.

In these intermediate phases, the appearance of substrate- or ligand-binding sites can be observed. In the final rate-limiting step, the protein achieves its native conformation with the emergence of functional properties. These final events correspond to the precise ordering of the elements of secondary structure, the correct packing of the hydrophobic core, the correct domain pairing in multidomain proteins, the reshuffling of disulfide bonds, cis-trans proline isomerization, and subunit assembly in oligomeric proteins. For several proteins, the rate-limiting step consists of the reorganization of misfolded species for reviews, see 2,6,15, Figure 1 illustrates a folding pathway with kinetic competition between correct folding and a side reaction leading to the formation of aggregates.

Domains are compact substructures within a protein molecule. They have been considered as folding units by Wetlaufer, forming structural modules that fold independently and assemble to generate the native structure.

Natural proteins: Sources, isolation, characterization and applications

In our laboratory, we have studied the role of structural domains in phosphoglycerate kinase whose structure is organized into two domains of approximately the same size Figure 2. The independently expressed engineered N- and C-domains have quasi-native structures and are capable of refolding cooperatively. The C-domain binds the ATP substrate with the same affinity as the native protein. However, even though these isolated domains can refold independently, it has not proved possible via a variety of experimental procedures to reproduce functionally active protein from the two separate domains.

The ability of independently folded domains to associate to yield a functional protein has been observed only with a few proteins, such as thioredoxin, elastase, and methionyl-t-RNA synthetase reviewed in Ref. Thus, it seems that, for many proteins, the correct folding of isolated domains is not sufficient to yield a functional ensemble. Rather, the interactions between domains are required during the folding process to allow the structural adjustments that yield a functional protein. Figure 2 - Structure of yeast phosphoglycerate kinase. The two tryptophans are colored in green and Cys97 in magenta.

In many proteins, the N and C termini are spatially adjacent in the folded state. In phosphoglycerate kinase, for example, circular permutations have been obtained by protein engineering that introduce a discontinuity into either one or the other domain. Such a change can modify the sequence of events in the folding process, but does not prevent the protein from achieving a native and functional conformation. It is likely that during evolution structural patterns of proteins consisting of continuous domains have been selected on the basis of thermodynamic stability.

However, proteins have enough plasticity to find their functional fold, even when the continuity of the domains has been artificially disrupted. It has been proposed that subdomains, which represent compact regions smaller than domains within a protein, might also fold autonomously, forming folded modules that assemble to generate the native protein These subdomains are proposed to be condensed states in which the close packing of the atoms in the hydrophobic core of the molecule has not yet taken place. Oas and Kim have reported that fragments from BPTI corresponding to subdomains fold autonomously and then associate.

The results obtained on the folding and complementation of fragments from barnase are also consistent with a modular model. In contrast, this model cannot account for the folding of barley chymotrypsin inhibitor 2. Likewise, fragments smaller than a domain cannot be considered as folding units in the SH2 domain of proteins p60 and p85, in staphylococcal nuclease, in tryptophan synthase, or in cytochrome c.

Several pairs of structural fragments from phosphoglycerate kinase have been obtained. Furthermore, several pairs of adjacent fragments have been found to give a functional complementation. Among them, at least one of the two fragments was not significantly folded when isolated. This demonstrates that the association of individual fragments with a non-native structure can favor subsequent rearrangements to functional native structures through long range interactions for a review, see Ref. Many phenomenological models have been thus proposed over the years; more recently a unified model of protein folding based on the effective energy surface of the polypeptide chain has emerged.

This so-called new view of protein folding arises from theoretical studies. Although simplified to take into account the computational limitations, several models have been proposed to overcome the Levinthal paradox by simulation of folding from random coil to the native structure.