The protein-folding problem: the native fold determines packing, but does packing determine the native fold?

Abstract

A globular protein adopts its native threedimensional structure spontaneously under physiological conditions. This structure is specified by a stereochemical code embedded within the amino acid sequence of that protein.Elucidation of this code is a major, unsolved challenge, known as the protein-folding problem. A critical aspect of the code is thought to involve molecular packing. Globular proteins have high packing densities, a consequence of the fact that residue side chains within the molecular interior fit together with an exquisite complementarity, like pieces of a three-dimensional jigsaw puzzle [Richards, F. M. (19T71)hAnnu. Rev. Biophys. Bioeng. 6, 151]. Such packing interactions are widely viewed as the principal determinant of the native structure. To test this view, we analyzed proteins of known structure for the presence of preferred interactions, reasoning that if side-chain complementarity is an important source of structural specificity, then sets of residues that interact favorably should be apparent. Our analysis leads to the surprising conclusion that high packing densities-so characteristic of globular proteins-are readily attainable among clusters of the naturally occurring hydrophobic amino acid residues. It is anticipated that this realization will simplify approaches to the protein-folding problem.It is well-known that a protein molecule will adopt its native three-dimensional structure spontaneously under normal physiological conditions (1). The transition to the native state from -a denatured state is called protein folding. Despite intense research, a generalized mechanistic understanding of the folding transition remains obscure. This important question is called the protein-folding problem.A key question-perhaps the key question-is the extent to which protein conformation is determined by packing interactions within the hydrophobic core. This question has its origins in the seminal work of Kauzmann (2), who used model compounds to argue that the burial of hydrophobic groups serves as a primary source of stabilization energy in folded proteins. Later, Richards showed that these buried groups are as well packed, on average, as crystals of small organic molecules, with packing densities more reminiscent of solids than of oil (3, 4). The inside of a typical protein contains side chains that fit together with a striking complementarity, like pieces of a three-dimensional jigsaw puzzle.The high packing densities seen in globular proteins are an experimental fact (3-6). This fact has been interpreted to mean that protein conformation is linked tightly to internal packing. According to this interpretation, for example, lysozyme does not have the same folded conformation as ribonuclease, although both proteins have approximately the same size and composition, because the lysozyme sequence cannot achieve efficient internal packing when organized into a ribonuclease fold. Such an interpretation of packing is consistent with classical studies of protein evolution, where the most conser...

Side‐chain entropy and packing in proteins

“…Side chains in this simple model of nuts and bolts packing (1) strongly oppose folding, compared to the linear chain; (2) only freeze completely into place and lose much entropy in the final approach to maximum compactness; (3) give rise to different contact frequencies among and between side chains and main chain in open states; (4) give rise to distributions of the different contact types in compact states similar to those observed in the PDB; (5) have no steric complementarities and therefore predict tolerance to mutations and relatively random distributions of mutually buried areas as observed by Behe et al (1991); and (6) do not by themselves lead to an entropy barrier that could account for the 2-state thermodynamics of protein folding. The SCM is simple enough to permit explorations of open conformations without approximation, including main-chain degrees of freedom, and to predict how configurational freedom and patterns of intrachain contacts depend on chain density.…”

“…There is further evidence in protein dynamics studies for the flexibility of protein interiors: small molecules rapidly diffuse to buried residues (Gurd & Rothgeb, 1979;Karplus & McCammon, 1981), and aromatic rings rotate with low activation energy barriers (Wiithrich & Wagner, 1978). Finally, studies of protein native structures show that neighboring core side chains have little or no tendency toward specific preferred mutually buried areas (Behe et al, 1991), and little preference for particular relative orientations of spatially neighboring hydrophobic side chains (Singh & Thornton, 1990, 1992. In these respects side-chain organization does not resemble the packing of a jigsaw puzzle.…”

A folding pathway for βpep‐4 peptide 33mer: From unfolded monomers and β‐sheet sandwich dimers to well‐structured tetramers

“…This should occur in a correlated fashion with good sidechain packing of the sandwiched hydrophobics-residues. Behe et al (1991) reported that hydrophobic interactions alone provide insufficient directionality and specificity for native-like folding. In ppep-4, the interfacial p-strand hydrogen bonds could direct the uniqueness of the fold.…”

Kinetic evidence for a two-stage mechanism of protein denaturation by guanidinium chloride

“…The role of packing interactions in the stability of proteins has been widely debated (43)(44)(45). Although hydrophobic interactions are considered the major determinant of protein stability, the observation of a state in which the core is loosely packed but dry highlights the importance of packing interactions for the stability of the protein fold.…”