scispace - formally typeset
Search or ask a question
Journal ArticleDOI

A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids

02 Nov 1990-Science (American Association for the Advancement of Science)-Vol. 250, Iss: 4981, pp 646-651
TL;DR: The relative thermodynamic stabilities of each of the 20 commonly occurring amino acids in the alpha-helical versus random coil states have been determined through the design of a peptide that forms a noncovalent alpha- Helical dimer, which is in equilibrium with a randomly coiled monomeric state.
Abstract: Amino acids have distinct conformational preferences that influence the stabilities of protein secondary and tertiary structures. The relative thermodynamic stabilities of each of the 20 commonly occurring amino acids in the alpha-helical versus random coil states have been determined through the design of a peptide that forms a noncovalent alpha-helical dimer, which is in equilibrium with a randomly coiled monomeric state. The alpha helices in the dimer contain a single solvent-exposed site that is surrounded by small, neutral amino acid side chains. Each of the commonly occurring amino acids was substituted into this guest site, and the resulting equilibrium constants for the monomer-dimer equilibrium were determined to provide a list of free energy difference (delta delta G degree) values.
Citations
More filters
PatentDOI
17 Apr 1998-Cell
TL;DR: The crystal structure of this complex, composed of the peptides N36 and C34, is a six-helical bundle that shows striking similarity to the low-pH-induced conformation of influenza hemagglutinin and likely represents the core of fusion-active gp41.

2,162 citations

Journal ArticleDOI
26 Nov 1993-Science
TL;DR: These studies demonstrate that conserved, buried residues in the GCN4 leucine zipper direct dimer formation are essential determinants of the global fold.
Abstract: Coiled-coil sequences in proteins consist of heptad repeats containing two characteristic hydrophobic positions. The role of these buried hydrophobic residues in determining the structures of coiled coils was investigated by studying mutants of the GCN4 leucine zipper. When sets of buried residues were altered, two-, three-, and four-helix structures were formed. The x-ray crystal structure of the tetramer revealed a parallel, four-stranded coiled coil. In the tetramer conformation, the local packing geometry of the two hydrophobic positions in the heptad repeat is reversed relative to that in the dimer. These studies demonstrate that conserved, buried residues in the GCN4 leucine zipper direct dimer formation. In contrast to proposals that the pattern of hydrophobic and polar amino acids in a protein sequence is sufficient to determine three-dimensional structure, the shapes of buried side chains in coiled coils are essential determinants of the global fold.

1,490 citations

Journal ArticleDOI
25 Oct 1991-Science
TL;DR: The crystal structure of the GCN4Leucine zipper suggests a key role for the leucine repeat, but also shows how other features of the coiled coil contribute to dimer formation.
Abstract: The x-ray crystal structure of a peptide corresponding to the leucine zipper of the yeast transcriptional activator GCN4 has been determined at 1.8 angstrom resolution. The peptide forms a parallel, two-stranded coiled coil of alpha helices packed as in the "knobs-into-holes" model proposed by Crick in 1953. Contacts between the helices include ion pairs and an extensive hydrophobic interface that contains a distinctive hydrogen bond. The conserved leucines, like the residues in the alternate hydrophobic repeat, make side-to-side interactions (as in a handshake) in every other layer of the dimer interface. The crystal structure of the GCN4 leucine zipper suggests a key role for the leucine repeat, but also shows how other features of the coiled coil contribute to dimer formation.

1,442 citations

Journal ArticleDOI
TL;DR: These studies suggest the possibility of creating “foldable” chain molecules other than proteins, and can account for the properties that characterize protein folding: two‐state cooperativity, secondary and tertiary structures, and multistage folding kinetics.
Abstract: General principles of protein structure, stability, and folding kinetics have recently been explored in computer simulations of simple exact lattice models. These models represent protein chains at a rudimentary level, but they involve few parameters, approximations, or implicit biases, and they allow complete explorations of conformational and sequence spaces. Such simulations have resulted in testable predictions that are sometimes unanticipated: The folding code is mainly binary and delocalized throughout the amino acid sequence. The secondary and tertiary structures of a protein are specified mainly by the sequence of polar and nonpolar monomers. More specific interactions may refine the structure, rather than dominate the folding code. Simple exact models can account for the properties that characterize protein folding: two-state cooperativity, secondary and tertiary structures, and multistage folding kinetics-fast hydrophobic collapse followed by slower annealing. These studies suggest the possibility of creating "foldable" chain molecules other than proteins. The encoding of a unique compact chain conformation may not require amino acids; it may require only the ability to synthesize specific monomer sequences in which at least one monomer type is solvent-averse.

1,433 citations

Journal ArticleDOI
TL;DR: This review focuses on the regulation of GRK activity by a variety of allosteric and other factors: agonist-stimulated GPCRs, beta gamma subunits of heterotrimeric GTP- binding proteins, phospholipid cofactors, the calcium-binding proteins calmodulin and recoverin, posttranslational isoprenylation and palmitoylation, autophosphorylation, and protein kinase C-mediated GRK phosphorylation.
Abstract: G protein-coupled receptor kinases (GRKs) constitute a family of six mammalian serine/threonine protein kinases that phosphorylate agonist-bound, or activated, G protein-coupled receptors (GPCRs) as their primary substrates. GRK-mediated receptor phosphorylation rapidly initiates profound impairment of receptor signaling, or desensitization. This review focuses on the regulation of GRK activity by a variety of allosteric and other factors: agonist-stimulated GPCRs, beta gamma subunits of heterotrimeric GTP-binding proteins, phospholipid cofactors, the calcium-binding proteins calmodulin and recoverin, posttranslational isoprenylation and palmitoylation, autophosphorylation, and protein kinase C-mediated GRK phosphorylation. Studies employing recombinant, purified proteins, cell culture, and transgenic animal models attest to the general importance of GRKs in regulating a vast array of GPCRs both in vitro and in vivo.

1,328 citations

References
More filters
Book ChapterDOI
TL;DR: The chapter reviews that the denaturation is a process in which the spatial arrangement of the polypeptide chains within the molecule is changed from that typical of the native protein to a more disordered arrangement.
Abstract: Publisher Summary This chapter explores that the changes that take place in the protein molecules during denaturation constitute one of the most interesting and complex classes of reactions that can be found either in nature or in the laboratory These reactions are important because of the information they can provide about the more intimate details of protein structure and function They are also significant because they challenge the chemist with a difficult area for the application of chemical principles The chapter reviews that the denaturation is a process in which the spatial arrangement of the polypeptide chains within the molecule is changed from that typical of the native protein to a more disordered arrangement The chapter also discusses the classification of protein structures: primary, secondary, and tertiary structures The primary structure is that expressed by the structural chemical formula and depends entirely on the chemical valence bonds that the classical organic chemist would write down for the protein molecule The secondary structure is the configuration of the polypeptide chain that results from the satisfaction of the hydrogen bonding potential between the peptide N-H and C=O groups The tertiary structure is the pattern according to which the secondary structures are packed together within the native protein molecule The term “denaturation” as used in this chapter is indented to include changes in both the secondary and tertiary structures

4,528 citations

Journal ArticleDOI
TL;DR: A procedure is presented which strongly reduces or elimi- nates these interactions, normalizes their absorption, and consequently permits a more precise analysis of tryptophan and tyrosine in proteins.
Abstract: A rapid method for the determination of tryptophan in proteins is presented. It is based on ab- sorbance measurements at 288 and 280 mp of the protein dissolved in 6 M guanidine hydrochloride. Blocked tryptophanyl (N-acetyl-L-tryptophanamide) and tyrosyl (glycyl-L-tyrosylglycine) compounds were selected as C urrent methods of protein amino acid analysis do not give quantitative values for tryptophan and conse- quently the amino acid compositions, which are other- wise complete, fail to report tryptophan values. The principal reason for this situation is that the standard procedure of protein hydrolysis in strong acid results in the destruction of tryptophan (Hill, 1965). Therefore a second procedure is required to measure tryptophan. Alkaline hydrolysis is less destructive but does not give quantitative recoveries generally (Spies and Chambers, 1949). Enzymatic hydrolysis of proteins can give quanti- tative yields of tryptophan but this method may not be generally valid (Hill and Schmidt, 1962). The hydrolytic problem can be circumvented by meas- uring tryptophan in the intact protein. A chemical method has been developed which has not been exploited adequately (Spies and Chambers, 1948, 1949). On the other hand, considerable effort has been expended in developing absorption spectroscopic procedures to measure tryptophan and tyrosine in unhydrolyzed pro- teins. Holiday (1936) and Goodwin and Morton (1946) have measured the absorption of proteins in 0.1 M NaOH and computed their tryptophan and tyrosine contents based on comparison with the absorption of the two amino acids. A modification of these techniques has been presented by Bencze and Schmid (1957). The pre- ceding three methods do not give quantitative results. The behavior of the chromophores has not been nor- malized and the two models, i.e., tryptophan and tyro- sine, are not completely adequate. A procedure is sug- gested in this report which strongly reduces or elimi- nates these interactions, normalizes their absorption, and consequently permits a more precise analysis of tryptophan and tyrosine in proteins.

3,323 citations

Journal ArticleDOI
16 Mar 1990-Science
TL;DR: Comparison of different sequences with similar messages can reveal key features of the code and improve understanding of how a protein folds and how it performs its function.
Abstract: An amino acid sequence encodes a message that determines the shape and function of a protein. This message is highly degenerate in that many different sequences can code for proteins with essentially the same structure and activity. Comparison of different sequences with similar messages can reveal key features of the code and improve understanding of how a protein folds and how it performs its function.

2,343 citations