Interhelical Interactions Research Articles

Protein destabilization by electrostatic repulsions in the two-stranded alpha-helical coiled-coil/leucine zipper.

The destabilizing effect of electrostatic repulsions on protein stability has been studied by using synthetic two-stranded alpha-helical coiled-coils as a model system. The native coiled-coil consists of two identical 35-residue polypeptide chains with a heptad repeat QgVaGbAcLdQeKf and a Cys residue at position 2 to allow formation of an interchain disulfide bridge. This peptide, designed to contain no intrahelical or interhelical electrostatic interactions, forms a stable coiled-coil structure at 20 degrees C in benign medium (50 mM KCl, 25 mM PO4, pH 7) with a [urea]1/2 value of 6.1 M. Four mutant coiled-coils were designed to contain one or two Glu substitutions for Gln per polypeptide chain. The resulting coiled-coils contained potential i to i' + 5 Glu-Glu interchain repulsions (denoted as peptide E2(15,20)), i to i' + 2 Glu-Glu interchain repulsions (denoted E2(20,22)), or no interchain ionic interactions (denoted E2(13,22) and E1(20)). The stabilities of the coiled-coils were determined by measuring the ellipticities at 222 nm as a function of urea or guanidine hydrochloride concentration at 20 degrees C in the presence and absence of an interchain disulfide bridge. At pH 7, in the presence of urea, the stabilities of E2(13,22) and E2(20,22) were identical suggesting that the potential i to i' + 2 interchain Glu-Glu repulsion in the E2(20,22) coiled-coil does not occur. In contrast, the mutant E2(15,20) is substantially less stable than E2(13,22) or E2(15,20) by 0.9 kcal/mol due to the presence of two i to i' + 5 interchain Glu-Glu repulsions, which destabilize the coiled-coil by 0.45 kcal/mol each. At pH 3 the coiled-coils were found to increase in stability as the number of Glu substitutions were increased. This, combined with reversed-phase HPLC results at pH 7 and pH 2, supports the conclusion that the protonated Glu side chains present at low pH are significantly more hydrophobic than Gln side chains which are in turn more hydrophobic than the ionized Glu side chains present at neutral pH. The protonated Glu residues increase the hydrophobicity of the coiled-coil interface leading to higher coiled-coil stability. The guanidine hydrochloride results at pH 7 show similar stabilities between the native and mutant coiled-coils indicating that guanidine hydrochloride masks electrostatic repulsions due to its ionic nature and that Glu and Gln in the e and g positions of the heptad repeat have very similar effects on coiled-coil stability in the presence of GdnHCl.

A strategy for the de novo design of helical proteins with stable folds.

This paper describes peptide analogs and the design strategy that were used to facilitate the final construction of a de novo-designed protein (ALIN) whose stable tertiary fold has been determined recently by NMR spectroscopy. Previous studies have suggested that the main problem in the de novo design of proteins is the attainment of a protein with a defined fold. To effectively overcome this mainchain multiconformation problem, three related steps, with experimental evaluation of the design hypotheses for each step, were pursued in the design process. Firstly, 15-residue sequences with experimentally verified high helicites were selected for the helical regions. Secondly, hydrophobic and electrostatic interhelical interactions as well as an interhelical disulfide bridge were designed to favor an antiparallel configuration of the helix axis. Finally, a loop with sufficient flexibility was inserted to stabilize the helices in the desired orientation. To assess the design strategy, peptides corresponding to each design step were synthesized and their structures verified experimentally by far-UV CD. As anticipated, ALIN was the most helical, and the SS-bridged dimeric peptides were more helical than their monomeric counterparts. The van't Hoff enthalpy change for ALIN computed from the CD denaturation curve and assuming a two-state model was 50 kJ/mol, a value close to that observed for helical coiled-coils. Overall, this report shows that small, simple proteins can be built using the current knowledge of protein structures.

A thermodynamic scale for leucine zipper stability and dimerization specificity: e and g interhelical interactions.

The leucine zipper is a dimeric coiled-coil protein structure composed of two amphipathic alpha-helices with the hydrophobic surfaces interacting to create the dimer interface. This structure has been found to mediate the dimerization of two abundant classes of DNA binding proteins: the bZIP and bHLH-Zip proteins. Several workers have reported that amino acids in the e and g positions of the coiled coil can modulate dimerization stability and specificity. Using the bZIP protein VBP as a host molecule, we report a thermodynamic scale (delta delta G) for 27 interhelical interactions in 35 proteins between amino acids in the g and the following e positions (g<==>e') of a leucine zipper coiled coil. We have examined the four commonly occurring amino acids in the e and g positions of bZIP proteins, lysine (K), arginine (R), glutamine (Q), glutamic acid (E), as well as the only other remaining charged amino acid aspartic acid (D), and finally alanine (A) as a reference amino acid. These results indicate that E<==>R is the most stable interhelical pair, being 0.35 kcal/mol more stable than E<==>K. A thermodynamic cycle analysis shows that the E<==>R pair is 1.33 kcal/mol more stable than A<==>A with -1.14 kcal/mol of coupling energy (delta delta Gint) coming from the interaction of E with R. The E<==>K coupling energy is only -0.14 kcal/mol. E interacts with more specificity than Q. The R<==>R pair is less stable than the K<==>K by 0.24 kcal/mol. R interacts with more specificity than K. Q forms more stable pairs with the basic amino acids K and R rather than with E. Changing amino acids in the e position to A creates bZIP proteins that form tetramers.

Solution structure of horse heart ferrocytochrome c determined by high-resolution NMR and restrained simulated annealing.

A model for the solution structure of horse heart ferrocytochrome c has been determined by nuclear magnetic resonance spectroscopy combined with hybrid distance geometry-simulated annealing calculations. Forty-four highly refined structures were obtained using a total of 1940 distance constraints based on the observed magnitude of nuclear Overhauser effects and 85 torsional angle restraints based on the magnitude of determined J-coupling constants. The all-residue root mean square deviation about the average structure is 0.47 +/- 0.09 A for the backbone N, C alpha, and C' atoms and 0.91 +/- 0.07 A for all heavy atoms. The overall topology of the model for solution structure is very similar to that seen in previously reported models for crystal structures of homologous c-type cytochromes. However, a detailed comparison between the model for the solution structure and the available model for the crystal structure of tuna ferrocytochrome c indicates significant differences in a number of secondary and tertiary structural features. For example, two of the three main helices display 3(10) to alpha-helical transitions resulting in bifurcation of main-chain hydrogen bond acceptor carbonyls. The N- and C-terminal helices are tightly packed and display several interhelical interactions not seen in previously reported models. The geometry of heme ligation is well-defined and completely consistent with the crystal structures of homologous cytochromes c as are the locations of four of six structural water molecules. Though the total solvent-accessible surface area of the protoporphyrin ring is similar to that seen in crystal studies of tuna ferrocytochrome c, the distribution is somewhat different. This is mainly due to a difference in packing of residues Phe-82 and Ile-81 such that Ile-81 crosses the edge of the heme in the solution structure. These and other observations help to explain a range of physical and biological data spanning the redox properties, folding, molecular recognition, and stability of the protein.

The Role of Interhelical Ionic Interactions in Controlling Protein Folding and Stability: De Novo Designed Synthetic Two-stranded α-Helical Coiled-Coils

The role of interchain ionic interactions in controlling protein folding and stability has been studied by using de novo designed synthetic two-stranded α-helical coiled-coils. The model coiled-coil (denoted as EK) consists of two identical 35-residue polypeptide chains with a heptad repeat KgLaGbAcLdEeKf and a Cys residue at position 2 and an Ala residue at position 16 in each chain. The Lys residues at positions "g" in one chain and Glu residues at positions "e" in the other chain are expected to form interchain ion-pairs in the coiled-coil structure. This peptide forms a stable coiled-coil structure in benign medium (50 mM KCl, 25 mM PO4, pH 7) with a [urea]1/2 value of 3·5 M. In contrast, two peptide analogs EE (EgLaGbAcLdEeKf) and KK (KgLaGbAcLdKeEf), which differ from EK in that EE contains only negatively charged Glu residues and KK contains only positively charged Lys residues at both positions e and g, each show a random coil structure in benign buffer. However, peptide EE or KK can form a stable coiled-coil structure if the interchain ionic repulsions are effectively suppressed either by changing pH or by using high salt concentrations. An equimolar mixture of these two peptides displays 100α α-helical content under the same conditions. These results demonstrate that although the interhelical ionic attractions are not essential for coiled-coil formation, a large number of these weak interactions can play an important role in the assembly of helices. Though interhelical ionic repulsions destabilize the homo-stranded coiled-coil, electrostatic attractions may stabilize the hetero-stranded coiled-coil. In addition, this study also suggests that the folding process for these synthetic model coiled-coils does not involve a single-stranded α-helix as a significantly populated folding intermediate.

Solution Structure of a de Novo Helical Protein by 2D-NMR Spectroscopy

The de novo design of proteins represents a critical test for our knowledge of protein structure. However, no structure of a successfully designed protein has yet been reported. This paper reports the design and the tertiary structure of a de novo 35-residue helix-loop-helix protein (ALIN), with helices arranged in an anti-parallel manner. For the helical region, we designed sequences that have high helicities even as isolated peptides. A flexible loop containing glycine residues was used to connect the two helices and the interhelical hydrophobic interaction was stabilized by the introduction of an SS-bridge. This arrangement of two consecutive helices bridged by a disulfide bond is not observed in any natural proteins. The protein is highly soluble and monomeric in aqueous solution. The structure ALIN, determined by 1H-NMR and distance geometry calculation, agrees well with the design. In addition, the exchange rates of amide protons indicate the presence of stable hydrogen bonds in the helical region. ALIN is the first de novo designed protein with a stable tertiary fold confirmed by NMR.

Interactions of coiled coils in transcription factors: where is the specificity?

Amphipathic α-helices create the dimerization interface in the bZIP and bHLH classes of DNA-binding proteins. These amphipathic helices have been shown to enter into a wide variety of specific dimerization interactions, and this large array of possible combinatorial interactions may provide for fine control of biological function. In bHLH-ZIP proteins, the addition of a leucine-zipper region immediately carboxyl-terminal to the helix-loop-helix region provides for an additional level of both dimerization specificity and control, again through the interaction of amphipathic α-helices. Interhelical electrostatic interactions have been implicated in regulating dimerization specificity.

Application of three-dimensional molecular hydrophobicity potential to the analysis of spatial organization of membrane protein domains. II. Optimization of hydrophobic contacts in transmembrane hairpin structures of Na+, K(+)-ATPase.

A method of packing of transmembrane hairpin helices in proteins is described. The procedure is based on the optimization of hydrophobic contacts calculated using the three-dimensional (3D) molecular hydrophobicity potential technique. To verify the validity of the computational scheme, we calculated relative orientations of membrane-spanning peptides in pairs L2-L3, M2-M3, and M4-M5 from L- and M-subunits of the photoreaction center of Rhodopseudomonas viridis and compared the predicted structures with those derived from atomic coordinates. The results of computer modeling agree with the X-ray data. We applied the approach proposed to study possible interhelical interactions in transmembrane hairpin structures of Na+, K(+)-ATPase.

Metal substitutions at the diiron sites of hemerythrin and myohemerythrin: contributions of divalent metals to stability of a four-helix bundle protein.

A general method is described for substitution of Mn(II) and Co(II) into the diiron sites of hemerythrin and myohemerythrin. Characterizations of these metal-substituted proteins show that their structures closely resemble those of the native proteins. In particular, the four-helix bundle structure appears to be maintained. The apomyohemerythrin retains most of the native helix content but is considerably less stable to denaturation than are the metal-containing proteins. The relative affinities of M(II) for apohemerythrin--namely, Co greater than Fe greater than Mn--parallel the stabilities of the M2myohemerythrins to denaturation by guanidinium chloride. These results indicate that for myohemerythrin (i) the majority of the helical structure found in the native protein does not require incorporation of M(II) and (ii) stabilization of the native structure relative to the fully unfolded structure appears to be due predominantly to M(II)-protein interactions, at least for M = Fe and Co. Incorporation of M(II) also generates unfolding cooperativity in myohemerythrin. This cooperativity can be attributed to interhelical interactions, which are prevented in the apoprotein by solvation of the seven metal ligand residues. The results are consistent with a minimal model for folding/unfolding of myohemerythrin and hemerythrin subunits consisting of the sequential equilibria, N in equilibrium with I in equilibrium with D, between native, intermediate, and fully unfolded states, respectively. The properties of apomyohemerythrin make it a candidate for the intermediate state, I.

An infrared study of 2H-bond variation in myoglobin revealed by high pressure.

A high-pressure Fourier-transform infrared technique was used to probe the evolution of 2H bonds inside the helical segments of myoglobin in relation to p2H, Tris concentration in the medium and iron-ligand nature. The analysis was focused on changes in the conformation-sensitive amide-I' band, reflecting the peptide C = O group stretching vibrations coupled to the in-plane N-2H bending and C = N stretching modes. From data obtained under high pressure, the strength of 2H bonds, inside the alpha-helical segments of the protein at atmospheric pressure, is not simply a function of p2H and salt concentration. At low Tris concentration (50 mM), the strength of these 2H bonds increases with p2H, whereas for a higher Tris concentration (100 mM) this strength is lower at p2H 7 than at p2H 6.0 or 8.5. It is also observed that the azidometmyoglobin molecule exhibits tighter intrahelical interactions and lower sensitivity to pressure than aquametmyoglobin. Information is also presented regarding interhelical interactions in relation to the solvent.

Structural changes in poly( d-alanine)

Investigations are reported on the possibility of the direct transformations from α-helices to β-sheets in poly( d-alanine) by heating and the immersion into formic acid, and were concluded that intrahelical hydrogen bonds in the α-helix were stable, while interhelical interactions in the α-helix crystal were weakened, and β-sheets did not transform directly from α-helices, but grew from random coils.

Direct effects of ionizing radiation on integral membrane proteins. Noncovalent energy transfer requires specific interpeptide interactions

The 12 transmembrane alpha helices (TMHs) of human erythrocyte glucose transporter were individually cut by pepsin digestion as membrane-bound 2.5-3.5-kDa peptide fragments. Radiation-induced chemical degradation of these fragments showed an average target size of 34 kDa. This is 10-12 x larger than the average size of an individual TMH, demonstrating that a significant energy transfer occurs among these TMHs in the absence of covalent linkage. Heating this TMH preparation at 100 degrees C for 15 min reduced the target size to 5 kDa or less, suggesting that the noncovalent energy transfer requires specific helix-helix interactions. Purified phospholamban, a small (6-kDa) integral membrane protein containing a single TMH, formed a pentameric assembly in sodium dodecyl sulfate. The chemical degradation target size of this phospholamban pentamer was 5-6 kDa, illustrating that not all integral membrane protein assemblies permit intersubunit energy transfer. These findings together with other published observations suggest strongly that significant noncovalent energy transfer can occur within the tertiary and quaternary structure of membrane proteins and that as yet undefined proper molecular interactions are required for such covalent energy transfer. Our results with pepsin-digested glucose transporter also illustrate the importance of the interhelical interaction as a predominating force in maintaining the tertiary structure of a transmembrane protein.

A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase at 2.5 Å

The three-dimensional crystal structure of seryl-transfer RNA synthetase from Escherichia coli, refined at 2.5 A resolution, is described. It has an N-terminal domain that forms an antiparallel alpha helical coiled-coil, stretching 60 A out into the solvent and stabilized by interhelical hydrophobic interactions and an active-site alpha-beta domain based around a seven-stranded antiparallel beta sheet. Unlike the three other known synthetase structures, the enzyme contains no classical nucleotide-binding fold, and is the first representative of a second class of aminoacyl-tRNA synthetase structures.

A Raman Study of Low Frequency Intrahelical Modes in A-, B-, and C-DNA

We have obtained low frequency (less than 200 cm-1) Raman spectra of calf-thymus DNA and poly(rI).poly(rC) as a function of water content and counterion species and of d(GGTATACC)2 and d(CGCGAATTCGCG)2 crystals. We have found that the Raman scattering from water in the first and second hydration shells does not contribute directly to the Raman spectra of DNA. We have determined the number of strong Raman active modes by comparing spectra for different sample orientations and polarizations and by obtaining fits to the spectra. We have found at least five Raman active modes in the spectra of A- and B-DNA. The frequencies of the modes above 40 cm-1 do not vary with counterion species, and there are only relatively small changes upon hydration. These modes are, therefore, almost completely internal. The mode near 34 cm-1 in A-DNA is mostly internal, whereas the mode near 25 cm-1 is dominated by interhelical interactions. The observed intensity changes upon dehydration were found to be due to the decrease in interhelical distance. Polymer length appears to play a role in the lowest frequency modes.

Letter: The structure of polydeoxyguanylic acid with polydeoxycytidylic acid.

B-A transition and DNA condensation are processes regulated by base sequence and water activity. The constraints imposed by interhelical interactions in condensation compromise the observation of the mechanism by which B and A base-stacking modes influence the global state of the molecule. We used a single-molecule approach to prevent aggregation and mechanical force to control the intramolecular chain association involved in condensation. Force-extension experiments with optical tweezers revealed that DNA stretches as B-DNA under ethanol and spermine concentrations that favor the A-form. Moreover, we found no contour-length change compatible with a cooperative transition between the A and B forms within the intrinsic-force regime. Experiments performed at constant force in the entropic-force regime with magnetic tweezers similarly did not show a bistable contraction of the molecules that could be attributed to the B-A transition when the physiological buffer was replaced by a water-ethanol mixture. A total, stepwise collapse was found instead, which is characteristic of DNA condensation. Therefore, a low-humidity-induced change from the B- to the A-form base-stacking alone does not lead to a contour-length shortening. These results support a mechanism for the B-A transition in which low-humidity conditions locally change the base-stacking arrangement and globally induce DNA condensation, an effect that may eventually stabilize a molecular contour-length reduction.

Hairpin bend and interhelical interactions in α-helical poly( l-alanine) in water

Conformational energy calculations were carried out to compute the properties of two antiparallel right-handed α-helical sections (with an intervening hairpin bend) of poly ( l-alanine) in water. Such a structure is stabilized by hydrophobic bonding to the extent of −0.25 kcal/mole residue, by electrostatic interaction between the antiparallel backbones to the extent of −0.35 kcal/mole residue, and by other contributions. The hydrophobic contribution comes from the dehydration of side-chain methyl groups of adjacent helices and from nonbonded (van der Waals) interaction between these same methyl groups. The calculations were carried out with hairpin bends consisting of four, five, and six residues, respectively. For the structure with a six-residue bend, the free energy involved in the transition from a straight α-helical structure of 54 residues to one with the antiparallel helical arrangement (with 24 residues per helix) is −0.69 kcal/mole residue. Consequently, this transition is a favorable one, and may account for the great stability of α-helical poly ( l-alanine) in water, and for the formation of incipient globularity in some proteins (whose folding may be initiated around such an antiparallel array of α-helices).