Helical Hydrophobic Moment Research Articles

SUR1 L0 and Kir6.2 M0 can Partner in KATP Gating: Evidences from Diabetogenic Mutations

Neonatal diabetes (ND) mutations in different domains of either KATP subunit overactivate KATP via different mechanisms. Mutations in the ABC core of SUR1 augment its Mg-nucleotide-dependent stimulation of Kir6.2. Mutations at the putative ATP site of Kir6.2 supposedly compromise the inhibitory nucleotide binding. Mutations at the putative gate reportedly stabilize its open state. Many ND mutations map to the putative L0 helix preceding the SUR1 core and to the M0 (‘slide’) helix of Kir6.2. We discovered that L0 controls spontaneous bursting and introduced a model in which L0 and M0 partner in KATP gating (Babenko & Bryan 2003). The model predicted that ND mutations in either amphipathic helix at the membrane-cytosol interface hyperactivate KATP by altering its intrinsic gating kinetics. Here we tested the idea. We compared the effects of severe ND mutations in the middle of either interface helix on spontaneous single-channel kinetics, ATP-inhibition, and Mg-nucleotide stimulation of KATP. We found that each of these mutations decreases the rate of burst termination while increasing the rate of burst initiation, thereby reducing the availability of the closed state with the lowest Kd for inhibitory ligands. This mechanism attenuates ATP inhibition but not Mg-nucleotide stimulation, thereby hyperactivating KATP in vivo, and uncouples sulfonylurea binding from Kir6.2 closure. Thus, in support of our model, perturbing either interface helix disrupts SUR1/Kir6.2 inhibitory coupling. Affinity photolabeling with I-azidoglibenclamide indicated that none of the ND mutations altered the proximity of L0 to M0. But each of these mutations changed the helical hydrophobic moment, implying that rotation of either helix along its axis disrupts L0/M0 interactions. We propose that the two interface helices have been optimized to interact and slide together to stabilize the long-lived closed state of SUR1/Kir6.2 complex.

Studies of the Minimum Hydrophobicity of α-Helical Peptides Required To Maintain a Stable Transmembrane Association with Phospholipid Bilayer Membranes

The effects of the hydrophobicity and the distribution of hydrophobic residues on the surfaces of some designed alpha-helical transmembrane peptides (acetyl-K2-L(m)-A(n)-K2-amide, where m + n = 24) on their solution behavior and interactions with phospholipids were examined. We find that although these peptides exhibit strong alpha-helix forming propensities in water, membrane-mimetic media, and lipid model membranes, the stability of the helices decreases as the Leu content decreases. Also, their binding to reversed phase high-performance liquid chromatography columns is largely determined by their hydrophobicity and generally decreases with decreases in the Leu/Ala ratio. However, the retention of these peptides by such columns is also affected by the distribution of hydrophobic residues on their helical surfaces, being further enhanced when peptide helical hydrophobic moments are increased by clustering hydrophobic residues on one side of the helix. This clustering of hydrophobic residues also increases peptide propensity for self-aggregation in aqueous media and enhances partitioning of the peptide into lipid bilayer membranes. We also find that the peptides LA3LA2 [acetyl-K2-(LAAALAA)3LAA-K2-amide] and particularly LA6 [acetyl-K2-(LAAAAAA)3LAA-K2-amide] associate less strongly with and perturb the thermotropic phase behavior of phosphatidylcholine bilayers much less than peptides with higher L/A ratios. These results are consistent with free energies calculated for the partitioning of these peptides between water and phospholipid bilayers, which suggest that LA3LA2 has an equal tendency to partition into water and into the hydrophobic core of phospholipid model membranes, whereas LA6 should strongly prefer the aqueous phase. We conclude that for alpha-helical peptides of this type, Leu/Ala ratios of greater than 7/17 are required for stable transmembrane associations with phospholipid bilayers.

Helix Packing Moments Reveal Diversity and Conservation in Membrane Protein Structure

Helical membrane proteins are more tightly packed and the packing interactions are more diverse than those found in helical soluble proteins. Based on a linear correlation between amino acid packing values and interhelical propensity, we propose the concept of a helix packing moment to predict the orientation of helices in helical membrane proteins and membrane protein complexes. We show that the helix packing moment correlates with the helix interfaces of helix dimers of single pass membrane proteins of known structure. Helix packing moments are also shown to help identify the packing interfaces in membrane proteins with multiple transmembrane helices, where a single helix can have multiple contact surfaces. Analyses are described on class A G protein-coupled receptors (GPCRs) with seven transmembrane helices. We show that the helix packing moments are conserved across the class A family of GPCRs and correspond to key structural contacts in rhodopsin. These contacts are distinct from the highly conserved signature motifs of GPCRs and have not previously been recognized. The specific amino acid types involved in these contacts, however, are not necessarily conserved between subfamilies of GPCRs, indicating that the same protein architecture can be supported by a diverse set of interactions. In GPCRs, as well as membrane channels and transporters, amino acid residues with small side-chains (Gly, Ala, Ser, Cys) allow tight helix packing by mediating strong van der Waals interactions between helices. Closely packed helices, in turn, facilitate interhelical hydrogen bonding of both weakly polar (Ser, Thr, Cys) and strongly polar (Asn, Gln, Glu, Asp, His, Arg, Lys) amino acid residues. We propose the use of the helix packing moment as a complementary tool to the helical hydrophobic moment in the analysis of transmembrane sequences.

Hydrophobic moments of tertiary protein structures.

The helical hydrophobic moment is a measure of the amphiphilicity of a segment of protein secondary structure. Such measure yields information of potential relevance for issues relating to cell surface binding and secondary structure function. The present article describes a global analog of the helical hydrophobic moment. The global moment provides a concise measure of the degree and direction of the amphiphilicity or hydrophobic imbalance across the entire protein tertiary structure. Therefore, this measure is a succinct representation of the spatial organization of residue hydrophobicity for each protein. With this measure, a simple comparison of the hydrophobic imbalance or segregation of different protein structures can be made. For example, two structures having the same fold and close in root-mean-square deviation may exhibit very different overall hydrophobic organization. Such difference is classified simply by the global moment. Furthermore, the direction of the global moment may point to regions of functional interest. Certain formal issues in the development of such moment are described, and a number of applications to particular protein structures are discussed.

Quantitative approaches to utilizing mutational analysis and disulfide crosslinking for modeling a transmembrane domain.

The transmembrane domain of chemoreceptor Trg from Escherichia coli contains four transmembrane segments in its native homodimer, two from each subunit. We had previously used mutational analysis and sulfhydryl cross-linking between introduced cysteines to obtain data relevant to the three-dimensional organization of this domain. In the current study we used Fourier analysis to assess these data quantitatively for periodicity along the sequences of the segments. The analyses provided a strong indication of alpha-helical periodicity in the first transmembrane segment and a substantial indication of that periodicity for the second segment. On this basis, we considered both segments as idealized alpha-helices and proceeded to model the transmembrane domain as a unit of four helices. For this modeling, we calculated helical crosslinking moments, parameters analogous to helical hydrophobic moments, as a quantitative way of condensing and utilizing a large body of crosslinking data. Crosslinking moments were used to define the relative separation and orientation of helical pairs, thus creating a quantitatively derived model for the transmembrane domain of Trg. Utilization of Fourier transforms to provide a quantitative indication of periodicity in data from analyses of transmembrane segments, in combination with helical crosslinking moments to position helical pairs should be useful in modeling other transmembrane domains.

Membrane interactions of synthetic peptides corresponding to amphipathic helical segments of the human immunodeficiency virus type-1 envelope glycoprotein.

The human and simian immunodeficiency virus envelope glycoproteins, which mediate virus-induced cell fusion, contain two putative amphipathic helical segments with large helical hydrophobic moments near their carboxyl-terminal ends. In an attempt to elucidate the biological role of these amphipathic helical segments, we have synthesized peptides corresponding to residues 768-788 and 826-854 of HIV-1/WMJ-22 gp160. Circular dichroism studies of the peptides showed that the alpha helicity of the peptides increased with the addition of dimyristoyl phosphatidylcholine (DMPC) indicating that the peptides form lipid-associating amphipathic helixes. The peptides solubilized turbid suspensions of DMPC vesicles, and electron microscopy of peptide-DMPC mixtures revealed the formation of discoidal complexes, suggesting that the peptides bind to and perturb lipid bilayers. The peptides were found to lyse lipid vesicles and caused carboxyfluorescein leakage from dye-entrapped egg phosphatidylcholine liposomes. The peptides also lysed human erythrocytes and were found to be toxic to cell cultures. At subtoxic concentrations, the peptides effectively inhibited the fusion of CD4+ cells infected with recombinant vaccinia virus expressing human immunodeficiency virus (HIV)-1 envelope proteins. Based on these results, and reported studies on the mutational analysis of HIV envelope proteins, we suggest that the amphipathic helical segments near the carboxyl terminus of HIV envelope proteins may play a role in lysis of HIV-infected cells and also may modulate the extent of cell fusion observed during HIV infection of CD4+ cells.

Location of helical regions in tetrapyrrole-containing proteins by a helical hydrophobic moment analysis. Application to phytochrome.

Helical regions in many tetrapyrrole proteins are highly amphiphilic, one side interacting with a hydrophobic core and another side interacting with the polar solvent. The mean helical hydrophobic moment is a measure of amphiphilicity of a helix. Helical regions in myoglobin, the alpha and beta subunits of C-phycocyanin, and cytochrome c can be distinguished from nonhelical regions by use of a hydrophobic moment analysis. 24 of 27 (89%) of the helical regions in these proteins were located by this analysis. Calculations were also performed on chymotrypsin, ribonuclease, and papain, which do not possess as pronounced a hydrophobic core as the tetrapyrrole-containing proteins. Less than 50% of the helical regions were correctly located, indicating a lack of amphiphilicity in the helices of these proteins. The hydrophobic moment analysis was also used to predict helical regions in phytochrome, the ubiquitous photoreceptor in plants. Additionally, this analysis is used to quickly locate internal hydrophilic residues which may be functionally important. The distribution of hydrophobic moments from a random sequence was determined so that qualitative and to some extent quantitative comparisons between different amphiphilic helices may be made.

The most highly amphiphilic α‐helices include two amino acid segments in human immunodeficiency virus glycoprotein 41

A search for highly amphiphilic alpha-helices has been made in a data base of protein sequences, using the helical hydrophobic moment as a criterion of amphiphilicity. The protein segments of largest hydrophobic moment have been analyzed. For the segments whose structures are known, they are in fact alpha-helices. Two of the segments having very large hydrophobic moments are from the smaller C-terminal portion of the human immunodeficiency virus (HIV) envelope glycoprotein gp41. Also, among segments having large hydrophobic moments, but not among the most extreme, are lytic peptides such as melittin. Melittin seeks surfaces between polar and apolar phases, including the membrane-water interface. It is conceivable that the gp41 segments of extreme hydrophobic moment may participate in one of the membrane-related functions of the HIV virus.

Identification of peptide hormones of the amphipathic helix class using the helical hydrophobic moment algorithm.

Eisenberg's helical hydrophobic moment (less than mu H greater than) algorithm was applied to the analysis of the primary structure of amphipathic alpha-helical peptide hormones and an optimal method for identifying other peptides of this class determined. We quantitate and compare known amphipathic helical peptide hormones with a second group of peptides with proven nonamphipathic properties and determine the best method of distinguishing between them. The respective means of the maximum 11 residue less than mu H greater than for the amphipathic helical and control peptides were 0.46 (+/-/-0.07) and 0.33 (0.07) (P + 0.004). To better reflect the amphipathic potential of the entire peptide, the percent of 11 residue segments in each peptide above a particular less than mu H greater than was plotted vs less than mu H greater than. The resulting curves are referred to as HM-C. The mean HM-C (of the two groups) was highly significantly different such that the HM-C method was superior to others in its ability to distinguish amphipathic from nonamphipathic peptides. Several potential new members of this structural class were identified using this approach. Molecular modeling of a portion of one of these, prolactin inhibitory factor, reveals a strongly amphipathic alpha helix at residues 4-21. This computer-based method may enable rapid identification of peptides of the amphipathic alpha-helix class.

Reduction in antiviral activity of human interferon-γ in acidic media with reference to structural change

The fluorescence intensity of a unique tryptohan 36 in human interferon-γ was drastically decreased below pH 4 with a concomitant decrease of antiviral activity. The region of residues 32–42 of human interferon-γ was found by calculation to have a low hydrophobicity together with a high helical hydrophobic moment, and the net electric charge of this region having an amphiphilic helical structure changed significantly near pH 4. These results suggest that the region of residues 32–42 plays am important role in exhibiting antiviral activity.

Differences in the hydrophobic properties of discrete alpha-helical domains of rat and human apolipoprotein A-IV

The primary structure of human apolipoprotein A-IV has been analyzed to identify amphipathic alpha-helical regions and compare their hydrophobic properties with analogous segments of rat apolipoprotein A-IV. Significant differences were found in the mean hydrophobicity and/or mean helical hydrophobic moment of several discrete alphα-helical domains of rat and human apolipoprotein A-IV, which may determine the differences in their biophysical and biological behavior.

Predicted calmodulin-binding sequence in the gamma subunit of phosphorylase b kinase.

A basic, amphiphilic alpha helix is a structural feature common to a variety of inhibitors of calmodulin and to the calmodulin-binding domains of myosin light chain kinases. To aid in recognizing this structural feature in sequences of peptides and proteins we have developed a computer algorithm which searches for sequences of appropriate length, hydrophobicity, helical hydrophobic moment, and charge to be considered as potential calmodulin-binding sequences. Such sequences occurred infrequently in proteins of known crystal structure. This algorithm was used to find the most likely site in the catalytic (gamma) subunit of phosphorylase b kinase for interaction with calmodulin (the delta subunit). A peptide corresponding to this site (residues 341-361 of the gamma subunit) was synthesized and found to bind calmodulin with approximately an 11 nM dissociation constant. A variant of this peptide in which an aspartic acid at position 7 in its sequence (347 of the gamma subunit) was replaced with an asparagine was found to bind calmodulin with approximately a 3 nM dissociation constant.

37] Recognition and characterization of calmodulin-binding sequences in peptides and proteins

Publisher Summary This chapter provides methods for the recognition and analysis of basic, amphiphilic calmodulin-binding regions in peptides and proteins. The first calmodulin-binding peptides were discovered through screening of peptide hormones for calmodulin-binding activity. Calmodulin also contains a hydrophobic patch that becomes more exposed upon calcium binding. Recent evidence has given credence to the premise that amphiphilic α helical peptides are good models for the calmodulin-binding site of target enzymes. A 27-residue peptide has been isolated from a CNBr digest of skeletal muscle myosin light chain kinase (MLCK), which appears to comprise this enzyme's calmodulin-binding domain. The helical wheel is a widely used qualitative method for locating potential calmodulin-binding sites within a protein sequence. A rapid method of quantitating the information presented on a helical wheel involves calculation of the average helical hydrophobic moment (μH), which is defined as the mean vector sum of the hydrophobicities of the residues in the helix. Binding of peptides to calmodulin can be determined in a number of ways that rely on monitoring changes in the physical and spectroscopic properties of calmodulin and/or peptides that accompany complex formation. Fluorescence spectroscopy is an excellent method for evaluating. It is also shown that peptides become more helical when they bind calmodulin and that this increase in helicity is readily measured by far-ultraviolet circular dichroism spectroscopy (CD).

Fluorescence quenching studies of apolipoprotein A-I in solution and in lipid-protein complexes: protein dynamics.

Fluorescence lifetime and intensity quenching studies of human plasma apolipoprotein A-I (apo A-I) in aqueous solution and in recombinant lipoprotein complexes with dimyristoylphosphatidylcholine (DMPC) indicate differences in conformational dynamics. In aqueous solution, the bimolecular quenching constants (k*) for lipid-free apo A-I fluorescence quenching by oxygen and acrylamide are 2.4 X 10(9) and 0.38 X 10(9) M-1 s-1, respectively. These values are independent of the oligomeric form of the protein. There is no correlation between the relatively small k* for apo A-I, which reflects rapid, low-amplitude protein fluctuations, and the labile conformational changes of apo A-I folding reactions, like denaturation, which occur on a slower time scale. In recombinant DMPC/apo A-I complexes (100:1 molar ratio) the protein increases in amphiphilic alpha-helical structure as it blankets the lipid matrix. The apparent k* for oxygen quenching of apo A-I fluorescence in the complex is large and increases in a temperature-dependent manner. We have introduced a two-compartment model, which discriminates the source of quencher molecules as aqueous or lipid, to describe oxygen quenching of DMPC/apo A-I fluorescence. The magnitude and temperature dependence of the apparent k* predominantly reflect the partitioning of oxygen between the two phases rather than being a probe of the lipid physical state. Calculations of the helical hydrophobic moment in apo A-I indicate that tryptophan residues 8 and 72 occur at the lipid-protein interface of amphiphilic alpha-helices, whereas the other two tryptophan residues (50, 108) lie on the nonpolar faces of amphiphilic helices.(ABSTRACT TRUNCATED AT 250 WORDS)

The helical hydrophobic moment avoids prolines in phospholipid-binding proteins

Proline residues appear to punctuate the distribution of amphiphilic phospholipid-binding regions of apolipoproteins. We have applied a quantitative test to this hypothesis and shown that the magnitude of the helical hydrophobic moment around proline residues is reduced in lipid-binding proteins and peptides.

The hydrophobic moment of the amphipathic helix of salmon calcitonin and biological potency.

The formation of an amphipathic helix in the central portion of calcitonin contributes to the potency of this hormone. We have synthesized a number of analogs of salmon calcitonin, containing deletions in the region of the peptide which is thought to form an amphipathic helix. There is no direct relationship between the hydrophobic moment of the helix and the biological activity of the peptide. For example, salmon des-Leu19-calcitonin and des-Ser13-calcitonin both have lower helical hydrophobic moments but have greater or equal biological potency compared with the native hormone. We suggest that other conformational features, such as flexibility and helix-forming potential, are also important in determining biological potency.

Use of hydrophobicity profiles to predict receptor binding domains on apolipoprotein E and the low density lipoprotein apolipoprotein B-E receptor.

We have used mean hydrophobicity and hydrophobic moment calculations to predict the receptor binding domains in apolipoprotein E and in the low density lipoprotein apolipoprotein B-E receptor. In apolipoprotein E, two receptor binding domains, residues 136-160 and 214-236, having a high hydrophilicity and a high mean helical hydrophobic moment, were identified. The first domain has been located experimentally and mutations influencing the hydrophobicity parameters of the binding site have been shown to affect the receptor binding. The second domain is probably, either separately or in combination with the first domain, involved in receptor binding or in heparin binding. In the low density lipoprotein apolipoprotein B-E receptor, six protein domains were identified. In the first domain (residues 1-371), eight hydrophilic maxima, organized in pairs through disulfide bonds, form the four experimentally observed receptor binding sites. These sites consist of repeats of 26 amino acids but differ from those reported by others [Yamamoto, T., Davis, C. G., Brown, M. S., Schneider, W. J., Casey, M. L., Goldstein, J. W. & Russell, D. W. (1984) Cell 39, 27-38]. The second, more hydrophobic, domain (residues 372-640) forms the core of the receptor, explaining its homology with the precursor of mouse epidermal growth factor, while the cysteine residues in the third domain (residues 641-699), interacting with those of the first domain, further stabilize the molecule. Beyond the fourth hydrophilic domain (residues 700-767), to which carbohydrates are linked, a very hydrophobic membrane spanning region (residues 768-789) could be detected easily. The last domain (residues 790-839), situated in the cytoplasma, contains hydrophilic maxima, as this region might interact with clathrin-related proteins. These data suggest that hydrophobicity analysis can detect and predict protein domains: hydrophilic receptor sites as well as hydrophobic core-forming and membrane-spanning regions.

Triangular matrix representation of dimensionless helical hydrophobic moment ratios

If the hydrophobicity of the ith residue in an α-helix is denoted by H i , one can (following Eisenberg) define a corresponding vector, h i = a i H i . Here a i is a unit vector directed radially from the helix axis through C i α . The vector sum of the h i for the N residues in an α-helix is denoted by h, and h 2 is the square of the magnitude of h. In the absence of any correlation in the h i we obtain h 2 = ∑ H i 2, where the sum extends over all N residues in the helix. The dimensionless ratio h 2/∑ H i 2 has the value 1 when the h i are uncorrected. However, if hydrophobic residues occur on the opposite surface of a helix from the hydrophilic residues, h 2/∑ H i 2 > 1. The h 2/∑ H i 2 for the n( n − 1)/2 helices that might occur in a chain of n residues are conveniently displayed as the elements in a symmetric n × n matrix. The jkth and kjth elements are h 2/∑ H i 2 for the helix that initiates at residue j and terminates at residue k. All of the h 2/∑ H i 2 are retained in either of the triangular matrices that together together constitute the symmetric matrix. The largest element in the triangular matrix for glucagon is the entry for a helix that is nearly identical with the major helix found by Wüthrich when the peptide is bound to a zwitterionic micelle. Three related hormonal peptides have their maximum h 2/∑ H i 2 in the same region of their respectively triangular matrices. The triangular matrix for α-tropomyosin shows that the h 2/∑ H i 2 are larger in the portion of the chain that forms the more stable helix in the in-register dimer.

Isolation and characterization of the human apolipoprotein A-II gene. Electron microscopic analysis of RNA:DNA hybrids, nucleotide sequence, identification of a polymorphic MspI site, and general structural organization of apolipoprotein genes.

Three cloned apolipoprotein A-II genes were isolated from a human genomic cosmid library constructed in our laboratory. An approximately 3-kilobase HindIII insert containing the entire gene was analyzed by RNA:DNA hybridization and electron microscopy. The apo-A-II gene was found to consist of 4 exons and 3 intervening sequences (IVS), and the lengths of each exon and IVS were estimated by direct observation of the hybrids. The entire approximately 3-kilobase HindIII insert was sequenced. The 5' end of the gene was determined by primer extension. The DNA sequence confirms the presence of 4 exons and 3 IVS: exon 1, 34 nucleotides; exon 2, 76 nucleotides; exon 3, 133 nucleotides; exon 4, 230 nucleotides; IVS-I, 169 nucleotides; IVS-II, 299 nucleotides; and IVS-III, 396 nucleotides. A "TATA box" is located at position -29 from the CAP site. A "CAT box" is present at position -78. A "TG" element consisting of (TG)19 is identified at the 3' end of IVS-III. Furthermore, an enhancer core sequence, CTTTCCA, is identified at position -355 in the 5' flanking sequence. At positions -497 to -471 upstream from the CAP site is a stretch of 27 nucleotides that show high homology to stretches of 5' flanking sequences in the apo-C-II, apo-A-I, apo-E, and apo-C-III genes. An Alu dimer sequence is located approximately 300 nucleotides from the 3' end of the gene. Within this Alu sequence, we have identified a polymorphic MspI site. Restriction fragment length polymorphism involving this site has been previously shown to correlate with apo-A-II levels and high density lipoprotein structure. Analysis of conformation by Chou-Fasman analysis and by the helical hydrophobic moment of Eisenberg et al. (Eisenberg, D., Weiss, R. M., and Tergwillager, T. C. (1982). Nature (Lond.) 299, 371-374) indicates that in all of the 5 apolipoproteins characterized at the nucleotide level to date, i.e. apo-C-II, apo-A-II, apo-E, apo-A-I, and apo-C-III, the 2 IVS within the peptide coding regions of the gene tend to occur at regions corresponding to the surface of the polypeptide chain and divide the protein into distinct functional domains.

Helical hydrophobic moment profiles in α and β tropomyosin

Averaged helical hydrophobic moment ratios have been evaluated in order to asses the potential of amphiphilic regions contributing to the helix-helix interaction responsible for stabilization of tropomyosin dimers. These ratios yield profiles that are higher in the amino-terminal half than in the carboxyl-terminal half of α and β tropomyosin chains. The higher profiles found in the amino-terminal half of α tropomyosin may contribute to the greater stability of the dimer in this region. Especially small helical hydrophobic moment ratios are found for fragments at each chain end and in the interior near Cys 190. These locations have previously been shown to be regions of instability in tropomyosin dimers