Physical characterization of lumazine proteins from Photobacterium

The physicochemical properties of Photobacterium lumazine proteins have been investigated. The molecular weights obtained by several physical techniques are in good agreement, and the averages are 2% and 8% higher than the minimum molecular weights from amino acid and ligand content. The average molecular weights, sedimentation coefficients, and molecular radii are respectively the following: Photobacterium leiognathi lumazine protein, 21 200 +/- 300, 2.18 S, and 22.9 A; Photobacterium phosphoreum lumazine protein, 21 300 +/- 500, 2.16 S, and 23.0 A. The hydrations of the lumazine proteins, estimated in several ways, indicate less hydration for P. leiognathi than for P. phosphoreum. The frictional ratios corrected for hydration give axial ratios less than 1.3 for both lumazine proteins. These values agree with those obtained by a combination of rotational and translational frictional parameters and elimination of the common hydrated volume terms. There is insufficient area on the exterior surface to accommodate hydration when the lumzine proteins are considered as smooth-surfaced ellipsoids. The required surface area can be accommodated however by surface roughness with a minimum of 30% internal water.     

Modeling the hydration of proteins: prediction of structural and hydrodynamic parameters from X-ray diffraction and scattering data

The implications of protein-water interactions are of importance for understanding the solution behavior of proteins and for analyzing the fine structure of proteins in aqueous solution. Starting from the atomic coordinates, by bead modeling the scattering and hydrodynamic properties of proteins can be predicted reliably (Debye modeling, program HYDRO). By advanced modeling techniques the hydration can be taken into account appropriately: by some kind of rescaling procedures, by modeling a water shell, by iterative comparisons to experimental scattering curves (ab initio modeling) or by special hydration algorithms. In the latter case, the surface topography of proteins is visualized in terms of dot surface points, and the normal vectors to these points are used to construct starting points for placing water molecules in definite positions on the protein envelope. Bead modeling may then be used for shaping the individual atomic or amino acid residues and also for individual water molecules. Among the tuning parameters, the choice of the scaling factor for amino acid hydration and of the molecular volume of bound water turned out to be crucial. The number and position of bound water molecules created by our hydration modeling program HYDCRYST were compared with those derived from X-ray crystallography, and the capability to predict hydration, structural and hydrodynamic parameters (hydrated volume, radius of gyration, translational diffusion and sedimentation coefficients) was compared with the findings generated by the water-shell approach CRYSOL. If the atomic coordinates are unknown, ab initio modeling approaches based on experimental scattering curves can provide model structures for hydrodynamic predictions.     

Sequence homology of the Ca2+-dependent regulator of cyclic nucleotide phosphodiesterase from rat testis with other Ca2+-binding proteins.

A Ca2+-dependent regulator protein of cyclic 3':5'-nucleotide phosphodiesterase (EC 3.1.4.17) has previously been isolated from rat testis and shown to be a heat-stable, Ca2+-binding protein with a molecular weight of approximately 17,000. The Ca2+-dependent regulator protein is also structurally similar to troponin-C, the Ca2+-binding component of muscle troponin and Ca2+ mediator of muscle contraction. The present report describes a partial amino acid sequence of the Ca2+-dependent regulator. The protein (148 amino acids) is 50% homologous with skeletal muscle troponin-C, but is 11 residues shorter than the muscle protein. The Ca2+-dependent regulator protein has an NH2-terminal sequence of acetyl-Ala-Asp-Glu, a COOH-terminal sequence of Thr-Ala-Lys and 1 residue of epsilon-trimethyllysine located at position 115. All of these properties are distinct from those of other homologous Ca2+-binding proteins. These properties may account for the biological specificities demonstrated by these proteins as compared to the Ca2+-dependent regulator protein. Based on the sequence and a comparison of the Ca2+-dependent regulator protein to other calcium-binding proteins, our data support the view that all of these moecules contain common sequences, especially at their proposed metal-binding sites.     

Proteins will Fold Anyway!!

Abstract

In order to investigate the environmental conditions of amino acid residues in protein molecules, four kinds of packing studies (atomic, geometric, hydrophobic and hydration) were formulated and tested on two proteins; bovine pancreatic trypsin inhibitor (BPTI) and bovine pancreatic ribonuclease S (RNase S). The inter-relationship of these packings on the fluctuations of amino acid residues was analysed by comparing the packing results with the dynamical studies, such as the root-mean-square-deviation values of atomic displacements obtained from the trajectories of molecular dynamics simulation, temperature factor information from crystal structures and residue fluctuations in proteins from continuum model. These analyses yield information about the most fluctuating and most stabilizing residue sites. Comparison of the results obtained by these methods indicate a good agreement, specifying an inverse correlation between the residue packing and fluctuations. This kind of study is helpful in identifying the specific residue sites such as nucleation, receptor binding and antigenic determining sites which in a way indirectly correlates with the functional residues in protein molecules.     

Nanometric design of extraordinary hydrophobic-induced pKa shifts for aspartic acid: Relevance to protein mechanisms

Commonly a key element enabling proteins to function is an amino acid residue or residues with functional side chains having shifted pKa values. This article reports the results on a set of protein-based polymers (model proteins) that exhibit hydrophobic folding and assembly transitions, and that have been designed for the purpose of achieving large hydrophobic-induced pKa shifts by selectively replacing Val residues by Phe residues. The high molecular weight polypentapeptides, actually poly (tricosapeptides) with six varied pentamers in fixed sequence, were designed and synthesized to have the same amino acid compositions but different proximities between a single aspartic acid residue and 5 Phe residues per 30 residues. With the 5 Phe residues distal from the Asp residue, the observed pKa shift was 2.9 when compared to the Val-containing reference. With the 5 Phe residues within 1 nm of the Asp residue, the pKa shift was 6.2. This represents a free energy of interaction of 8 kcal/moles. To our knowledge, this is the largest pKa shift documented for an Asp residue in a polypeptide– or protein–water system. Data are reviewed that do not support the usual electrostatic arguments for pKa shifts of charge–charge repulsion and/or unfavorable ion self-energies arising from displacement of water by hydrophobic moieties, but rather the data are interpreted to indicate the presence of an apolar–polar repulsive free energy of hydration, which results from a potentially highly cooperative competition between apolar and polar species for hydration. © 1994 John Wiley & Sons, Inc.     

Structural and energetic parameters of Ca2+ binding to peptides and proteins

The characteristics of Ca²⁺-binding sites and of the structural reorganization induced by Ca²⁺-binding in storage proteins and ion carriers are being studied as models for molecular mechanisms in Ca²⁺ channels and in Ca²⁺-dependent modulatory proteins. A first step in the study was the development of energy parameters for Ca²⁺ compatible with those in the CHARMM package of computer simulation software. Such parameters were obtained from an analytical fit to the potential surface for [(Ca)(OCH₂)₄]²⁺ calculated with an ab initio molecular orbital method. The resulting parametrization was tested for the hexapeptide cyclo-(Pro-Gly)₃, and a 75 residue long calcium binding protein from bovine intestine (ICaBP). The geometrical parameters calculated for the hexapeptide and its 2:1 complex with Ca²⁺ were in good agreement with experimental data from crystallography and nmr. Similarly, the structure of ICaBP optimized with CHARMM using the new Ca²⁺ parameters showed good agreement with the x-ray structure both in the local structures of the calcium-binding sites and in the overall shape of the protein.     

Light scattering and hydrodynamic properties of linear and circular bacteriophage lambda DNA

Low-angle light scattering, sedimentation velocity, and intrinsic viscosity measurements have been made on circular and linear forms of lambda (λ) bacteriophage DNA. Available equations, used to relate hydrodynamic parameters of both forms to the molecular weight, give relatively consistent values of particle weights which essentially agree with the light-scattering results. An average molecular weight of (34 ± 3) × 10⁶ for λ DNA was obtained in good agreement with literature values of (31–33) × 10⁶. The linear λ DNA has a larger root-mean-square radius than the circular molecule, when determined by light scattering, but the difference does not appear to be us large as expected from hydrodynamic data. The two forms also show significantly different angular distrbutions of scattered light intensities which agree only qualitatively with those derived from existing theory. The light-scattering results suggest that further experiments and modifications of available theories should be undertaken.     

A 13C-NMR study on the conformational and dynamical properties of a cereal seed storage protein,C-hordein,and its model peptides

We have recorded the ¹³C CP-MAS and DD-MAS nmr spectra of dry and hydrated barley storage protein, C-hordein, as a model for wheat S-poor prolamins, together with those of model synthetic peptides (Pro)₂(Gln)₆(I) and (Pro-Gln-Gln-Pro-Phe-Pro-Gln-Gln)₃(II) under dry or hydrated conditions. The spectral features of C-hordein as well as these peptides were appreciably different from each other depending on the extent of hydration, reflecting different domains that adopt different types of conformations as well as dynamics. In particular, considerable proportions of the peak intensities were lost in the CP-MAS spectra, and well-resolved ¹³C-nmr signals emerged in DD-MAS nmr spectra owing to acquisition of molecular motions by swelling. It was shown that local β-turn or (Pro)_n type II conformation is more preferable for individual Pro residues and β-sheet type conformation is dominant for individual Gln residues in the dry and hydrated systems. In addition, two types of Gln environments are originated in C-hordein that differ in their mobility. Further, ¹³C spin-lattice relaxation times (T₁'s) of C- hordein and peptide II were reduced by more than one order of magnitude by hydration, reflecting the presence of well-swollen molecular chains. In contrast, theT₁ values of peptide I upon hydration remained one third of those in the dry state. Carbon-resolved proton spin-lattice relaxation times in the rotating frame (T_1ρ's) were also decreased by about 50% upon hydration, although these parameters were less sensitive as compared to T₁ values. In addition, the ¹³C-nmr signals of the aromatic side chain of Phe residues disappeared on hydration owing to interference between the frequency of the acquired flip-flop motion and the proton decoupling frequency. This information gives a new insight into establishing the structural properties of the studied protein system. A model may be put forward for a gel-type structure in which the more rigid part of the system involves intermolecular hydrogen-bonded Gln side chains as well as some hydrophobic “pockets” involving Pro and Phe residues. The liquid-like domain is characterized by considerable backbone and side-chain motion as well as rapid ring-puckering motion in Pro residues. © 1997 John Wiley & Sons, Inc.     

Soluble microtubule proteins of the sea urchin embryo: partial characterization of the proteins and behavior of the pool in early development

A partial characterization of the soluble microtubule proteins of sea urchin eggs and embryos is presented. Vinblastine precipitation yielded a pellet with a high colchicine binding activity. This precipitate when electrophoresed on an alkaline SDS/urea gel system yields two protein bands which correspond to molecular weights of 57,000 ± 2000 and 52,000 ± 2000. These values are very close to our values and to the published values for axonemal microtubule proteins. Electrophoresis of the vinblastine precipitated proteins on a neutral SDS system without urea yielded only one band with an apparent molecular weight of 52,000 ± 2000. The amino acid composition of the vinblastine-precipitated microtubule protein was determined to be similar to that of axonemal protein.The pool of microtubule proteins was found to remain constant in size throughout early development in both control and actinomycin-treated embryos. Soluble microtubule proteins comprise about 0.37% of the total protein of the sea urchin (Arbacia) egg. Approximately 20% of the total microtubule protein in the egg appears to be particle bound.     

Compressibility-structure relationship of globular proteins

The adiabatic compressibility, -beta s, of 11 globular proteins in water was determined by means of sound velocity measurements at 25 degrees C. All the proteins studied except for subtilisin showed positive -beta s values, indicating the large internal compressibility of the protein molecules. The intrinsic compressibility of proteins free from the hydration effect appeared to be comparable to that of normal ice. The compressibility data for 25 proteins, including 14 reported previously [Gekko, K., & Noguchi, H. (1979) J. Phys. Chem. 83, 2706-2714], were statistically analyzed to examine the correlation of the compressibility with some structural parameters and the amino acid compositions of proteins. It was found that -beta s increases with increasing partial specific volume and hydrophobicity of proteins. The helix element also seemed to be a dynamic domain to increase -beta s. Four amino acid residues (Leu, Glu, Phe, and His) greatly increased -beta s, and another four (Asn, Gly, Ser, and Thr) decreased it. Some empirical equations were derived for the estimation of the -beta s values of unknown proteins on the basis of their amino acid compositions. The volume fluctuations of proteins revealed by the compressibility data were in the range of 30-200 mL/mol, which corresponded to about 0.3% of the total protein volume. The conformational fluctuation seemed to enhance the thermal stability of proteins.     

An endogenous inhibitor protein of synaptic plasma membrane (Ca2+ + Mg2+)-ATPase

An inhibitor protein of synaptic plasma membrane (Ca2+ + Mg2+)-ATPase was purified to apparent homogeneity from rat cerebrum by a molecular weight cut followed by chromatography of cytosol proteins with molecular weights between 10 000 and 3500 on DEAE-Sephadex at pH 5.2. The inhibitor could be partially inactivated by proteinases and dithiothreitol, but was heat-stable. Gel filtration gave a molecular weight of about 6000. Like the (Ca2+ + Mg2+)-ATPase inhibitor protein isolated from erythrocytes, the inhibitor from brain contains a characteristic high proportion of glutamic acid (36%) and glycine (37%) residues. Synaptic plasma membrane Mg2+-ATPase and microsomal membrane (Ca2+ + Mg2+)-ATPase did not respond to the inhibitor. Synaptic plasma membrane and erythrocyte membrane (Ca2+ + Mg2+)-ATPases, however, were affected. Inhibitory influence on synaptic membrane (Ca2+ + Mg2+)-ATPase was reversible, since inhibition could be relieved upon removal of inhibitor from saturable sites on the membrane. The inhibitor is not a calmodulin-binding protein, since the concentration of calmodulin for half-maximal activation of the ATPase was unaffected by its presence. Mode of inhibition of the (Ca2+ + Mg2+)-ATPase by the inhibitor was non-competitive.     

Comprehensive analysis of the numbers,lengths and amino acid compositions of transmembrane helices in prokaryotic,eukaryotic and viral integral membrane proteins of high-resolution structure

We report a comprehensive analysis of the numbers, lengths and amino acid compositions of transmembrane helices in 235 high-resolution structures of integral membrane proteins. The properties of 1551 transmembrane helices in the structures were compared with those obtained by analysis of the same amino acid sequences using topology prediction tools. Explanations for the 81 (5.2%) missing or additional transmembrane helices in the prediction results were identified. Main reasons for missing transmembrane helices were mis-identification of N-terminal signal peptides, breaks in α-helix conformation or charged residues in the middle of transmembrane helices and transmembrane helices with unusual amino acid composition. The main reason for additional transmembrane helices was mis-identification of amphipathic helices, extramembrane helices or hairpin re-entrant loops. Transmembrane helix length had an overall median of 24 residues and an average of 24.9 ± 7.0 residues and the most common length was 23 residues. The overall content of residues in transmembrane helices as a percentage of the full proteins had a median of 56.8% and an average of 55.7 ± 16.0%. Amino acid composition was analysed for the full proteins, transmembrane helices and extramembrane regions. Individual proteins or types of proteins with transmembrane helices containing extremes in contents of individual amino acids or combinations of amino acids with similar physicochemical properties were identified and linked to structure and/or function. In addition to overall median and average values, all results were analysed for proteins originating from different types of organism (prokaryotic, eukaryotic, viral) and for subgroups of receptors, channels, transporters and others.     

Molecular cloning and expression of human neurochondrin-1 and -2.

Human neurochondrins have been cloned from a brain cDNA library. The human neurochondrin-1 and -2 predict leucine-rich (15.8 and 15.9%) proteins of 729 and 712 amino acid residues, with molecular weights of 78.9 and 77.2 kDa, respectively. The deduced amino acid sequence indicates 98% identity among human, mouse and rat species. Northern analysis indicates that about 4 kb human neurochondrin mRNAs are abundant in the fetal and the adult brain.     

Complete primary structure of a human plasma membrane Ca2+ pump

cDNAs coding for a plasma membrane Ca2+ pump were isolated from a human teratoma library and sequenced. The translated sequence contained 1,220 amino acids with a calculated molecular weight of 134,683. All regions of functional importance known from other ion-transporting ATPases could be identified. The translated sequence also contained, near the carboxyl terminus, the calmodulin-binding domain and two domains which are very rich in glutamic acid and aspartic acid. These two domains resemble calmodulin somewhat and one of them may play a role in the binding of Ca2+. The enzyme also contains domains rich in serine and threonine, one of which has a sequence matching those of good cAMP-dependent protein kinase substrates. The carboxyl-terminal region is important for regulation by calmodulin, proteolysis, and phosphorylation. Near the amino terminus are two domains which are very rich in lysine and glutamic acid, as well as two domains resembling EF hands, one of which also has some resemblance to calmodulin. Comparison of the cloned sequence with peptide sequences from the erythrocyte Ca2+ pump showed that the two proteins have a very high proportion of identical residues but are not 100% identical, indicating that they represent different isozymes.     

The CLS2 gene encodes a protein with multiple membrane-spanning domains that is important Ca2+ tolerance in yeast

Genetic screening of Saccharomyces cerevisiae mutants defective in Ca²⁺ homeostasis identified cls2, which exhibits a specific Ca²⁺-sensitive growth phenotype. We describe here the CLS2 gene and a multicopy suppressor (named BCL21, for bypass of CLS2) of the cls2 mutation. The CLS2 gene encodes a polypeptide of 410 amino acid residues, and its hydropathy profile indicates that the predicted Cls2 protein (Cls2p) contains ten putative membrane spanning regions. Immunofluorescent staining of the yeast cells expressing epitopetagged Cls2p suggests that Cls2p is localized to endoplasmatic reticulum (ER) membrane. A cls2 disruption strain is viable, but shows a Ca²⁺-sensitive phenotype like the original cls2 mutants. BCL21 suppresses the cls2 disruption mutation, indicating that the multicopy suppression does not require the Cls2p. Suppression of cls2 was observed even after introduction of a singlecopy plasmid harboring BCL21. The BCL21 gene encodes a protein of 382 amino acid residues and is identical to the SUR1 gene. sur1 was originally isolated as a suppressor of rvs161, which has reduced viability in nutrient starvation conditions. Possible mechanisms of the multicopy suppression are discussed.     

Rise and fall of the delta globin gene

The complete nucleotide sequence of the gene phoE, which codes for the phosphate limitation inducible outer membrane pore protein of Escherichia coli K12 was established. The results show that PhoE protein is synthesized in a precursor form with a 21 amino acid residue amino-terminal extension. This peptide has the general characteristics of a signal sequence. The promoter region of phoE has no homlogy with the consensus sequence of E. coli promoter regions, but homologous sequences with the promoter region of phoA, the structural gene for alkaline phosphatase, were observed. The deduced amino acid sequence showed that the mature PhoE protein is composed of 330 amino acid residues with a calculated molecular weight of 36,782. A number of 81 charged amino acids was found scattered throughout the protein while no large stretches of hydrophobic amino acids were observed. Hydrophobicity and hydration profiles of PhoE protein showed five pronounced hydrophilic maxima which are all located in the region from the amino terminus to residue 212.When the deduced amino acid sequence of PhoE protein was compared with the established sequence of the OmpF pore protein, a number of 210 identical residues was found. Some aspects of the structure-function relationship of PhoE protein are discussed in view of the hydrophobicity and hydration profiles, and the homology between PhoE protein and OmpF protein.     

Isolation and NH2-terminal amino acid sequences of rat serum carrier proteins for insulin-like growth factors

Three N-glycosylated carrier proteins (CP) for insulin-like growth factors (apparent molecular weights 30-32, 42 and 45 kDa) were isolated from adult rat serum. They share the same amino terminus (up to amino acid 31) and are constituents of the growth hormone-dependent native 150-200 kDa IGF carrier complex. Residues 12-31 display 60 and 50% sequence homology, respectively, to residues 2-21 of fetal rat and to residues 4-22 of a human amniotic fluid IGF carrier protein. No homology exists with the type I or II IGF receptors. Adult rat serum also contains a fourth IGF CP (24 kDa) whose 9 NH2-terminal amino acids are identical to those of the fetal form. Our findings suggest that the three N-glycosylated components originate from the same IGF carrier protein (adult form) and that the 24 kDa protein is a separate (fetal) species.     

Purification and properties of an acidic protein from chromaffin granules of bovine adrenal medulla

1. A soluble protein has been purified from an aqueous extract of bovine adrenal chromaffin granules by chromatography on Sephadex G-200. This protein comprises 25% of the total protein of the granules and gave a single band on gel electrophoresis. 2. The protein is unusually rich in acidic amino acids, notably glutamic acid (26.0%, w/w); it is also relatively rich in proline (8.6%, w/w) but poor in cystine (0.35%, w/w). 3. A molecular weight of 77000 was obtained from sedimentation and diffusion measurements on the protein, and approach-to-equilibrium measurements gave apparent molecular weights of the same order. 4. A molecular weight 7 times that given above was estimated from the results of chromatography on a column of Sephadex G-200 that had been calibrated with globular proteins. However, good agreement between the ultracentrifuge and Sephadex experiments was obtained on the assumption that Sephadex chromatography depends on the effective hydrodynamic radii of proteins and not on their molecular weights. 5. The hydrodynamic properties of the protein differed from those of a typical globular protein. Thus the protein had a high intrinsic viscosity, a high frictional ratio and a large effective hydrodynamic volume. 6. The hydrodynamic properties of the protein, but not its molecular weight, were dependent on the ionic strength of the solvent. Increasing the ionic strength caused an increase in the sedimentation and diffusion coefficients, but a decrease in the intrinsic viscosity and in the frictional ratio of the protein. 7. Optical-rotatory-dispersion measurements indicated that only a small part of the polypeptide chain was in an alpha-helical conformation. 8. These results are compatible with the protein's having a conformation approaching that of a random-coil polypeptide, the volume occupied by the molecule being determined by electrostatic repulsion between the excess of negative charges.     

Interaction of metal cations with Ca2+-transport sites of the plasma membrane Ca2+ pump of secretory cells of gastric glands

Investigation of Ca2+ transport by calcium pump of the cell plasma membrane of the gastric glands isolated from guinea pigs and its inhibition by metal cations has been performed. The mainly competitive type of Ca2+ translocation inhibition by the calcium pump by metals cations (0.025-1.00 mM) was determined. Potency of inhibition increases in such an order (I50, mM): Ba2+ (0.336) < Sr2+ (0.251) < Mn2+ (0.099) < Co2+ (0.029) < Cd2+ (0.016). It was shown by one-factor dispersion analysis that potency of inhibition depends on ionic radii and hydration enthalpy of metal cations and also on stability constants of their complexes with oxygen-containing bioligands (acetic, aspartic and glutamic acid) (hx2 = 83.73-85.95). Dependence of the inhibition constants (I50) on ionic radii is most adequately described by the parabolic equation, such a dependence on hydration enthalpy and stability constants with oxygen-containing bioligands--by exponential or multiplicative equations. The conclusion has been made that selective Ca2+ translocation by the calcium pump and its inhibition by metal cations is determined by the interaction between energy of their interaction with cation-binding sites of the transport system and energy of hydration. Energetics of such interactions depends on the steric factors. The physicochemical model of the Ca2+ selective translocation by calcium pump and its inhibition by metal cations has been proposed.     

Polymorphism of rat seminal vesicle secretory proteins: Characterization of svp-1 and svp-2 and their identification with the major secretory proteins IV and V

The proteins secreted by the rat seminal vesicle can be separated into five major fractions (namely, RSV-I through V) by gel electrophoresis in denaturing conditions. Two polymorphic proteins, svp-1 and svp-2, also present in the mouse, are produced by the seminal vesicle as well, but the procedure used for their identification makes it impossible to ascertain whether they correspond to any of the major fractions mentioned above. We show here that, on the basis of molecular weight measurements and of amino acid composition determinations, svp-1 and RSV-V are indeed the same protein. We also show that svp-2 is strictly related to another major secretory protein, RSV-IV, whose amino acid composition is almost identical, but for a few amino acid residues, to that of svp-2. We thus conclude that the latter protein is a variant of RSV-IV that can be expressed only in rats homozygous for a given allele at the svp-2 locus. This paper thus brings together published information on the genetics of the loci coding for svp-1 and for svp-2 and on the molecular biology of RSV-IV and RSV-V and of their corresponding gene.This work was supported by a CNR grant from Progetto Finalizzato Ingegneria Genetica e Basi Molecolari delle Malattie genetiche.