Biomedical subjects

Oliviero Carugo

Publications and source records attributed to Oliviero Carugo.

11 recordsLinked to original sources

PubMed2003

Oxidative folding intermediates with nonnative disulfide bridges between adjacent cysteine residues.

The oxidative folding of the Amaranthus alpha-amylase inhibitor, a 32-residue cystine-knot protein with three disulfide bridges, was studied in vitro in terms of the disulfide content of the intermediate species. A nonnative vicinal disulfide bridge between cysteine residues 17 and 18 was found in three of five fully oxidized intermediates. One of these, the most abundant folding intermediate (MFI), was further analyzed by (1)H NMR spectroscopy and photochemically induced dynamic nuclear polarization, which revealed that it has a compact structure comprising slowly interconverting conformations in which some of the amino acid side chains are ordered. NMR pulsed-field gradient diffusion experiments confirmed that its hydrodynamic radius is indistinguishable from that of the native protein. Molecular modeling suggested that the eight-membered ring of the vicinal disulfide bridge in MFI may be located in a loop region very similar to those found in experimentally determined 3D structures of other proteins. We suggest that the structural constraints imposed on the folding intermediates by the nonnative disulfides, including the vicinal bridge, may play a role in directing the folding process by creating a compact fold and bringing the cysteine residues into close proximity, thus facilitating reshuffling to native disulfide bridges.

Cysteine↗

PubMed2003

DPX: for the analysis of the protein core.

SUMMARY: In order to obtain an accurate description of the protein interior, we describe a simple and fast algorithm that measures the depth of each atom in a protein (dpx), defined as its distance (A) from the closest solvent accessible atom. The program reads a PDB file containing the atomic solvent accessibility in the B-factor field, and writes a file in the same format, where the B-factor field now contains the dpx value. Output structure files can be thus directly displayed with molecular graphics programs like RASMOL, MOLMOL, Swiss-PDB View and colored according to dpx values. AVAILABILITY: The algorithm is implemented in a standalone program written in C and its source is freely available at ftp.icgeb.trieste.it/pub/DPX or on request from the authors.

Algorithms↗

PubMed2003

Atom depth in protein structure and function.

Atom depth, originally defined as the distance between a protein atom and the nearest water molecule surrounding a protein, is a simple but valuable geometrical descriptor of the protein interior. It can be easily computed from the 3D structure of a protein, thus complementing the information provided by the calculation of the solvent accessible surface area and buried surface area. Depth has been found to be correlated with several molecular, residue and atomic properties, such as average protein domain size, protein stability, free energy of formation of protein complexes, amino acid type hydrophobicity, residue conservation and hydrogen/deuterium amide proton exchange rates.

Algorithms↗

PubMed2003

Atom depth as a descriptor of the protein interior.

Atom depth, defined as the distance (dpx, A) of a nonhydrogen atom from its closest solvent-accessible protein neighbor, provides a simple but precise description of the protein interior. Mean residue depths can be easily computed and are very sensitive to structural features. From the analysis of the average and maximum atom depths of a set of 136 protein structures, we derive a limit of approximately 200 residues for protein and protein domain size. The average and maximum atom depths in a protein are related to its size but not to the fold type. From the same set of structures, we calculated the mean residue depths for the 20 amino acid types, and show that they correlate well with hydrophobicity scales. We show that dpx values can be used to partition atoms in discrete layers according to their depth and to identify atoms that, although buried, are potential targets for posttranslational modifications like phosphorylation. Finally, we find a correlation between highly conserved residues in structural neighbors of the same fold type, and their mean residue depth in the reference structure.

Algorithms↗

PubMed2003

Vicinal disulfide turns.

The formation of a disulfide bond between adjacent cysteine residues is accompanied by the formation of a tight turn of the protein backbone. In nearly 90% of the structures analyzed a type VIII turn was found. The peptide bond between the two cysteines is in a distorted trans conformation, the omega torsion angle ranges from 159 to -133 degrees, with an average value of 171 degrees. The constrained nature of the vicinal disulfide turn and the pronounced difference observed between the oxidized and reduced states, suggests that vicinal disulfides may be employed as a 'redox-activated' conformational switch.

Cysteine↗

PubMed2003

Prediction of polypeptide fragments exposed to the solvent.

A method is presented to predict those polypeptide segments within a globular protein that are more likely to be exposed to the solvent. The protein amino acidic sequence is the only information needed by this new algorithm. It uses a consensus hydrophobicity scale, derived from 28 known scales, and it is based on the comparison between the average hydrophobicity of a polypeptide fragment and the average hydrophobicity expected for a segment containing the same number of residues. The latter values are pre-computed from a non-redundant set of single chain protein structural domains. The comparison between the two average values results in a t value that readily provides the prediction with a statistical significance. A jack-knife validation analysis indicates that the protein segment predicted to be the most solvent exposed is actually solvent exposed and amongst the fragments that are most exposed. The source of a stand-alone program, written in C language, that allows the prediction of the most likely solvent exposed segment in a globular protein is available from the author.

Algorithms↗

PubMed2002

Protein fold similarity estimated by a probabilistic approach based on C(alpha)-C(alpha) distance comparison.

The distribution of the C(alpha)-C(alpha) distances between residues separated by three to 30 amino acid residues is highly characteristic of protein folds and makes it possible to identify them from a straightforward comparison of the distance histograms. The comparison is carried out by contingency table analysis and yields a probability of identity (PRIDE score), with values between zero and 1. For closely related structures, PRIDE is highly correlated with the root-mean-square distance between C(alpha) atoms, but it provides a correct classification even for unrelated structures for which a structural alignment is not meaningful. For example, an analysis of the CATH database of fold structures showed that 98.8% of the folds fall into the correct CATH homologous superfamily category, based on the highest PRIDE score obtained. Structural alignment and secondary-structure assignment are not necessary for the calculation of PRIDE, which is fast enough to allow the scanning of large databases.

Animals↗

PubMed2002

The evolution of structural databases.

Starting with the Protein Data Bank (PDB) as a common ancestor, the evolution of structural databases has been driven by the rapprochement of the structural world and the practical applications. The result is an impressive number of secondary structural databases that is welcomed by structural biologists and bioinformaticians but runs the risk of producing an embarrassment of riches among non-specialist users. Given that any profit depends on the number of customers, efficient interfaces between many structural data banks must be available to make their contents easily accessible. Increasing the information content of central structural repositories might be the best way to guide users through the many, sometimes overlapping databases.

Computer Communication Networks↗

PubMed2002

CX, an algorithm that identifies protruding atoms in proteins.

MOTIVATION: A simple and fast algorithm is described that calculates a measure of protrusion (cx) for atoms in protein structures, directly useable with the common molecular graphics programs. RESULTS: A sphere of predetermined radius is centered around each non-hydrogen atom, and the volume occupied by the protein and the free volume within the sphere (internal and external volumes, respectively) are calculated. Atoms in protruding regions have a high ratio (cx) between the external and the internal volume. The program reads a PDB file, and writes the output in the same format, with cx values in the B factor field. Output structure files can be directly displayed with standard molecular graphics programs like RASMOL, MOLMOL, Swiss-PDB Viewer and colored according to cx values. We show the potential use of this program in the analysis of two protein-protein complexes and in the prediction of limited proteolysis sites in native proteins. AVAILABILITY: The algorithm is implemented in a standalone program written in C and its source is freely available at ftp.icgeb.trieste.it/pub/CX or on request from the authors.

Algorithms↗

PubMed2002

Recent progress in protein 3D structure comparison.

Quantitation of protein 3-D structure similarity is crucial in such fields as evolutionary studies, structural modeling and prediction of biological function. There are various approaches, many of which are tailored to specific problems. This review summarizes the recent developments in this field with particular interest in two main areas: i) improvements to and statistical interpretation of the root-man-square distance between equivalent atoms, rmsd; and ii) methods of protein structural classification based on geometrical features. Special attention is given to fast methods capable of analyzing large structural databases.

Amino Acid Motifs↗

PubMed1996

Synthesis, Structure, and Reactivity of Model Complexes of Copper Nitrite Reductase.

The copper(I) and copper(II) complexes with the nitrogen donor ligands bis[(1-methylbenzimidazol-2-yl)methyl]amine (1-BB), bis[2-(1-methylbenzimidazol-2-yl)ethyl]amine (2-BB), N-acetyl-2-BB (AcBB), and tris[2-(1-methylbenzimidazol-2-yl)ethyl]nitromethane (TB) have been studied as models for copper nitrite reductase. The copper(II) complexes form adducts with nitrite and azide that have been isolated and characterized. The Cu(II)-(1-BB) and Cu(II)-AcBB complexes are basically four-coordinated with weak axial interaction by solvent or counterion molecules, whereas the Cu(II)-(2-BB) and Cu(II)-TB complexes prefer to assume five-coordinate structures. A series of solid state structures of Cu(II)-(1-BB) and -(2-BB) complexes have been determined. [Cu(1-BB)(DMSO-O)(2)](ClO(4))(2): triclinic, P&onemacr; (No. 2), a = 9.400(1) Å, b = 10.494(2) Å, c = 16.760(2) Å, alpha = 96.67(1) degrees, beta = 97.10(1) degrees, gamma = 108.45(1) degrees, V = 1534.8(5) Å(3), Z = 2, number of unique data [I >/= 3sigma(I)] = 4438, number of refined parameters = 388, R = 0.058. [Cu(1-BB)(DMSO-O)(2)](BF(4))(2): triclinic, P&onemacr; (No. 2), a = 9.304(5) Å, b = 10.428(4) Å, c = 16.834(8) Å, alpha = 96.85(3) degrees, beta = 97.25(3) degrees, gamma = 108.21(2) degrees, V = 1517(1) Å(3), Z = 2, number of unique data [I >/= 2sigma(I)] = 3388, number of refined parameters = 397, R = 0.075. [Cu(1-BB)(DMSO-O)(NO(2))](ClO(4)): triclinic, P&onemacr; (No. 2), a = 7.533(2) Å, b = 8.936(1) Å, c = 19.168(2) Å, alpha = 97.66(1) degrees, beta = 98.62(1) degrees, gamma = 101.06(1) degrees, V = 1234.4(7) Å(3), Z = 2, number of unique data [I >/= 2sigma(I)] = 3426, number of refined parameters = 325, R = 0.081. [Cu(2-BB)(MeOH)(ClO(4))](ClO(4)): triclinic, P&onemacr; (No. 2), a = 8.493(3) Å, b = 10.846(7) Å, c = 14.484(5) Å, alpha = 93.71(4) degrees, beta = 103.13(3) degrees, gamma = 100.61(4) degrees, V = 1270(1) Å(3), Z = 2, number of unique data [I>/= 2sigma(I)] = 2612, number of refined parameters = 352, R = 0.073. [Cu(2-BB)(N(3))](ClO(4)): monoclinic, P2(1)/n (No. 14), a = 12.024(3) Å, b = 12.588(5) Å, c = 15.408(2) Å, beta = 101,90(2) degrees, V = 2282(1) Å(3), Z = 4, number of unique data [I >/= 2sigma(I)] = 2620, number of refined parameters = 311, R = 0.075. [Cu(2-BB)(NO(2))](ClO(4))(MeCN): triclinic, P&onemacr; (No. 2), a = 7.402(2) Å, b = 12.500(1) Å, c = 14.660(2) Å, alpha = 68.14(1) degrees, beta = 88.02(2) degrees, gamma = 78.61(1) degrees, V = 1233.0(4) Å(3), Z = 2, number of unique data [I>/= 2sigma(I)] = 2088, number of refined parameters = 319, R = 0.070. In all the complexes the 1-BB or 2-BB ligands coordinate the Cu(II) cations through their three donor atoms. The complexes with 2-BB appear to be more flexible than those with 1-BB. The nitrito ligand is bidentate in [Cu(2-BB)(NO(2))](ClO(4))(MeCN) and essentially monodentate in [Cu(1-BB)(DMSO-O)(NO(2))](ClO(4)). The copper(I) complexes exhibit nitrite reductase activity and react rapidly with NO(2)(-) in the presence of stoichiometric amounts of acid to give NO and the corresponding copper(II) complexes. Under the same conditions the reactions between the copper(I) complexes and NO(+) yield the same amount of NO, indicating that protonation and dehydration of bound nitrite are faster than its reduction. The NO evolved from the solution was detected and quantitated as the [Fe(EDTA)(NO)] complex. The order of reactivity of the Cu(I) complexes in the nitrite reduction process is [Cu(2-BB)](+) > [Cu(1-BB)](+) > [Cu(TB)](+) > [Cu(AcBB)](+).

Journal Article↗