Classification of proteins based on similarity of two-dimensional protein maps

Albrecht, Birgit; Grant, Guy H.; Sisu, Cristina; Richards, W. Graham

doi:10.1016/j.bpc.2008.08.004

Cited by 4 publications

(2 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Neural networks using AA sequence data have been ineffectual in predicting α-helical domains in peptide structures [15]. Nevertheless, successful parameterizations of more complex molecular patterns which include helices have been reported [16] [17]. Redundancy and periodicity also occur in one or two loops of an α-helix.…”

Section: Biochemical Consequencesmentioning

confidence: 99%

Consequences of Non-Uniformity in the Stoichiometry of Component Fractions within One and Two Loops Models of α-Helical Peptides

Schmidt¹,

Hapeman²,

Wachira³

et al. 2014

JBPC

View full text Add to dashboard Cite

A 3-D electrostatic density map generated using the Wavefront Topology System and Finite Element Method clearly demonstrates the non-uniformity and periodicity present in even a single loop of an α-helix. The four dihedral angles (N-C*-C-N, C*-C-N-C*, and C-N-C*-C) fully define a helical shape independent of its length: the three dihedral angles, φ = −33.5˚, ω = 177.3˚, and Ψ = −69.4˚, generate the precise (and identical) redundancy in a one loop (or longer) α-helical shape (pitch = 1.59 Å/residue; r = 2.25 Å). Nevertheless the pattern of dihedral angles within an 11 and a 22-peptide backbone atom sequence cannot be distributed evenly because the stoichiometry in fraction of four atoms never divides evenly into 11 or 22 backbone atoms. Thus, three sequential sets of 11 backbone atoms in an α-helix will have a discretely different chemical formula and correspondingly different combinations of molecular forces depending upon the assigned starting atom in an 11-step sequence. We propose that the unit cell of one loop of an α-helix occurs in the peptide backbone sequence C-(N-C*-C)3-N which contains an odd number of C* plus even number of amide groups. A two-loop pattern (C*-C-N) 7-C* contains an even number of C* atoms plus an odd number of amide groups. Dividing the two-loop pattern into two equal lengths, one fraction will have an extra half amide (N-H) and the other fraction will have an extra half amide C=O, i.e., the stoichiometry of each half will be different. Also, since the length of N-C*-C-N, C*-C-N-C*, and C-N-C*-C are unequal, the summation of the number of each in any fraction of n loops of an α-helix in sequence will always have unequal length, depending upon the starting atom (N, C*, or C).

show abstract

Section: Biochemical Consequencesmentioning

confidence: 99%

Consequences of Non-Uniformity in the Stoichiometry of Component Fractions within One and Two Loops Models of α-Helical Peptides

Schmidt¹,

Hapeman²,

Wachira³

et al. 2014

JBPC

View full text Add to dashboard Cite

show abstract

“…Then a web server to make a pattern based search, using interaction matrix representation of protein structures [13], was developed. Albrecht et al [15] propose a different approach and apply data reduction techniques directly to the protein structure and convert 3D data into 2D so accelerating the structural comparisons between proteins. Zotenko et al [14] propose an approach to speed up protein structure comparison by mapping a protein structure to a high dimensional vector and approximating structural similarity by distances between the corresponding vectors.…”

mentioning

confidence: 99%

Search of protein structural blocks through secondary structure triplets

Cantoni

Ferone

Ozbudak

et al. 2012

2012 3rd International Conference on Image Processing Theory, Tools and Applications (IPTA)

View full text Add to dashboard Cite

This paper presents an approach for protein motif retrieval founded on protein secondary structures (SSs) in 3D. This is a new way to analyze the protein 3D structure. In this approach, based on the Generalized Hough Transform (GHT), the primitives are the triangles defined by the midpoints of three SSs. The three distances between each SSs couple are used in searching and in the voting process. The barycenter of the motif is assigned as the Reference Point (RP). All motif triangles are compared with all possible triangles in the macromolecule. The lengths of triangle edges are used as selective parameters. For every correspondence a vote is given to the point which is figured out as motif barycenter with a special mapping rule and the point having most votes is determined as candidate RP. In this paper we made some experiments for retrieval of four- and five-SSs motif from the macromolecule. Experimental results showed that the RP is determined with precision and this new approach to retrieve the motif is simple to implement, computationally efficient and fast

show abstract

Correlation to Protein Conformation of Wide-Angle X-ray Scatter Parameters

2010

View full text Add to dashboard Cite

In the last decade, several studies have reported that Wide-Angle X-ray Scattering (WAXS) from protein in solution contains valuable information about protein secondary and tertiary structures. Nevertheless, the use of such information will remain limited until a clear understanding of the correlation between protein structural elements and WAXS profile regions is established. In this work, large number of possible protein conformations is generated using comparative modeling (LOOPP & PHYRE servers) of nine different proteins representing six main protein classes (SCOP database). After model validation (SAVES server), protein structural elements of the selected models are retrieved (Swiss PDB Viewer & VORONOIA) and their corresponding WAXS profiles are generated (CRYSOL). The correlations between seven elements of protein structure (alpha helix, beta sheet and random coil content, alpha to beta ratio, alpha to random coil ratio, average packing density and number of residues) and seven WAXS profile parameters (Full Width at Half Maximum of two main scattering peaks of interest, their areas, positions and ratio of intensities) are investigated. Results revealed high (up to 0.75) and moderate (0.30-0.50) correlations between some of the suggested profile parameters and investigated protein structural elements indicating that these parameters represent a useful probe of protein conformation. Moreover, a high observed correlation between the degree of fitting of model to reference structures and the degree of fitting of their corresponding WAXS profiles suggests that the latter can be used in experimental model validation.

show abstract

Classification of proteins based on similarity of two-dimensional protein maps

Cited by 4 publications

References 28 publications

Consequences of Non-Uniformity in the Stoichiometry of Component Fractions within One and Two Loops Models of α-Helical Peptides

Consequences of Non-Uniformity in the Stoichiometry of Component Fractions within One and Two Loops Models of α-Helical Peptides

Search of protein structural blocks through secondary structure triplets

Correlation to Protein Conformation of Wide-Angle X-ray Scatter Parameters

Contact Info

Product

Resources

About