Proteins as Networks: A Mesoscopic Approach Using Haemoglobin Molecule as Case Study

Giuliani, Alessandro; Paola, Luisa Di; Setola, Roberto

doi:10.2174/157016409789973743

Cited by 31 publications

(37 citation statements)

References 76 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…This approach results useful to analyze chemico-physical and functional protein properties [18,24,26,[31][32][33][34][35][36][37].…”

Section: Protein Contact Graph and General Topological Indexesmentioning

confidence: 99%

Structural and Functional Analysis of Hemoglobin and Serum Albumin Through Protein Long-Range Interaction Networks

Paci¹,

Paola²,

Santoni³

et al. 2012

Self Cite

View full text Add to dashboard Cite

Long-range contacts in protein structures were demonstrated to be predictive of different physiological properties of hemoglobin and albumin proteins. Complex networks based approach was demonstrated to highlight basic principles of protein folding and activity. The presence of a natural scaling region ending at an approximate threshold of 120-150 residues shared by proteins of different size and quaternary structure was highlighted. This threshold is reminiscent of the typical size for a macromolecule to have a binding site sensible to environmental regulation.

show abstract

“…This approach results useful to analyze chemico-physical and functional protein properties [18,24,26,[31][32][33][34][35][36][37].…”

Section: Protein Contact Graph and General Topological Indexesmentioning

confidence: 99%

Structural and Functional Analysis of Hemoglobin and Serum Albumin Through Protein Long-Range Interaction Networks

Paci¹,

Paola²,

Santoni³

et al. 2012

Self Cite

View full text Add to dashboard Cite

show abstract

“…Thus, this quantum dynamics does also manifest as an elastodynamics, the latter being the physical field which in the usual take is associated to allosterics. So, to resume, these adaptable stereochemical modifications point out to the importance of topology -yet associated to a torsion geometry-both defined by the wave function (Rapoport, 2007), and secondly and most important, that these topologies may be changing themselves (Giuliani, 2009). The non-orientable MB and KB topologies of stereochemistry has been claimed to yield a new paradigm to organic chemistry (Sokolov, 2009;Herges, 2006;Bonchev and Rouvray, 2000), and in (Rapoport, 2011c) it was argued it plays a core role in cell biology and embryology, having them all the same organizing principle.…”

Section: Non-orientable Self-referentialmentioning

confidence: 99%

Surmounting the Cartesian Cut: Klein Bottle Logophysics, The Dirac Algebra and the Genetic Code

Rapoport¹

2011

Neuroquantology

View full text Add to dashboard Cite

We reintroduce the Klein Bottle (KB) logophysics at the foundations of the unification of quantum geometry, cell biology, embryology and evolution, to extend it to the genetic code and allosteric recognition. We find that the genetic code has three possible fractal topologies: two different families of KBs embedded in HyperKBs, or still a 2-torus, depending which pair of three subalphabets for the genetic "letters" is chosen; this does not require the double helix. We complete the genetic codification of embryological differentiation introduced in an accompanying article. We discuss the Hadamard-KB representation of this codification and discuss its robustness and that of embryological development with respect to environmental noise. We discuss this KB codification of the 64 codons with its isomorphic representation in terms of the Dirac Algebra (DA) of Quantum Mechanics, in the Nilpotent Universal Computational Rewrite System (NUCRS), a self-referential syntax that generates much of mathematics and the fundamental symmetries of physics. We show that the double helix can be obtained from the duplication of the KB associated with the bistable perception of the tetrahedron representation of the four genetic letters. The DA and its double tetrahedron codification in NUCRS is found to be associated with a pair of superposed KBs, yielding the double 3D (space and momentum) space of physics, and the double helix of DNA, which thus appears related to a pair of KBs, being the case that only one is necessary to construct the genome. We show that the depth-time variable of visual perception materializes as space Thus, the DA is derivable from two KBs, and the purported dualism of physics as presented in NUCRS, is rendered to be based in the non-dualistic KBL. We discuss the relations with a theory of evolutions, and between biological periodicities and the KB of the Mendeleev table (Boeyens). We present relations between metacognition and the HyperKlein Bottle, and evolution in terms of time waves defining in toto the different structures. We present rudiments of the ontoepistemology of the Hyper KB Logic, its relations with the anthropic principles and the universal physical constants, which are found to be contextual.

show abstract

“…In recent works [1,20], we deal with the translation of the 3D structure of proteins into a Protein Contact Network (PCN), adopting a contact distance cutoff between 4 and 8 Å, focusing strictly on the α carbons, as nodes of the corresponding network. In this way, the protein structure is translated into the corresponding graph, whose invariants are possibly connected to some key features of the protein molecule.…”

Section: Introductionmentioning

confidence: 99%

Sym-Bio GUI: A graphical user interface to analyze protein aminoacid residue contact networks

Giuliani

Paola

Russo

2012

2012 25th IEEE International Symposium on Computer-Based Medical Systems (CBMS)

Self Cite

View full text Add to dashboard Cite

Proteomics impact on drug design strongly relies on the availability of fast and efficient tools to analyze protein structures. Within this framework, a promising approach deals with the topological analysis of between-residue contact networks. In this paper, we present SymBio, a tool modelled via two Graphical User Interfaces (GUI), aimed at translating the 3D structure of the target protein, fed in the standard PDB format, into an adjacency list, formatted in a custom fashion (NWB file), that is further transmitted to a Network Analysis Toolkit (NAT), and an adjacency matrix for the dedicated clustering analysis. Both classical network invariants (computed by NAT) and a clustering procedure of the nodes (computed by GUI's), provide potentially relevant topological information at both single residue and entire structure levels.

show abstract

Proteins as Networks: A Mesoscopic Approach Using Haemoglobin Molecule as Case Study

Cited by 31 publications

References 76 publications

Structural and Functional Analysis of Hemoglobin and Serum Albumin Through Protein Long-Range Interaction Networks

Structural and Functional Analysis of Hemoglobin and Serum Albumin Through Protein Long-Range Interaction Networks

Surmounting the Cartesian Cut: Klein Bottle Logophysics, The Dirac Algebra and the Genetic Code

Sym-Bio GUI: A graphical user interface to analyze protein aminoacid residue contact networks

Contact Info

Product

Resources

About