Structural analysis of heme proteins: implications for design and prediction

Ting Li; Bonkovsky, Herbert L.; Jun-tao Guo
January 2011
BMC Structural Biology;2011, Vol. 11 Issue 1, p13
Academic Journal
Background: Heme is an essential molecule and plays vital roles in many biological processes. The structural determination of a large number of heme proteins has made it possible to study the detailed chemical and structural properties of heme binding environment. Knowledge of these characteristics can provide valuable guidelines in the design of novel heme proteins and help us predict unknown heme binding proteins. Results: In this paper, we constructed a non-redundant dataset of 125 heme-binding protein chains and found that these heme proteins encompass at least 31 different structural folds with all-a class as the dominating scaffold. Heme binding pockets are enriched in aromatic and non-polar amino acids with fewer charged residues. The differences between apo and holo forms of heme proteins in terms of the structure and the binding pockets have been investigated. In most cases the proteins undergo small conformational changes upon heme binding. We also examined the CP (cysteine-proline) heme regulatory motifs and demonstrated that the conserved dipeptide has structural implications in protein-heme interactions. Conclusions: Our analysis revealed that heme binding pockets show special features and that most of the heme proteins undergo small conformational changes after heme binding, suggesting the apo structures can be used for structure-based heme protein prediction and as scaffolds for future heme protein design.


Related Articles

  • A novel mode of sensory transduction in archaea: binding protein-mediated chemotaxis towards osmoprotectants and amino acids. Kokoeva, Maia V.; Storch, Kai-Florian; Klein, Christian; Oesterhelt, Dieter // EMBO Journal;5/15/2002, Vol. 21 Issue 10, p2312 

    Directly upstream of the Halobacterium salinarum transducer genes basT and htpIV we identified two open reading frames (orfs) with significant homologies to genes encoding binding proteins for amino acids and compatible solutes, respectively. Behavioral testing of deletion mutants indicates that...

  • The Role of Pseudo-Endoglucanases in the Evolution of Nematode Cell Wall-Modifying Proteins. Haegeman, Annelies; Kyndt, Tina; Gheysen, Godelieve // Journal of Molecular Evolution;May2010, Vol. 70 Issue 5, p441 

    In this article, the characterization and evolution of pseudo-endoglucanases and a putative expansin-like gene in the migratory nematode Ditylenchus africanus are described. Four genes were cloned with a very high similarity to the endoglucanase Da- eng1, which, however, lack a part of the...

  • Engineering novel binding proteins from nonimmunoglobulin domains. Binz, H. Kaspar; Amstutz, Patrick; Pl├╝ckthun, Andreas // Nature Biotechnology;Oct2005, Vol. 23 Issue 10, p1257 

    Not all adaptive immune systems use the immunoglobulin fold as the basis for specific recognition molecules: sea lampreys, for example, have evolved an adaptive immune system that is based on leucine-rich repeat proteins. Additionally, many other proteins, not necessarily involved in adaptive...

  • Prediction of FAD Binding Residues with Combined Features from Primary Sequence. Chun Fang; Noguchi, Tamotsu; Yamana, Hayato // International Proceedings of Computer Science & Information Tech;2012, Vol. 34, p147 

    In order to analyze the impact of different characteristics of protein sequence on small nucleotide binding site prediction, this paper proposed four sequence-based methods for identifying FAD binding residues of flavin binding proteins (FBP) by means of support vector machine (SVM). We used the...

  • Discovery of EST-SSRs in Lung Cancer: Tagged ESTs with SSRs Lead to Differential Amino Acid and Protein Expression Patterns in Cancerous Tissues. Bakhtiarizadeh, Mohammad Reza; Ebrahimi, Mansour; Ebrahimie, Esmaeil // PLoS ONE;2011, Vol. 6 Issue 11, p1 

    Tandem repeats are found in both coding and non-coding sequences of higher organisms. These sequences can be used in cancer genetics and diagnosis to unravel the genetic basis of tumor formation and progression. In this study, a possible relationship between SSR distributions and lung cancer was...

  • Soluble expression of proteins correlates with a lack of positively-charged surface. Pedro Chan; Curtis, Robin A.; Warwicker, Jim // Scientific Reports;11/29/2013, p1 

    Prediction of protein solubility is gaining importance with the growing use of protein molecules as therapeutics, and ongoing requirements for high level expression. We have investigated protein surface features that correlate with insolubility. Non-polar surface patches associate to some degree...

  • Calgranulin C is Overexpressed in Lesional Psoriasis. Mirmohammadsadegh, Alizera; Tschakarjan, Etiena; Ljoljic, Antonia; Bohner, Katja; Michel, Gunter; Ruzicka, Thomas; Goos, Manfred; Hengge, Ulrich R. // Journal of Investigative Dermatology;Jun2000, Vol. 114 Issue 6, p1207 

    Examines the expression of calgranulin C, a calcium-binding protein, in lesional psoriasis. Implication of the proteins for the calcium-dependent regulation of cellular activities; Number of amino acids; Details on molecular weight.

  • Cooperation of basolateral epithelial amino acid transporters TAT1 and LAT2 investigated in a double knock out mouse model. Boiadjieva, E. B.; Vilches, C.; Bodoy, S.; Guetg, A.; Verrey, F.; Palacin, M. // Proceedings of the Physiological Society;2013, p521P 

    Transcellular transport of amino acids by epithelial tissues includes their import across apical membranes and sequential export through basolateral membranes. In the cell, the basolateral efflux step is driven by the amino acid concentration gradient and is strictly regulated by the cooperative...

  • Research highlights. Eggleston, Angela K; Hodges, Maria; Lall, Sabbi // Nature Structural & Molecular Biology;Sep2010, Vol. 17 Issue 9, p1036 

    The article discusses several studies related to molecular biology. It states that a research by Patla and colleagues showed the existence of hundreds of heterogeneous particles at the center of focal adhesions which allow adhesions' stimuli adaptation. It says that Chandler and associates have...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics