Structural analysis of heme proteins: implications for design and prediction
© Li et al; licensee BioMed Central Ltd. 2011
Received: 26 October 2010
Accepted: 3 March 2011
Published: 3 March 2011
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.
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-α 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.
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.
This year marks the 50th anniversary of the publication of the very first two protein structures, myoglobin and hemoglobin, two prototype heme proteins involved in oxygen storage and transport [1, 2]. Heme proteins, or hemoproteins, are a group of proteins carrying heme as the prosthetic group. Heme proteins are ubiquitous in biological systems and exhibit diverse biological activities. These include the classical functions of diatomic gas transportation/storage and electron transfer as exemplified by myoglobin, hemoglobin and cytochrome c[3, 4]. More recent studies continue to reveal more pleiotropic roles of heme proteins in transcriptional regulation [5, 6], ion channel chemosensing , circadian clock control , and microRNA processing .
The identification of human Rev-erb nuclear receptors as heme sensing transcription factors represents an important addition to the heme protein family [10, 11]. Rev-erbα (NR1D1) and Rev-erbβ (NR1D2) have been implicated in the regulation of circadian rhythms, lipid and glucose metabolism, and diseases [12–15]. They were previously categorized as orphan receptors with no known physiological ligand. Computational modeling and X-ray crystallization of the ligand binding domain (LBD) of Rev-erbs provided incentives for proposing heme as the bona fide ligand. However, the proposal was largely based on the homology between Rev-erb LBD and that of a known heme sensing protein E75, a Drosophila nuclear receptor; and the authenticity of heme as a ligand remained elusive at the time due to the lack of unified information on heme binding sites and heme-protein interaction. Therefore detailed analysis and prediction were not possible. Yet the Rev-erb story prompted us to ask: can we predict heme proteins? The worldwide structural genomics projects have produced a large number of new structures with unknown functions or annotated as hypothetical proteins [16, 17]. Owing to the ubiquitous and essential nature of heme in life, we hypothesize that some "orphan" structures in Protein Data Bank (PDB)  are heme proteins.
As a first step towards a long term goal to develop methodologies for predicting and designing novel heme proteins, a field of interest with great potential in medicine and green energy [27, 30], we set out to investigate the common characteristics of heme binding sites and the conformational differences between apo (without heme) and holo heme proteins, aiming at consolidating and synthesizing a large body of experimental data and extracting useful information and novel integrative insights.
We take into consideration two key questions crucial to the structure-function paradigm of heme proteins. The first concerns the structural implications of the heme-interactive sequence motifs. CXXCH represents the classic type-c heme binding motif in which the two vinyl groups of heme form covalent bonds with two cysteine residues in proteins [27, 28]. Recently, a heme regulatory motif CP (for cysteine-proline dipeptide) has received increasing attention [31–35]. But up to the present the functional importance of this CP heme sensing or regulatory motif has been studied only through mutational experiments on a limited number of proteins. It is still not clear from a structural point of view how the CP motif is involved in regulation of heme binding as has been established for the CXXCH heme c motif.
The second question concerns the structural environment or the physiochemical features of the heme binding pockets. Of particular importance is the conformational difference between the apo and holo forms of heme proteins since, in most cases, only apo structures will be available for prediction. Even though the global and local conformational changes induced by ligand binding in general have been surveyed by a number of studies [36–39], such systematic studies on heme proteins have not been reported. In this study, we compiled a non-redundant dataset of apo-holo pairs to examine the conformational and pocket changes in heme proteins after heme binding.
The diversity and conservation of interactions between heme and proteins have been analyzed previously by Schneider et al. . However they used a redundant dataset with 68 type-b heme proteins (based on 60% sequence identity cutoff) due largely to the limited availability of heme protein structures [27, 40]. A very recent study performed analysis on a smaller dataset of 34 heme proteins, each of which represents one CATH homologous family or a SCOP family . There are seven different heme groups in the 34 heme proteins with heme b and heme c as the dominant forms . Here we performed structural analysis on a larger, non-redundant dataset of heme proteins containing heme b and/or c types. Heme proteins are found in at least 31 different structural folds in all the four major classes based on SCOP classifications , attesting to the diversity and complexity of heme-protein interactions. The heme binding pockets are enriched in aromatic amino acids and relatively depleted with respect to the charged residues, glutamic acid, aspartic acid, and lysine. We also found that the CP motif has structural implications in heme-protein interactions.
Two non-redundant datasets were generated in this study. The first dataset, containing 125 heme-binding protein chains, was used for analysis of heme binding environment. This set was culled from protein structures in the Protein Data Bank (PDB, November 24, 2009)  with HEM (for heme b) or HEC (for heme c) as ligands with the following criteria: experimental method = X-ray crystallography, maximum resolution = 3 Å, and maximum R-value = 0.3. The protein chains that interact with heme molecules (described in next section "Analysis of heme interacting residues") were selected, and a non-redundant set of 125 heme-binding protein chains was generated using PISCES  with a sequence identity cutoff of 25% (Additional file 1, Table S1). The second dataset has 5596 protein chains in which each pair of protein chains has less than 25% sequence identity and each structure has a resolution of 2.5 Å or better and an R-factor of 0.3 or better. This set was used for calculating background frequencies of amino acids, secondary structure types, and relative solvent accessibility. The sequences for the protein chains derived from the PDB "SEQRES" records may have cloning and expression artifacts such as His-tags at the N- or C-terminus and some of the protein chains have missing residues [44, 45]. To avoid such artifacts and incomplete sequences, the amino acid frequencies were calculated using the full-length protein sequences through mapping PDB chains to Uniprot entries with PDBSWS .
Analysis of heme interacting residues
A residue is considered as a heme axial ligand if the distance between the nitrogen, sulfur or oxygen of the residue and the heme iron is within 3 Å. Residues having heavy atoms within 4.5 Å of any non-hydrogen atoms of the heme molecule are identified as heme interacting amino acids. A protein chain is considered as heme binding if it has residue(s) as axial ligand(s) to the heme iron or has at least ten residue interactions with the heme molecule. DSSP was used to assign each residue to one of three secondary structure states, helix, strand, and coil . Following the widely used convention, H (α-helix), G (310-helix) and I (π-helix) from DSSP are classified as helix type while E (extended strand) and B (residue in isolated-bridge) states are classified as strand type. All the other states from DSSP are considered as coils. The relative solvent accessibility was calculated by dividing the absolute value of exposed area from DSSP over the maximum accessibility of each residue . We employ a three-state classification for relative solvent accessibility: buried (≤7%), intermediate (>7% and ≤37%), and exposed (>37%), as described previously .
Structural comparisons between apo and holo heme proteins
To maximize the number of possible apo-holo heme protein pairs, each of the heme protein chains was first compared with all the non-heme protein chains derived from PISCES pdbaaent file using BLAST . There are a number of ligands that are similar to heme b or c in PDB, so structures with these heme-like ligands are not considered as apo proteins for our apo-holo comparisons. Based on HIC-Up keyword search using heme and porphyrin  and SuperLigands ligand structure similarity search , we identified 55 heme-like ligands in PDB (Additional file 1, Table S2). The highly similar apo-holo heme protein pairs (cutoffs set at 90% sequence identity and 95% sequence alignment overlap) were then culled to generate a list of 15 non-redundant apo-holo pairs using PISCES with a sequence identity cutoff of 25% . Five of the 15 apo proteins that contain other non-heme ligands in the heme-binding pockets were removed from the list as they are not truly "apo" forms with respect to the heme binding sites. The structural differences were evaluated with two structure alignment programs, FAST  and CE  for structure comparisons. The similarity/difference between two structures is measured by the RMSD (root mean square deviation) of the Cα atoms of aligned residues. The pocket/cavity was predicted using the CASTp server (Computed Atlas of Surface Topography of proteins). To compare the shape of the pockets, Rvs, the ratio between the volume and the surface area is used.
Results and Discussion
Non-redundant dataset of heme binding proteins
SCOP fold classes of the 125 heme binding protein chains in the non-redundant dataset
# of Chains
SCOP Fold Name
Nuclear receptor ligand-binding domain
Four-helical up-and-down bundle
Indolic compounds 2,3-dioxygenase-like
GST C-terminal domain-like
Common fold of diphtheria toxin/transcription factors...
Tryptophan synthase β subunit-like PLP-dependent enzymes
Cytochrome b5-like heme/steroid binding domain
Nitric oxide (NO) synthase oxygenase domain
Ligand-binding domain in NO signalling & Golgi transport
Heme iron utilization protein-like
Heme-binding four-helical bundle
Cytochrome c oxidase subunit I-like
Structural environment of the heme binding pockets
The conserved interactions between protein residues and heme were previously studied by calculating either the frequencies of residues that are in van der Waals contact with heme for each fold class of b-type heme proteins  or by calculating the mean number per binding site . Smith et al also applied normalized amino acid profiles to assess the composition and conservation of heme binding sites . Here we explored the residue preferences in the heme binding pockets through calculating the relative frequencies of heme binding residues in our non-redundant dataset. The relative frequency of each amino acid is normalized to its background frequency.
Normally, the background frequencies used for comparisons are calculated from a non-redundant protein dataset. However, due to the dominant presence of all-α folds, it is not clear whether the residue distribution in heme proteins is different from that in other proteins. Therefore we first compared the residue distributions between non-redundant heme proteins and non-redundant all proteins. To avoid issues with missing residues and cloning artifacts (His-tags etc.) associated with PDB sequences, we used native full-length protein sequences to calculate residue compositions by mapping the PDB chains to Uniprot entries with PDBSWS . The relative residue frequencies between heme proteins and all proteins show that heme proteins tend to contain more alanine, phenylalanine, histidine, methionine, and tryptophan residues and fewer cysteine, aspartic acid, isoleucine, lysine, asparagine, and serine residues (Additional file 2, Figure S1). Statistical analysis (χ2) revealed a significant difference between these two frequency profiles (data not shown). In order to have a meaningful description of the enrichment or deficiency of residues in the heme interacting environment, we used the background frequencies from the non-redundant set of heme proteins as references.
Consistent with earlier reports, the aromatic residues (phenylalanine, tyrosine, and tryptophan) play important roles in protein-heme interactions through stacking interactions with the porphyrin[27, 41]. One exception is tryptophan in heme c proteins, which showed a similar level of occurrences compared to the background (Figure 4A). Leucine, isoleucine, and valine, which make hydrophobic interactions with the heme ring structure, are slightly increased over the background frequencies. The residues with the fewest occurrences, aspartic acid, glutamic acid, and lysine are charged residues, suggesting the heme binding pocket is mainly a hydrophobic environment. In contrast, arginine, a positively charged residue that has been considered a major player in anchoring the heme propionates, has a much higher occurrence than other charged amino acids and shows a similar (HEM) or slightly higher (HEC) level of frequency to the background (Figure 4A) .
Heme binding sequence motifs
Another motif worthy of note, G X[HR]XC[PLAV]G, comes from the heme b proteins with cysteine as axial ligands (Figure 6B). The motif represents the classic CYP signature heme binding motif FXXGXXCXG in bacteria, plant, and mammalian cytochrome P450 s [59–61]. At the -4 and +2 positions (with ligand cysteine as reference position) are small amino acids (glycine) while the -2 position prefers a positively charged amino acid such as histidine or arginine. These positively charged residues interact electronically with the negatively charged heme propionates (Figure 6C and 6D). The small glycine residue at the -4 position may provide the flexibility needed for positioning the positively charged residues close to heme propionate groups. The +1 position is dominated by proline and hydrophobic amino acids, leucine, alanine, valine and isoleucine. Six of the eighteen cases have proline right after the axial ligand cysteine, reminiscent of the dipeptide CP motif being implicated in heme sensing and regulation [31–35, 62]. While the importance of CP motif has been studied through deletion or site-directed mutation experiments in several important proteins, including transcription repressor Bach1, iron regulatory protein 2 (IRP2) , circadian factor period 2 (Per2)  and δ-aminolevulinic acid synthase (ALAS) , the possible role of the CP motif in heme interaction from a structural point of view remains unclear as the structures for most of these proteins with such CP motifs are unknown.
CP dipeptides have also been implicated in indirect interaction with heme. Ragsdale and colleagues reported a novel role for CP motifs in heme oxygenase 2 (HMOX-2) as a thiol/disulfide redox switch that localizes outside the heme-binding pocket [62, 64, 65], therefore regulating heme-protein interaction via sensing redox status in the environment. There are a total of twenty-nine CP dipeptides in our dataset. Less than a quarter of them (in 7 protein chains including 2PBJA) show physical interactions with heme molecules. It would be impractical at this point to predict the functional role of the remaining CP dipeptides in heme-protein interaction, mainly due to the limited sample size and the lack of structural details on heme pocket-CP interaction. Here we made use of statistical analysis to indirectly assess the functional relevance of CP dipeptides in heme interaction. The rationale behind the assay is that, if CP dipeptides are important heme signatures for heme interaction, the expected occurrences of CP dipeptides in hemoproteins should be higher compared to control population. We found no statistically significant difference between the presence of CP dipeptides in heme proteins and non-heme proteins (data not shown), suggesting other yet to be identified factors may exist to help determine the role CP dipeptides play in heme binding . It should be noted that we do not exclude the possibility that in the control sample there exist unknown hemoproteins; however for them to significantly affect the frequency of CP signals there would have to be a considerably large fraction of the control proteins being analyzed to be heme-interacting, which we anticipate as less likely.
Structure comparison between apo and holo heme proteins
Comparisons between apo and holo heme protein structures
surface area (Å2)
It should be noted that the above comparisons are based on heme proteins that have stable apo structures solved through X-ray crystallography. For some proteins, as in the case of hemoglobin, the absence of ligand(s) can increase the flexibility and cause partial unfolding of the protein structure, making it difficult for structure determination [70, 71]. Furthermore, intrinsically disordered or unstructured regions are considered to be responsible for many important cellular functions such as ligand binding [72, 73]. However the existence of such flexible apo structures would not interfere with our goal in structure-based heme protein prediction as we aim to take the existing apo structures in PDB as inputs .
Other features useful for comparing apo-holo heme proteins are the pocket size and shape. Due to different heme binding modes (partially exposed or fully embedded, Additional file 2 Figure S3) and the difficulty in identifying the exact heme binding pocket from existing automatic programs, the sizes of heme binding pockets vary from small (~400 Å3) to very large (over 2000 Å3) (Table 2). In addition, the changes in absolute pocket volumes after heme binding are variable. Small changes are seen in 2ITFA-2ITEB, 2R7AA-2RG7 D, and 2ZDOA-1XBWD. Other pairs exhibited significant changes in volume despite the minimal conformational change (Table 2). To take the shape into consideration we calculated the Rvs value (the ratio of pocket volume over the pocket surface area) of each pocket. Most of the apo or holo proteins have Rvs values around 1.4. To further investigate whether the binding pocket can be used as one of the characteristics for heme protein prediction, we compared the Rvs distributions between heme binding pockets and pockets in non-heme proteins (proteins that don't have heme ligand(s) and are not homologous to heme proteins) with similar sizes ranging from 350 to 2000Å3. The Rvs of heme binding pockets has a narrow distribution whereas the Rvs from similar pocket sizes of non-heme proteins has a wide spread with a long right tail (Additional file 2, Figure S4-A). We also investigated the distribution of Rvs normalized to a sphere shape as introduced by Sonavane and Chakrabarti . A similar trend was found (Additional file 2, Figure S4-B). It should be pointed out that, even though unknown heme proteins may be included in the non-heme dataset, many non-heme proteins share similar pocket characteristics.
In this study, we surveyed the known heme protein structures for the purpose of structure-based heme protein prediction and novel heme protein design. We first compiled a non-redundant dataset of 125 heme (type b and c) binding protein chains that encompass a large number of protein structural folds, reflecting the diversified roles of heme proteins. Structural analysis revealed that the residues interacting with heme are mainly non-polar, especially aromatic amino acids, providing a hydrophobic environment for the heme ring structure. We also investigated the possible structural roles of CP motifs that are implicated in the regulation of heme binding and have received much attention recently. While the CP dipeptide is not as strong a signature for heme binding as the classic CXXCH heme c binding motif, the proline in the heme-interacting CP dipeptides assume important structural roles when CP is conserved and the cysteine functions as an axial ligand with heme iron. Indirect interaction between CP motifs and heme binding has also been reported in HMOX-2 protein, in which CP dipeptides form thiol/disulfide redox switch away from the heme binding pocket [62, 64], suggesting the heterogeneity of CP-heme interactions.
Comparisons between the apo and holo heme proteins indicate that most of the heme proteins undergo small conformational changes after heme binding, suggesting the apo structure can be used for structure-based heme protein prediction and as a scaffold for heme protein design. In addition our analysis on the heme binding pockets showed that despite the different sizes, the Rvs values of heme binding pockets are confined in a small range, whereas the data from non-heme binding proteins spread over a large range. We will apply the results from this study to investigate if any of the hypothetical proteins in PDB are potential heme proteins through computational prediction and experimental validations in the near future.
List of abbreviations used
lipid binding domain
structural classification of proteins
protein data bank
root mean square deviation
ratio of volume over area.
The authors thank Dr. Dennis Livesay and Dr. Laura Schrum for comments on this manuscript. This research was partly supported by the NSF CAREER grant (DBI#0844749) to JTG, the NIH 5R01DK038825 to HLB, and the CMC-UNC Charlotte Collaborative Grants Program (09-002) to TL and JTG.
- Kendrew JC, Dickerson RE, Strandberg BE, Hart RG, Davies DR, Phillips DC, Shore VC: Structure of myoglobin: A three-dimensional Fourier synthesis at 2 A. resolution. Nature 1960, 185(4711):422–427. 10.1038/185422a0View ArticlePubMed
- Perutz MF, Rossmann MG, Cullis AF, Muirhead H, Will G, North AC: Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-A. resolution, obtained by X-ray analysis. Nature 1960, 185(4711):416–422. 10.1038/185416a0View ArticlePubMed
- Poulos TL: The Janus nature of heme. Nat Prod Rep 2007, 24(3):504–510. 10.1039/b604195gView ArticlePubMed
- Paoli M, Marles-Wright J, Smith A: Structure-function relationships in heme-proteins. DNA Cell Biol 2002, 21(4):271–280. 10.1089/104454902753759690View ArticlePubMed
- Sun J, Hoshino H, Takaku K, Nakajima O, Muto A, Suzuki H, Tashiro S, Takahashi S, Shibahara S, Alam J, Taketo MM, Yamamoto M, Igarashi K: Hemoprotein Bach1 regulates enhancer availability of heme oxygenase-1 gene. The EMBO journal 2002, 21(19):5216–5224. 10.1093/emboj/cdf516PubMed CentralView ArticlePubMed
- Zenke-Kawasaki Y, Dohi Y, Katoh Y, Ikura T, Ikura M, Asahara T, Tokunaga F, Iwai K, Igarashi K: Heme induces ubiquitination and degradation of the transcription factor Bach1. Molecular and cellular biology 2007, 27(19):6962–6971. 10.1128/MCB.02415-06PubMed CentralView ArticlePubMed
- Tang XD, Xu R, Reynolds MF, Garcia ML, Heinemann SH, Hoshi T: Haem can bind to and inhibit mammalian calcium-dependent Slo1 BK channels. Nature 2003, 425(6957):531–535. 10.1038/nature02003View ArticlePubMed
- Kaasik K, Lee CC: Reciprocal regulation of haem biosynthesis and the circadian clock in mammals. Nature 2004, 430(6998):467–471. 10.1038/nature02724View ArticlePubMed
- Faller M, Matsunaga M, Yin S, Loo JA, Guo F: Heme is involved in microRNA processing. Nature structural & molecular biology 2007, 14(1):23–29.View Article
- Raghuram S, Stayrook KR, Huang P, Rogers PM, Nosie AK, McClure DB, Burris LL, Khorasanizadeh S, Burris TP, Rastinejad F: Identification of heme as the ligand for the orphan nuclear receptors REV-ERBalpha and REV-ERBbeta. Nature structural & molecular biology 2007, 14(12):1207–1213.View Article
- Yin L, Wu N, Curtin JC, Qatanani M, Szwergold NR, Reid RA, Waitt GM, Parks DJ, Pearce KH, Wisely GB, Lazar MA: Rev-erbalpha, a heme sensor that coordinates metabolic and circadian pathways. Science 2007, 318(5857):1786–1789. 10.1126/science.1150179View ArticlePubMed
- Coste H, Rodriguez JC: Orphan nuclear hormone receptor Rev-erbalpha regulates the human apolipoprotein CIII promoter. J Biol Chem 2002, 277(30):27120–27129. 10.1074/jbc.M203421200View ArticlePubMed
- Migita H, Morser J, Kawai K: Rev-erbalpha upregulates NF-kappaB-responsive genes in vascular smooth muscle cells. FEBS letters 2004, 561(1–3):69–74. 10.1016/S0014-5793(04)00118-8View ArticlePubMed
- Preitner N, Damiola F, Lopez-Molina L, Zakany J, Duboule D, Albrecht U, Schibler U: The orphan nuclear receptor REV-ERBalpha controls circadian transcription within the positive limb of the mammalian circadian oscillator. Cell 2002, 110(2):251–260. 10.1016/S0092-8674(02)00825-5View ArticlePubMed
- Yang X, Lamia KA, Evans RM: Nuclear receptors, metabolism, and the circadian clock. Cold Spring Harb Symp Quant Biol 2007, 72: 387–394. 10.1101/sqb.2007.72.058View ArticlePubMed
- Watson JD, Sanderson S, Ezersky A, Savchenko A, Edwards A, Orengo C, Joachimiak A, Laskowski RA, Thornton JM: Towards fully automated structure-based function prediction in structural genomics: a case study. Journal of molecular biology 2007, 367(5):1511–1522. 10.1016/j.jmb.2007.01.063PubMed CentralView ArticlePubMed
- Pazos F, Sternberg MJ: Automated prediction of protein function and detection of functional sites from structure. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(41):14754–14759. 10.1073/pnas.0404569101PubMed CentralView ArticlePubMed
- Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic acids research 2000, 28(1):235–242. 10.1093/nar/28.1.235PubMed CentralView ArticlePubMed
- Reedy CJ, Gibney BR: Heme protein assemblies. Chem Rev 2004, 104(2):617–649. 10.1021/cr0206115View ArticlePubMed
- Isogai Y, Ishida M: Design of a novel heme protein with a non-heme globin scaffold. Biochemistry 2009, 48(34):8136–8142. 10.1021/bi900518qView ArticlePubMed
- Koder RL, Anderson JL, Solomon LA, Reddy KS, Moser CC, Dutton PL: Design and engineering of an O(2) transport protein. Nature 2009, 458(7236):305–309. 10.1038/nature07841PubMed CentralView ArticlePubMed
- Lu Y, Yeung N, Sieracki N, Marshall NM: Design of functional metalloproteins. Nature 2009, 460(7257):855–862. 10.1038/nature08304PubMed CentralView ArticlePubMed
- Lin YW, Yeung N, Gao YG, Miner KD, Tian S, Robinson H, Lu Y: Roles of glutamates and metal ions in a rationally designed nitric oxide reductase based on myoglobin. Proceedings of the National Academy of Sciences of the United States of America 2010, 107(19):8581–8586. 10.1073/pnas.1000526107PubMed CentralView ArticlePubMed
- Choma CT, Lear JD, Nelson MJ, Dutton PL, Robertson DE, Degrado WF: Design of a heme-binding 4-helix bundle. Journal of the American Chemical Society 1994, 116(3):856–865. 10.1021/ja00082a005View Article
- Robertson DE, Farid RS, Moser CC, Urbauer JL, Mulholland SE, Pidikiti R, Lear JD, Wand AJ, DeGrado WF, Dutton PL: Design and synthesis of multi-haem proteins. Nature 1994, 368(6470):425–432. 10.1038/368425a0View ArticlePubMed
- Reedy CJ, Elvekrog MM, Gibney BR: Development of a heme protein structure-electrochemical function database. Nucleic acids research 2008, (36 Database):D307–313.
- Schneider S, Marles-Wright J, Sharp KH, Paoli M: Diversity and conservation of interactions for binding heme in b-type heme proteins. Nat Prod Rep 2007, 24(3):621–630. 10.1039/b604186hView ArticlePubMed
- Bowman SE, Bren KL: The chemistry and biochemistry of heme c: functional bases for covalent attachment. Nat Prod Rep 2008, 25(6):1118–1130. 10.1039/b717196jPubMed CentralView ArticlePubMed
- Murray JW, Delumeau O, Lewis RJ: Structure of a nonheme globin in environmental stress signaling. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(48):17320–17325. 10.1073/pnas.0506599102PubMed CentralView ArticlePubMed
- Razeghifard R, Wallace BB, Pace RJ, Wydrzynski T: Creating functional artificial proteins. Curr Protein Pept Sci 2007, 8(1):3–18. 10.2174/138920307779941479View ArticlePubMed
- Igarashi J, Murase M, Iizuka A, Pichierri F, Martinkova M, Shimizu T: Elucidation of the heme binding site of heme-regulated eukaryotic initiation factor 2alpha kinase and the role of the regulatory motif in heme sensing by spectroscopic and catalytic studies of mutant proteins. J Biol Chem 2008, 283(27):18782–18791. 10.1074/jbc.M801400200View ArticlePubMed
- Ishikawa H, Kato M, Hori H, Ishimori K, Kirisako T, Tokunaga F, Iwai K: Involvement of heme regulatory motif in heme-mediated ubiquitination and degradation of IRP2. Molecular cell 2005, 19(2):171–181. 10.1016/j.molcel.2005.05.027View ArticlePubMed
- Lathrop JT, Timko MP: Regulation by heme of mitochondrial protein transport through a conserved amino acid motif. Science 1993, 259(5094):522–525. 10.1126/science.8424176View ArticlePubMed
- Yang J, Kim KD, Lucas A, Drahos KE, Santos CS, Mury SP, Capelluto DG, Finkielstein CV: A novel heme-regulatory motif mediates heme-dependent degradation of the circadian factor period 2. Molecular and cellular biology 2008, 28(15):4697–4711. 10.1128/MCB.00236-08PubMed CentralView ArticlePubMed
- Zhang L, Guarente L: Heme binds to a short sequence that serves a regulatory function in diverse proteins. The EMBO journal 1995, 14(2):313–320.PubMed CentralPubMed
- Brylinski M, Skolnick J: What is the relationship between the global structures of apo and holo proteins? Proteins 2008, 70(2):363–377. 10.1002/prot.21510View ArticlePubMed
- Karthikeyan S, Zhou Q, Osterman AL, Zhang H: Ligand binding-induced conformational changes in riboflavin kinase: structural basis for the ordered mechanism. Biochemistry 2003, 42(43):12532–12538. 10.1021/bi035450tView ArticlePubMed
- Najmanovich R, Kuttner J, Sobolev V, Edelman M: Side-chain flexibility in proteins upon ligand binding. Proteins 2000, 39(3):261–268. 10.1002/(SICI)1097-0134(20000515)39:3<261::AID-PROT90>3.0.CO;2-4View ArticlePubMed
- Zavodszky MI, Kuhn LA: Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis. Protein Sci 2005, 14(4):1104–1114. 10.1110/ps.041153605PubMed CentralView ArticlePubMed
- Dessailly BH, Nair R, Jaroszewski L, Fajardo JE, Kouranov A, Lee D, Fiser A, Godzik A, Rost B, Orengo C: PSI-2: structural genomics to cover protein domain family space. Structure 2009, 17(6):869–881. 10.1016/j.str.2009.03.015PubMed CentralView ArticlePubMed
- Smith LJ, Kahraman A, Thornton JM: Heme proteins--diversity in structural characteristics, function, and folding. Proteins 2010, 78(10):2349–2368. 10.1002/prot.22747View ArticlePubMed
- Murzin AG, Brenner SE, Hubbard T, Chothia C: SCOP: a structural classification of proteins database for the investigation of sequences and structures. Journal of molecular biology 1995, 247(4):536–540.PubMed
- Wang G, Dunbrack RL Jr: PISCES: a protein sequence culling server. Bioinformatics 2003, 19(12):1589–1591. 10.1093/bioinformatics/btg224View ArticlePubMed
- Carson M, Johnson DH, McDonald H, Brouillette C, Delucas LJ: His-tag impact on structure. Acta Crystallogr D Biol Crystallogr 2007, 63(Pt 3):295–301. 10.1107/S0907444906052024View ArticlePubMed
- Kim R, Guo JT: Systematic analysis of short internal indels and their impact on protein folding. BMC Struct Biol 2010, 10(1):24. 10.1186/1472-6807-10-24PubMed CentralView ArticlePubMed
- Martin AC: Mapping PDB chains to UniProtKB entries. Bioinformatics 2005, 21(23):4297–4301. 10.1093/bioinformatics/bti694View ArticlePubMed
- Kabsch W, Sander C: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22(12):2577–2637. 10.1002/bip.360221211View ArticlePubMed
- Miller S, Janin J, Lesk AM, Chothia C: Interior and surface of monomeric proteins. Journal of molecular biology 1987, 196(3):641–656. 10.1016/0022-2836(87)90038-6View ArticlePubMed
- Kim D, Xu D, Guo JT, Ellrott K, Xu Y: PROSPECT II: protein structure prediction program for genome-scale applications. Protein engineering 2003, 16(9):641–650. 10.1093/protein/gzg081View ArticlePubMed
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. Journal of molecular biology 1990, 215(3):403–410.View ArticlePubMed
- Kleywegt GJ: Crystallographic refinement of ligand complexes. Acta Crystallogr D Biol Crystallogr 2007, 63(Pt 1):94–100.PubMed CentralView ArticlePubMed
- Michalsky E, Dunkel M, Goede A, Preissner R: SuperLigands-a database of ligand structures derived from the Protein Data Bank. BMC bioinformatics 2005, 6: 122. 10.1186/1471-2105-6-122PubMed CentralView ArticlePubMed
- Zhu J, Weng Z: FAST: a novel protein structure alignment algorithm. Proteins 2005, 58(3):618–627. 10.1002/prot.20331View ArticlePubMed
- Shindyalov IN, Bourne PE: Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein engineering 1998, 11(9):739–747. 10.1093/protein/11.9.739View ArticlePubMed
- Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J: CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic acids research 2006, (34 Web Server):W116–118. 10.1093/nar/gkl282
- Sonavane S, Chakrabarti P: Cavities and atomic packing in protein structures and interfaces. PLoS Comput Biol 2008, 4(9):e1000188. 10.1371/journal.pcbi.1000188PubMed CentralView ArticlePubMed
- Yamada T, Takusagawa F: PGH2 degradation pathway catalyzed by GSH-heme complex bound microsomal prostaglandin E2 synthase type 2: the first example of a dual-function enzyme. Biochemistry 2007, 46(28):8414–8424. 10.1021/bi700605mView ArticlePubMed
- Medlock AE, Carter M, Dailey TA, Dailey HA, Lanzilotta WN: Product release rather than chelation determines metal specificity for ferrochelatase. Journal of molecular biology 2009, 393(2):308–319. 10.1016/j.jmb.2009.08.042PubMed CentralView ArticlePubMed
- Nelson DR: Cytochrome P450 and the individuality of species. Archives of biochemistry and biophysics 1999, 369(1):1–10. 10.1006/abbi.1999.1352View ArticlePubMed
- Chapple C: Molecular-genetic analysis of plant cytochrome P450-dependent monooxygenases. Annu Rev Plant Physiol Plant Mol Biol 1998, 49: 311–343. 10.1146/annurev.arplant.49.1.311View ArticlePubMed
- Otyepka M, Skopalik J, Anzenbacherova E, Anzenbacher P: What common structural features and variations of mammalian P450 s are known to date? Biochimica et biophysica acta 2007, 1770(3):376–389.View ArticlePubMed
- Yi L, Jenkins PM, Leichert LI, Jakob U, Martens JR, Ragsdale SW: Heme regulatory motifs in heme oxygenase-2 form a thiol/disulfide redox switch that responds to the cellular redox state. J Biol Chem 2009, 284(31):20556–20561. 10.1074/jbc.M109.015651PubMed CentralView ArticlePubMed
- Ogawa K, Sun J, Taketani S, Nakajima O, Nishitani C, Sassa S, Hayashi N, Yamamoto M, Shibahara S, Fujita H, Igarashi K: Heme mediates derepression of Maf recognition element through direct binding to transcription repressor Bach1. The EMBO journal 2001, 20(11):2835–2843. 10.1093/emboj/20.11.2835PubMed CentralView ArticlePubMed
- Yi L, Morgan JT, Ragsdale SW: Identification of a thiol/disulfide redox switch in the human BK channel that controls its affinity for heme and CO. J Biol Chem 2010, 285(26):20117–20127. 10.1074/jbc.M110.116483PubMed CentralView ArticlePubMed
- Yi L, Ragsdale SW: Evidence that the heme regulatory motifs in heme oxygenase-2 serve as a thiol/disulfide redox switch regulating heme binding. J Biol Chem 2007, 282(29):21056–21067. 10.1074/jbc.M700664200PubMed CentralView ArticlePubMed
- Pardee KI, Xu X, Reinking J, Schuetz A, Dong A, Liu S, Zhang R, Tiefenbach J, Lajoie G, Plotnikov AN, Botchkarev A, Krause HM, Edwards A: The structural basis of gas-responsive transcription by the human nuclear hormone receptor REV-ERBbeta. PLoS Biol 2009, 7(2):e43. 10.1371/journal.pbio.1000043View ArticlePubMed
- Tsai CJ, del Sol A, Nussinov R: Allostery: absence of a change in shape does not imply that allostery is not at play. Journal of molecular biology 2008, 378(1):1–11. 10.1016/j.jmb.2008.02.034PubMed CentralView ArticlePubMed
- Okazaki K, Takada S: Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms. Proceedings of the National Academy of Sciences of the United States of America 2008, 105(32):11182–11187. 10.1073/pnas.0802524105PubMed CentralView ArticlePubMed
- Boehr DD, Nussinov R, Wright PE: The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 2009, 5(11):789–796. 10.1038/nchembio.232PubMed CentralView ArticlePubMed
- Leutzinger Y, Beychok S: Kinetics and mechanism of heme-induced refolding of human alpha-globin. Proceedings of the National Academy of Sciences of the United States of America 1981, 78(2):780–784. 10.1073/pnas.78.2.780PubMed CentralView ArticlePubMed
- Culbertson DS, Olson JS: Role of heme in the unfolding and assembly of myoglobin. Biochemistry 2010, 49(29):6052–6063. 10.1021/bi1006942PubMed CentralView ArticlePubMed
- Dunker AK, Brown CJ, Obradovic Z: Identification and functions of usefully disordered proteins. Unfolded Proteins 2002, 62: 25–49. full_text
- Dyson HJ, Wright PE: Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 2005, 6(3):197–208. 10.1038/nrm1589View ArticlePubMed
- Crooks GE, Hon G, Chandonia JM, Brenner SE: WebLogo: a sequence logo generator. Genome research 2004, 14(6):1188–1190. 10.1101/gr.849004PubMed CentralView ArticlePubMed
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