1
|
Menozzi I, Polverini E, Berni R. Deciphering protein dynamics changes along the pathway of retinol uptake by cellular retinol-binding proteins 1 and 2. Arch Biochem Biophys 2018; 645:107-116. [PMID: 29567208 DOI: 10.1016/j.abb.2018.03.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 03/12/2018] [Accepted: 03/18/2018] [Indexed: 12/11/2022]
Abstract
Four Cellular Retinol-binding Proteins (CRBP 1, 2, 3, 4) are encoded in the human genome. CRBP 1 and 2, sharing a 56% amino acid sequence identity, exhibit the highest binding affinities for retinol. Previous NMR studies provided some insights into the mechanism of retinol uptake, but details of such mechanism remain to be elucidated. Herein, the results of molecular dynamics simulations for the uptake of retinol by CRBP 1 and 2 are consistent with the presence of two different retinol entry points, both involving the 'cap region' (α-helices I and II and neighboring loops). We observed that a hydrophobic patch at the surface of the 'portal region' (α-helix II, CD and EF loops) of CRBP 1 attracts retinol, which accesses the binding cavity through an opening generated by the concerted movements of Arg58 and Phe57, present in the CD loop. In CRBP 2 a different distribution of the surface residues of the 'cap region' allows retinol to access the binding cavity by sinking in a hydrophobic matrix between the two α-helices. Polar interactions mainly affect retinol movements inside the β-barrel cavities of both CRBPs. The interaction energy profiles are in agreement with the different behavior of the two protein systems.
Collapse
Affiliation(s)
- Ilaria Menozzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze, 23/A, University of Parma, 43124 Parma, Italy
| | - Eugenia Polverini
- Department of Mathematical, Physical and Computer Sciences, Parco Area delle Scienze, 7/A, University of Parma, 43124 Parma, Italy.
| | - Rodolfo Berni
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze, 23/A, University of Parma, 43124 Parma, Italy.
| |
Collapse
|
2
|
Bradley ME, Benner SA. Integrating protein structures and precomputed genealogies in the Magnum database: examples with cellular retinoid binding proteins. BMC Bioinformatics 2006; 7:89. [PMID: 16504077 PMCID: PMC1475641 DOI: 10.1186/1471-2105-7-89] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2005] [Accepted: 02/23/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND When accurate models for the divergent evolution of protein sequences are integrated with complementary biological information, such as folded protein structures, analyses of the combined data often lead to new hypotheses about molecular physiology. This represents an excellent example of how bioinformatics can be used to guide experimental research. However, progress in this direction has been slowed by the lack of a publicly available resource suitable for general use. RESULTS The precomputed Magnum database offers a solution to this problem for ca. 1,800 full-length protein families with at least one crystal structure. The Magnum deliverables include 1) multiple sequence alignments, 2) mapping of alignment sites to crystal structure sites, 3) phylogenetic trees, 4) inferred ancestral sequences at internal tree nodes, and 5) amino acid replacements along tree branches. Comprehensive evaluations revealed that the automated procedures used to construct Magnum produced accurate models of how proteins divergently evolve, or genealogies, and correctly integrated these with the structural data. To demonstrate Magnum's capabilities, we asked for amino acid replacements requiring three nucleotide substitutions, located at internal protein structure sites, and occurring on short phylogenetic tree branches. In the cellular retinoid binding protein family a site that potentially modulates ligand binding affinity was discovered. Recruitment of cellular retinol binding protein to function as a lens crystallin in the diurnal gecko afforded another opportunity to showcase the predictive value of a browsable database containing branch replacement patterns integrated with protein structures. CONCLUSION We integrated two areas of protein science, evolution and structure, on a large scale and created a precomputed database, known as Magnum, which is the first freely available resource of its kind. Magnum provides evolutionary and structural bioinformatics resources that are useful for identifying experimentally testable hypotheses about the molecular basis of protein behaviors and functions, as illustrated with the examples from the cellular retinoid binding proteins.
Collapse
Affiliation(s)
- Michael E Bradley
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, USA
- Division of Biological Sciences, Department of Ecology and Evolution, University of Chicago, 1101 East 57Street, Chicago, IL, 60615, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, 1115 NW 14Avenue, Gainesville, FL, 32601, USA
| |
Collapse
|
3
|
Polverini E, Fornabaio M, Fasano A, Carlone G, Riccio P, Cavatorta P. The pH-dependent unfolding mechanism of P2 myelin protein: an experimental and computational study. J Struct Biol 2005; 153:253-63. [PMID: 16427315 DOI: 10.1016/j.jsb.2005.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Revised: 11/04/2005] [Accepted: 11/10/2005] [Indexed: 10/25/2022]
Abstract
The P2 protein is a small, extrinsic protein of the myelin membrane in the peripheral nervous system that structurally belongs to the fatty acid binding proteins (FABPs) family, sharing with them a 10 strands beta-barrel structure. FABPs appear to be involved in cellular fatty acid transport, but very little is known about the role of P2 in the metabolism of peripheral myelin lipids. Study of protein conformation at different pHs is a useful tool for the characterization of the unfolding mechanisms and the intrinsic conformational properties of the protein, and may give insight into factors that guide protein folding pathways. In particular, low pH conditions have been shown to induce partially folded states in several proteins. In this paper, the acidic unfolding of purified P2 protein was studied with both spectroscopic techniques and molecular dynamics simulation. Both experimental and computational results indicate the presence of a partly folded state at low pH, which shows structural changes mainly involving the lid that is formed by the helix-turn-helix domain. The opening of the lid, together with a barrel relaxation, could regulate the ligand exchanges near the cell membrane, supporting the hypothesis that the P2 protein may transport fatty acids between Schwann cells and peripheral myelin.
Collapse
Affiliation(s)
- Eugenia Polverini
- Dipartimento di Fisica, CNR-INFM and CNISM, Università di Parma, Parco Area delle Scienze, 7/A, 43100 Parma, Italy.
| | | | | | | | | | | |
Collapse
|
4
|
Lu J, Cistola DP, Li E. Two homologous rat cellular retinol-binding proteins differ in local conformational flexibility. J Mol Biol 2003; 330:799-812. [PMID: 12850148 DOI: 10.1016/s0022-2836(03)00629-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Cellular retinol-binding protein I (CRBP I) and cellular retinol-binding protein II (CRBP II) are closely homologous proteins that play distinct roles in the maintenance of vitamin A homeostasis. The solution structure and dynamics of CRBP I and CRBP II were compared by multidimensional NMR techniques. These studies indicated that differences in the mean backbone structures of CRBP I and CRBP II were localized primarily to the alphaII helix. Intraligand NOE cross-peaks were detected for the hydroxyl proton in the NOESY spectrum of CRBP I-bound retinol, but not for CRBP II-bound retinol, indicating that the conformational dynamics of retinol binding are different for these two proteins. As determined by Lipari-Szabo formalism, both the apo and holo forms of CRBP I and CRBP II are conformationally rigid on the pico- to nanosecond timescale. transverse relaxation optimized spectroscopy-Carr-Purcell-Meiboom-Gill -based 15N relaxation dispersion experiments at both 500 MHz and 600 MHz magnetic fields revealed that 84 and 62 residues for apo-CRBP I and II, respectively, showed detectable conformational exchange on a micro- to millisecond timescale, in contrast to three and seven residues for holo-CRBP I and II, respectively. Thus binding of retinol markedly reduced conformational flexibility in both CRBP I and CRBP II on the micro- to millisecond timescale. The 15N relaxation dispersion curves of apo-CRBP I and II were fit to a two-state conformational exchange model by a global iterative fitting process and by an individual (residue) fitting process. In the process of carrying out the global fit, more than half of the residue sites were eliminated. The individual chemical exchange rates k(ex), and chemical shift differences, Deltadelta, were increased in the putative portal region (alphaII helix and betaC-betaD turn) of apo-CRBP II compared to apo-CRBP I. These differences in conformational flexibility likely contribute to differences in how CRBP I and CRBP II interact with ligands, membranes and retinoid metabolizing enzymes.
Collapse
Affiliation(s)
- Jianyun Lu
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | | |
Collapse
|
5
|
Tsuzuki S, Honda K, Uchimaru T, Mikami M, Tanabe K. Origin of the Attraction and Directionality of the NH/π Interaction: Comparison with OH/π and CH/π Interactions. J Am Chem Soc 2000. [DOI: 10.1021/ja001901a] [Citation(s) in RCA: 335] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Seiji Tsuzuki
- Contribution from the National Institute of Materials and Chemical Research, Tsukuba, Ibaraki 305-8565, Japan
| | - Kazumasa Honda
- Contribution from the National Institute of Materials and Chemical Research, Tsukuba, Ibaraki 305-8565, Japan
| | - Tadafumi Uchimaru
- Contribution from the National Institute of Materials and Chemical Research, Tsukuba, Ibaraki 305-8565, Japan
| | - Masuhiro Mikami
- Contribution from the National Institute of Materials and Chemical Research, Tsukuba, Ibaraki 305-8565, Japan
| | - Kazutoshi Tanabe
- Contribution from the National Institute of Materials and Chemical Research, Tsukuba, Ibaraki 305-8565, Japan
| |
Collapse
|
6
|
Affiliation(s)
- M E Newcomer
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | | | | |
Collapse
|
7
|
Guo Y, Bozic D, Malashkevich VN, Kammerer RA, Schulthess T, Engel J. All-trans retinol, vitamin D and other hydrophobic compounds bind in the axial pore of the five-stranded coiled-coil domain of cartilage oligomeric matrix protein. EMBO J 1998; 17:5265-72. [PMID: 9736606 PMCID: PMC1170854 DOI: 10.1093/emboj/17.18.5265] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The potential storage and delivery function of cartilage oligomeric matrix protein (COMP) for cell signaling molecules was explored by binding hydrophobic compounds to the recombinant five-stranded coiled-coil domain of COMP. Complex formation with benzene, cyclohexane, vitamin D3 and elaidic acid was demonstrated through increases in denaturation temperatures of 2-10 degreesC. For all-trans retinol and all-trans retinoic acid, an equilibrium dissociation constant KD = 0.6 microM was evaluated by fluorescence titration. Binding of benzene and all-trans retinol into the hydrophobic axial pore of the COMP coiled-coil domain was proven by the X-ray crystal structures of the corresponding complexes at 0.25 and 0.27 nm resolution, respectively. Benzene binds with its plane perpendicular to the pore axis. The binding site is between the two internal rings formed by Leu37 and Thr40 pointing into the pore of the COMP coiled-coil domain. The retinol beta-ionone ring is positioned in a hydrophobic environment near Thr40, and the 1.1 nm long isoprene tail follows a completely hydrophobic region of the pore. Its terminal hydroxyl group complexes with a ring of the five side chains of Gln54. A mutant in which Gln54 is replaced by Ile binds all-trans retinol with affinity similar to the wild-type, demonstrating that hydrophobic interactions are predominant.
Collapse
Affiliation(s)
- Y Guo
- Abteilung für Biophysikalische Chemie, Biozentrum, Universität Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | | | | | | | | | | |
Collapse
|
8
|
Parkinson G, Gunasekera A, Vojtechovsky J, Zhang X, Kunkel TA, Berman H, Ebright RH. Aromatic hydrogen bond in sequence-specific protein DNA recognition. NATURE STRUCTURAL BIOLOGY 1996; 3:837-41. [PMID: 8836098 DOI: 10.1038/nsb1096-837] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
9
|
Plesniak LA, Wakarchuk WW, McIntosh LP. Secondary structure and NMR assignments of Bacillus circulans xylanase. Protein Sci 1996; 5:1118-35. [PMID: 8762143 PMCID: PMC2143425 DOI: 10.1002/pro.5560050614] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Bacillus circulans xylanase (BCX) is a member of the family of low molecular weight endo-beta-(1,4)-xylanases. The main-chain 1H, 13C, and 15N resonances of this 20.4-kDa enzyme were assigned using heteronuclear NMR experiments recorded on a combination of selectively and uniformly labeled protein samples. Using chemical shift, NOE, J coupling, and amide hydrogen exchange information, 14 beta-strands, arranged in a network of three beta-sheets, and a single alpha-helix were identified in BCX. The NMR-derived secondary structure and beta-sheet topology agree closely with that observed in the crystal structure of this protein. The HN of Ile 118 has a strongly upfield-shifted resonance at 4.03 ppm, indicative of a potential amide-aromatic hydrogen bond to the indole ring of Trp 71. This interaction, which is conserved in all low molecular weight xylanases of known structure, may play an important role in establishing the active site conformation of these enzymes. Following hen egg white and bacteriophage T4 lysozymes, B. circulans xylanase represents the third family of beta-glycanases for which extensive NMR assignments have been reported. These assignments provide the background for detailed studies of the mechanism of carbohydrate recognition and hydrolysis by this bacterial xylanase.
Collapse
Affiliation(s)
- L A Plesniak
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | | | | |
Collapse
|