1
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Enikeev AD, Abramov PM, Elkin DS, Komelkov AV, Beliaeva AA, Silantieva DM, Tchevkina EM. Opposite Effects of CRABP1 and CRABP2 Homologs on Proliferation of Breast Cancer Cells and Their Sensitivity to Retinoic Acid. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:2107-2124. [PMID: 38462454 DOI: 10.1134/s0006297923120131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 03/12/2024]
Abstract
Resistance of tumor cells to retinoic acid (RA), a promising therapeutic agent, is the major factor limiting the use of RA in clinical practice. The mechanisms of resistance to RA are still poorly understood. Cellular Retinoic Acid Binding Proteins, CRABP1 and CRABP2, are essential mediators of RA signaling, but role of the two CRABP homologs in regulating cellular sensitivity to RA has not been well studied. In addition, the effects of CRABP1 and CRABP2 on cell proliferation have not been compared. Here, using a broad panel of breast cancer cell lines with different levels of RA sensitivity/resistance, we show for the first time that in the RA-sensitive cells, CRABP1 expression is restricted by methylation, and protein levels are highly variable. In the moderately-RA-resistant cell lines, high level of CRABP1 is observed both at the mRNA and protein levels, unchanged by inhibition of DNA methylation. The cell lines with maximum resistance to RA are characterized by complete repression of CRABP1 expression realized at transcriptional and posttranscriptional levels, and exogenous expression of each of the CRABP homologs has no effect on the studied characteristics. CRABP1 and CRABP2 proteins have opposing effects on proliferation and sensitivity to RA. In particular, CRABP1 stimulates and CRABP2 reduces proliferation and resistance to RA in the initially RA-sensitive cells, while in the more resistant cells the role of each homolog in both of these parameters is reversed. Overall, we have shown for the first time that CRABP proteins exert different effects on the growth and sensitivity to RA of breast cancer cells (stimulation, suppression, or no effect) depending on the baseline level of RA-sensitivity, with the effects of CRABP1 and CRABP2 homologs on the studied properties always being opposite.
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Affiliation(s)
- Adel D Enikeev
- Federal State Budgetary Institution "N. N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, 115522, Russia
| | - Pavel M Abramov
- Federal State Budgetary Institution "N. N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, 115522, Russia
| | - Danila S Elkin
- Federal State Budgetary Institution "N. N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, 115522, Russia
| | - Andrey V Komelkov
- Federal State Budgetary Institution "N. N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, 115522, Russia
| | - Anastasiya A Beliaeva
- Federal State Budgetary Institution "N. N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, 115522, Russia
| | - Darya M Silantieva
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Elena M Tchevkina
- Federal State Budgetary Institution "N. N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, 115522, Russia.
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2
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Toke O. Structural and Dynamic Determinants of Molecular Recognition in Bile Acid-Binding Proteins. Int J Mol Sci 2022; 23:ijms23010505. [PMID: 35008930 PMCID: PMC8745080 DOI: 10.3390/ijms23010505] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 12/12/2022] Open
Abstract
Disorders in bile acid transport and metabolism have been related to a number of metabolic disease states, atherosclerosis, type-II diabetes, and cancer. Bile acid-binding proteins (BABPs), a subfamily of intracellular lipid-binding proteins (iLBPs), have a key role in the cellular trafficking and metabolic targeting of bile salts. Within the family of iLBPs, BABPs exhibit unique binding properties including positive binding cooperativity and site-selectivity, which in different tissues and organisms appears to be tailored to the local bile salt pool. Structural and biophysical studies of the past two decades have shed light on the mechanism of bile salt binding at the atomic level, providing us with a mechanistic picture of ligand entry and release, and the communication between the binding sites. In this review, we discuss the emerging view of bile salt recognition in intestinal- and liver-BABPs, with examples from both mammalian and non-mammalian species. The structural and dynamic determinants of the BABP-bile–salt interaction reviewed herein set the basis for the design and development of drug candidates targeting the transcellular traffic of bile salts in enterocytes and hepatocytes.
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Affiliation(s)
- Orsolya Toke
- Laboratory for NMR Spectroscopy, Structural Research Centre, Research Centre for Natural Sciences, 2 Magyar Tudósok Körútja, H-1117 Budapest, Hungary
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3
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Subadini S, Bera K, Hritz J, Sahoo H. Polyethylene glycol perturbs the unfolding of CRABP I: A correlation between experimental and theoretical approach. Colloids Surf B Biointerfaces 2021; 202:111696. [PMID: 33770701 DOI: 10.1016/j.colsurfb.2021.111696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/25/2021] [Accepted: 03/11/2021] [Indexed: 10/21/2022]
Abstract
The importance of macromolecules paves the way towards a detailed molecular level investigation as all most all cellular processes occurring at the interior of cells in the form of proteins, enzymes, and other biological molecules are significantly affected because of their crowding. Thus, exploring the role of crowding environment on the denaturation and renaturation kinetics of protein molecules is of great importance. Here, CRABP I (cellular retinoic acid binding protein I) is employed as a model protein along with different molecular weights of Polyethylene glycol (PEG) as molecular crowders. The experimental evaluations are done by accessing the protein secondary structure analysis using circular dichroism (CD) spectroscopy and unfolding kinetics using intrinsic fluorescence of CRABP I at 37 °C to mimic the in vivo crowding environment. The unfolding kinetics results indicated that both PEG 2000 and PEG 4000 act as stabilizers by retarding the unfolding kinetic rates. Both kinetic and stability outcomes presented the importance of crowding environment on stability and kinetics of CRABP I. The molecular dynamics (MD) studies revealed that thirteen PEG 2000 molecules assembled during the 500 ns simulation, which increases the stability and percentage of β-sheet. The experimental findings are well supported by the molecular dynamics simulation results.
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Affiliation(s)
- Suchismita Subadini
- Biophysical and Protein Chemistry Lab, Department of Chemistry, NIT Rourkela, Rourkela, 769008, India
| | - Krishnendu Bera
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Jozef Hritz
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic; Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Harekrushna Sahoo
- Biophysical and Protein Chemistry Lab, Department of Chemistry, NIT Rourkela, Rourkela, 769008, India; Center of Nanomaterials, NIT Rourkela, Rourkela, 769008, India.
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4
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Bhattacharya S, Xu L, Thompson D. Long-range Regulation of Partially Folded Amyloidogenic Peptides. Sci Rep 2020; 10:7597. [PMID: 32371882 PMCID: PMC7200734 DOI: 10.1038/s41598-020-64303-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 04/15/2020] [Indexed: 01/20/2023] Open
Abstract
Neurodegeneration involves abnormal aggregation of intrinsically disordered amyloidogenic peptides (IDPs), usually mediated by hydrophobic protein-protein interactions. There is mounting evidence that formation of α-helical intermediates is an early event during self-assembly of amyloid-β42 (Aβ42) and α-synuclein (αS) IDPs in Alzheimer’s and Parkinson’s disease pathogenesis, respectively. However, the driving force behind on-pathway molecular assembly of partially folded helical monomers into helical oligomers assembly remains unknown. Here, we employ extensive molecular dynamics simulations to sample the helical conformational sub-spaces of monomeric peptides of both Aβ42 and αS. Our computed free energies, population shifts, and dynamic cross-correlation network analyses reveal a common feature of long-range intra-peptide modulation of partial helical folds of the amyloidogenic central hydrophobic domains via concerted coupling with their charged terminal tails (N-terminus of Aβ42 and C-terminus of αS). The absence of such inter-domain fluctuations in both fully helical and completely unfolded (disordered) states suggests that long-range coupling regulates the dynamicity of partially folded helices, in both Aβ42 and αS peptides. The inter-domain coupling suggests a form of intra-molecular allosteric regulation of the aggregation trigger in partially folded helical monomers. This approach could be applied to study the broad range of amyloidogenic peptides, which could provide a new path to curbing pathogenic aggregation of partially folded conformers into oligomers, by inhibition of sites far from the hydrophobic core.
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Affiliation(s)
- Shayon Bhattacharya
- Department of Physics, Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Liang Xu
- Department of Physics, Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland.
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5
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Pobre KFR, Powers DL, Ghosh K, Gierasch LM, Powers ET. Kinetic versus thermodynamic control of mutational effects on protein homeostasis: A perspective from computational modeling and experiment. Protein Sci 2019; 28:1324-1339. [PMID: 31074892 DOI: 10.1002/pro.3639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/06/2019] [Indexed: 01/05/2023]
Abstract
The effect of mutations in individual proteins on protein homeostasis, or "proteostasis," can in principle depend on the mutations' effects on the thermodynamics or kinetics of folding, or both. Here, we explore this issue using a computational model of in vivo protein folding that we call FoldEcoSlim. Our model predicts that kinetic versus thermodynamic control of mutational effects on proteostasis hinges on the relationship between how fast a protein's folding reaction reaches equilibrium and a critical time scale that characterizes the lifetime of a protein in its environment: for rapidly dividing bacteria, this time scale is that of cell division; for proteins that are produced in heterologous expression systems, this time scale is the amount of time before the protein is harvested; for proteins that are synthesized in and then exported from the eukaryotic endoplasmic reticulum, this time scale is that of protein secretion, and so forth. This prediction was validated experimentally by examining the expression yields of the wild type and several destabilized mutants of a model protein, the mouse ortholog of cellular retinoic acid-binding protein 1.
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Affiliation(s)
- Kristine Faye R Pobre
- Departments of Biochemistry & Molecular Biology and Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, 01003
| | - David L Powers
- Department of Mathematics, Clarkson University, Potsdam, New York, 13699
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, Colorado, 80208
| | - Lila M Gierasch
- Departments of Biochemistry & Molecular Biology and Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, 01003
| | - Evan T Powers
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, 92037
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6
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Thakur AK, Meng W, Gierasch LM. Local and non-local topological information in the denatured state ensemble of a β-barrel protein. Protein Sci 2018; 27:2062-2072. [PMID: 30252171 DOI: 10.1002/pro.3516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 11/06/2022]
Abstract
The folding of predominantly β-sheet proteins is complicated by the presence of a large number of non-local interactions in their native states, which increase the ruggedness of their folding energy landscapes. However, forming non-local contacts early in folding or even in the unfolded state can smooth the energy landscape and facilitate productive folding. We report that several sequence regions of a β-barrel protein, cellular retinoic acid-binding protein 1 (CRABP1), populate native-like secondary structure to a significant extent in the denatured state in 8 M urea. In addition, we provide evidence for both local and non-local interactions in the denatured state of CRABP1. NMR chemical shift perturbations (CSPs) under denaturing conditions upon substitution of single residues by mutation support the presence of several non-local interactions in topologically key sites, arguing that the denatured state is conformationally restricted and contains topological information for the native fold. Among the most striking non-local interactions are those between the N- and C-terminal regions, which are involved in closure of the native β-barrel. In addition, CSPs support the presence of two features in the denatured state: a major hydrophobic cluster involving residues from various parts of the sequence and a native-like interaction similar to one identified in previous studies as forming early in folding (Budyak et al., Structure 21, 476 [2013]). Taken together, our data support a model in which transient structures involving nonlocal interactions prime early folding interactions in CRABP1, determine its barrel topology, and may protect this predominantly β-sheet protein against aggregation.
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Affiliation(s)
- Abhay K Thakur
- Departments of Biochemistry & Molecular Biology and Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
| | - Wenli Meng
- Departments of Biochemistry & Molecular Biology and Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
| | - Lila M Gierasch
- Departments of Biochemistry & Molecular Biology and Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
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7
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Yageta S, Shibuya R, Imamura H, Honda S. Conformational and Colloidal Stabilities of Human Immunoglobulin G Fc and Its Cyclized Variant: Independent and Compensatory Participation of Domains in Aggregation of Multidomain Proteins. Mol Pharm 2017; 14:699-711. [DOI: 10.1021/acs.molpharmaceut.6b00983] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Seiki Yageta
- Department of Computational
Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, AIST Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Risa Shibuya
- Department of Computational
Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Hiroshi Imamura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, AIST Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Shinya Honda
- Department of Computational
Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, AIST Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
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8
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Mascarenhas NM, Gosavi S. Protein Domain-Swapping Can Be a Consequence of Functional Residues. J Phys Chem B 2016; 120:6929-38. [PMID: 27331242 DOI: 10.1021/acs.jpcb.6b03968] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Monomer topology has been implicated in domain-swapping, a potential first step on the route to disease-causing protein aggregation. Despite having the same topology (β1-α1-β2-β3-β4-β5), the cysteine protease inhibitor stefin-B domain swaps more readily than a single-chain variant of the heterodimeric sweet protein monellin (scMn). Here, we computationally study the folding of stefin-B and scMn in order to understand the molecular basis for the difference in their domain-swapping propensities. In agreement with experiments, our structure-based simulations show that scMn folds cooperatively without the population of an intermediate while stefin-B populates an equilibrium intermediate state. Since the simulation intermediate has only one domain structured (β3-β4-β5), it can directly lead to domain-swapping. Using computational variants of stefin-B, we show that the population of this intermediate is caused by regions of stefin-B that have been implicated in protease inhibition. We also find that the protease-binding regions are located on two structural elements and localized in space. In contrast, the residues that contribute to the sweetness of monellin are not localized to a few structural elements but are distributed over the protein fold. We conclude that the distributed functional residues of monellin do not induce large local perturbations in the protein structure, eliminating the formation of folding intermediates and in turn domain-swapping. On the other hand, the localized protease-binding regions of stefin-B promote the formation of a folding intermediate which can lead to domain-swapping. Thus, domain-swapping can be a direct consequence of the constraints that function imposes on the protein structure.
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Affiliation(s)
- Nahren Manuel Mascarenhas
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bangalore 560065, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bangalore 560065, India
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9
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Sugita M, Matsuoka M, Kikuchi T. Topological and sequence information predict that foldons organize a partially overlapped and hierarchical structure. Proteins 2015; 83:1900-13. [PMID: 26248725 DOI: 10.1002/prot.24874] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 06/23/2015] [Accepted: 07/29/2015] [Indexed: 11/09/2022]
Abstract
It has been suggested that proteins have substructures, called foldons, which can cooperatively fold into the native structure. However, several prior investigations define foldons in various ways, citing different foldon characteristics, thereby making the concept of a foldon ambiguous. In this study, we perform a Gō model simulation and analyze the characteristics of substructures that cooperatively fold into the native-like structure. Although some results do not agree well with the experimental evidence due to the simplicity of our coarse-grained model, our results strongly suggest that cooperatively folding units sometimes organize a partially overlapped and hierarchical structure. This view makes us easy to interpret some different proposal about the foldon as a difference of the hierarchical structure. On the basis of this finding, we present a new method to assign foldons and their hierarchy, using structural and sequence information. The results show that the foldons assigned by our method correspond to the intermediate structures identified by some experimental techniques. The new method makes it easy to predict whether a protein folds sequentially into the native structure or whether some foldons fold into the native structure in parallel.
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Affiliation(s)
- Masatake Sugita
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Masanari Matsuoka
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Takeshi Kikuchi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
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10
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Individual and collective contributions of chaperoning and degradation to protein homeostasis in E. coli. Cell Rep 2015; 11:321-33. [PMID: 25843722 DOI: 10.1016/j.celrep.2015.03.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/29/2015] [Accepted: 03/07/2015] [Indexed: 11/24/2022] Open
Abstract
The folding fate of a protein in vivo is determined by the interplay between a protein's folding energy landscape and the actions of the proteostasis network, including molecular chaperones and degradation enzymes. The mechanisms of individual components of the E. coli proteostasis network have been studied extensively, but much less is known about how they function as a system. We used an integrated experimental and computational approach to quantitatively analyze the folding outcomes (native folding versus aggregation versus degradation) of three test proteins biosynthesized in E. coli under a variety of conditions. Overexpression of the entire proteostasis network benefited all three test proteins, but the effect of upregulating individual chaperones or the major degradation enzyme, Lon, varied for proteins with different biophysical properties. In sum, the impact of the E. coli proteostasis network is a consequence of concerted action by the Hsp70 system (DnaK/DnaJ/GrpE), the Hsp60 system (GroEL/GroES), and Lon.
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11
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Gershenson A, Gierasch LM, Pastore A, Radford SE. Energy landscapes of functional proteins are inherently risky. Nat Chem Biol 2014; 10:884-91. [PMID: 25325699 PMCID: PMC4416114 DOI: 10.1038/nchembio.1670] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 09/19/2014] [Indexed: 01/08/2023]
Abstract
Evolutionary pressure for protein function leads to unavoidable sampling of conformational states that are at risk of misfolding and aggregation. The resulting tension between functional requirements and the risk of misfolding and/or aggregation in the evolution of proteins is becoming more and more apparent. One outcome of this tension is sensitivity to mutation, in which only subtle changes in sequence that may be functionally advantageous can tip the delicate balance toward protein aggregation. Similarly, increasing the concentration of aggregation-prone species by reducing the ability to control protein levels or compromising protein folding capacity engenders increased risk of aggregation and disease. In this Perspective, we describe examples that epitomize the tension between protein functional energy landscapes and aggregation risk. Each case illustrates how the energy landscapes for the at-risk proteins are sculpted to enable them to perform their functions and how the risks of aggregation are minimized under cellular conditions using a variety of compensatory mechanisms.
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Affiliation(s)
- Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Lila M Gierasch
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Annalisa Pastore
- Department of Clinical Neurosciences, King’s College London, Denmark Hill Campus, London, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
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12
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Sarkar S, Chattopadhyay K. Studies of Early Events of Folding of a Predominately β-Sheet Protein Using Fluorescence Correlation Spectroscopy and Other Biophysical Methods. Biochemistry 2014; 53:1393-402. [DOI: 10.1021/bi4014837] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Suparna Sarkar
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, India
| | - Krishnananda Chattopadhyay
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, India
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13
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Ferrolino MC, Zhuravleva A, Budyak IL, Krishnan B, Gierasch LM. Delicate balance between functionally required flexibility and aggregation risk in a β-rich protein. Biochemistry 2013; 52:8843-54. [PMID: 24236614 DOI: 10.1021/bi4013462] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Susceptibility to aggregation is general to proteins because of the potential for intermolecular interactions between hydrophobic stretches in their amino acid sequences. Protein aggregation has been implicated in several catastrophic diseases, yet we still lack in-depth understanding about how proteins are channeled to this state. Using a predominantly β-sheet protein whose folding has been explored in detail, cellular retinoic acid-binding protein 1 (CRABP1), as a model, we have tackled the challenge of understanding the links between a protein's natural tendency to fold, 'breathe', and function with its propensity to misfold and aggregate. We identified near-native dynamic species that lead to aggregation and found that inherent structural fluctuations in the native protein, resulting in opening of the ligand-entry portal, expose hydrophobic residues on the most vulnerable aggregation-prone sequences in CRABP1. CRABP1 and related intracellullar lipid-binding proteins have not been reported to aggregate inside cells, and we speculate that the cellular concentration of their open, aggregation-prone conformations is sufficient for ligand binding but below the critical concentration for aggregation. Our finding provides an example of how nature fine-tunes a delicate balance between protein function, conformational variability, and aggregation vulnerability and implies that with the evolutionary requirement for proteins to fold and function, aggregation becomes an unavoidable but controllable risk.
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Affiliation(s)
- Mylene C Ferrolino
- Department of Biochemistry and Molecular Biology, ‡Program in Molecular and Cellular Biology, and §Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
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14
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The Role of Aromatic-Aromatic Interactions in Strand-Strand Stabilization of β-Sheets. J Mol Biol 2013; 425:3522-35. [PMID: 23810905 DOI: 10.1016/j.jmb.2013.06.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 06/12/2013] [Accepted: 06/18/2013] [Indexed: 11/21/2022]
Abstract
Aromatic-aromatic interactions have long been believed to play key roles in protein structure, folding, and binding functions. However, we still lack full understanding of the contributions of aromatic-aromatic interactions to protein stability and the timing of their formation during folding. Here, using an aromatic ladder in the β-barrel protein, cellular retinoic acid-binding protein 1 (CRABP1), as a case study, we find that aromatic π stacking plays a greater role in the Phe65-Phe71 cross-strand pair, while in another pair, Phe50-Phe65, hydrophobic interactions are dominant. The Phe65-Phe71 pair spans β-strands 4 and 5 in the β-barrel, which lack interstrand hydrogen bonding, and we speculate that it compensates energetically for the absence of strand-strand backbone interactions. Using perturbation analysis, we find that both aromatic-aromatic pairs form after the transition state for folding of CRABP1, thus playing a role in the final stabilization of the β-sheet rather than in its nucleation as had been earlier proposed. The aromatic interaction between strands 4 and 5 in CRABP1 is highly conserved in the intracellular lipid-binding protein (iLBP) family, and several lines of evidence combine to support a model wherein it acts to maintain barrel structure while allowing the dynamic opening that is necessary for ligand entry. Lastly, we carried out a bioinformatics analysis and found 51 examples of aromatic-aromatic interactions across non-hydrogen-bonded β-strands outside the iLBPs, arguing for the generality of the role played by this structural motif.
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