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Taank Y, Randhawa V, Agnihotri N. Ergosterol and its metabolites as agonists of Liver X receptor and their anticancer potential in colorectal cancer. J Steroid Biochem Mol Biol 2024; 243:106572. [PMID: 38908720 DOI: 10.1016/j.jsbmb.2024.106572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/10/2024] [Accepted: 06/20/2024] [Indexed: 06/24/2024]
Abstract
Aberrant cholesterol homeostasis is a well-recognized hallmark of cancer and is implicated in metastasis as well as chemotherapeutic resistance, the two major causes of cancer associated mortality. Liver X receptors (LXRs) are the key transcription factors that induce cholesterol efflux via enhancing the expression of ABCA1 and ABCG1. Therefore, a comprehensive analysis of several novel sterols namely ergosta-7,22,24(28)-trien-3β-ol (Erg1), ergosta-5,22,25-trien-3-ol (Erg2), ergosta-5,7,22,24(28)-tetraen-3β-ol (Erg3), and ergosta-7,22-dien-3β-ol (Erg4) as LXR agonists has been performed. Molecular docking studies have shown that these sterols possess higher binding affinities for LXRs as compared to the reference ligands (GW3965 and TO901317) and also formed critical activating interactions. Molecular dynamic (MD) simulations further confirmed that docking complexes made of these sterols possess significant stability. To assess the extent of LXR activation, ABCA1 promoter was cloned into luciferase reporter plasmid and transfected into HCT116 cells. It was observed that treatment with Erg, Erg2 and Erg4 led to a significant LXR activation with an EC50 of 5.64 µM, 4.83 and 3.03 µM respectively. Furthermore, a significant increase in mRNA expression of NR1H2 and LXR target genes i.e. ABCA1, ABCG1 and ApoE was observed upon Erg treatment. Flow cytometric analysis have revealed a significant increase in the accumulation of ABCA1 upon Erg treatment. Cytotoxicity studies conducted on colorectal cancer cell and normal epithelial cell line showed that these sterols are selectively toxic towards cancer cells. Taken together, our findings suggests that ergosterol activates LXRs, have significant anticancer activity and could be a likely candidate to manage aberrant cholesterol homeostasis.
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Affiliation(s)
- Yogain Taank
- Department of Biochemistry (Sector 25), Panjab University, Chandigarh 160014, India
| | - Vinay Randhawa
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Navneet Agnihotri
- Department of Biochemistry (Sector 25), Panjab University, Chandigarh 160014, India.
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2
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Hollmann F, Sanchis J, Reetz MT. Learning from Protein Engineering by Deconvolution of Multi-Mutational Variants. Angew Chem Int Ed Engl 2024; 63:e202404880. [PMID: 38884594 DOI: 10.1002/anie.202404880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/18/2024]
Abstract
This review analyzes a development in biochemistry, enzymology and biotechnology that originally came as a surprise. Following the establishment of directed evolution of stereoselective enzymes in organic chemistry, the concept of partial or complete deconvolution of selective multi-mutational variants was introduced. Early deconvolution experiments of stereoselective variants led to the finding that mutations can interact cooperatively or antagonistically with one another, not just additively. During the past decade, this phenomenon was shown to be general. In some studies, molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) computations were performed in order to shed light on the origin of non-additivity at all stages of an evolutionary upward climb. Data of complete deconvolution can be used to construct unique multi-dimensional rugged fitness pathway landscapes, which provide mechanistic insights different from traditional fitness landscapes. Along a related line, biochemists have long tested the result of introducing two point mutations in an enzyme for mechanistic reasons, followed by a comparison of the respective double mutant in so-called double mutant cycles, which originally showed only additive effects, but more recently also uncovered cooperative and antagonistic non-additive effects. We conclude with suggestions for future work, and call for a unified overall picture of non-additivity and epistasis.
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Affiliation(s)
- Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, Netherlands
| | - Joaquin Sanchis
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Manfred T Reetz
- Max-Plank-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45481, Mülheim, Germany
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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3
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Pei R, Zhang J, Tan J, Luo Y, Ye S. Fermi Resonance of the N-D Stretching Mode Probing the Local Hydrogen-Bonding Environment in Proteins. J Phys Chem B 2024; 128:5658-5666. [PMID: 38836292 DOI: 10.1021/acs.jpcb.4c00390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Local H-bonding interactions are crucial for proteins to undergo various structural transitions and form different secondary structures. However, identifying slight distinctions in the local H-bonding of proteins is rather challenging. Here, we demonstrate that the Fermi resonance of the N-D stretching mode can provide an effective probe for the localized H-bonding environment of proteins both at the surface/interface and in the bulk. Using sum frequency generation vibrational spectroscopy and infrared spectroscopy, we established a correlation between the Fermi resonance of the N-D mode and protein secondary structures. The H-bond of N-D···C═O splits the N-D modes into two peaks (∼2410 and ∼2470 cm-1). The relative strength ratio (R) between the ∼2410 cm-1 peak and the ∼2470 cm-1 peak is very sensitive to H-bond strength and protein secondary structure. R is less than 1 for α-helical peptides, while R is greater than 1 for β-sheet peptides. For R < 2.5, both α-helical/loop structures and β-sheet structures exhibit almost identical Fermi coupling strengths (W = 28 cm-1). For R > 2.5, W decreases from 28 to 14 cm-1 and depends on the aggregation degree of the β-sheet oligomers or fibrils. The initial local H-bonding status impacts the misfolding dynamics of proteins at the lipid bilayer interface.
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Affiliation(s)
- Ruoqi Pei
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Jiahui Zhang
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Junjun Tan
- Hefei National Laboratory, University of Science and Technology of China, Hefei, Anhui 230088, China
| | - Yi Luo
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei, Anhui 230088, China
| | - Shuji Ye
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei, Anhui 230088, China
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4
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Yang X, Jiang W. Enantioselective Recognition of Functional Organic Molecules in Water by Biomimetic Macrocyclic Hosts. J Am Chem Soc 2024; 146:3900-3909. [PMID: 38294833 DOI: 10.1021/jacs.3c11492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Enantioselective recognition of functional organic molecules in water is routine in nature but remains a formidable challenge for synthetic hosts. Here, we reported two pairs of chiral naphthotubes with chiral centers located in the neighborhood of the inward-directing amide groups. These naphthotubes, with a chiral twisted cavity, show highly enantioselective recognition in water to a wide scope of organic molecules (90 chiral guests). The highest enantioselectivity of 34 was achieved with neotame. Small differences between all of the noncovalent interactions shielded in the hydrophobic cavity were revealed to be responsible for the enantioselective recognition in water, which is different from the traditional views. Moreover, these hosts can differentiate the analogues of aspartame using fluorescence spectroscopy. These chiral naphthotubes have made unprecedented achievements in enantioselective recognition, providing the basis for their applications in chiral analysis and separations.
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Affiliation(s)
- Xiran Yang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology (SUSTech), Xueyuan Blvd 1088, Shenzhen 518055, China
| | - Wei Jiang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology (SUSTech), Xueyuan Blvd 1088, Shenzhen 518055, China
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Ugrani S. Inhibitor design for TMPRSS2: insights from computational analysis of its backbone hydrogen bonds using a simple descriptor. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:27-46. [PMID: 38157015 PMCID: PMC10853362 DOI: 10.1007/s00249-023-01695-4] [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: 09/05/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 01/03/2024]
Abstract
Transmembrane protease serine 2 (TMPRSS2) is an important drug target due to its role in the infection mechanism of coronaviruses including SARS-CoV-2. Current understanding regarding the molecular mechanisms of known inhibitors and insights required for inhibitor design are limited. This study investigates the effect of inhibitor binding on the intramolecular backbone hydrogen bonds (BHBs) of TMPRSS2 using the concept of hydrogen bond wrapping, which is the phenomenon of stabilization of a hydrogen bond in a solvent environment as a result of being surrounded by non-polar groups. A molecular descriptor which quantifies the extent of wrapping around BHBs is introduced for this. First, virtual screening for TMPRSS2 inhibitors is performed by molecular docking using the program DOCK 6 with a Generalized Born surface area (GBSA) scoring function. The docking results are then analyzed using this descriptor and its relationship to the solvent-accessible surface area term ΔGsa of the GBSA score is demonstrated with machine learning regression and principal component analysis. The effect of binding of the inhibitors camostat, nafamostat, and 4-guanidinobenzoic acid (GBA) on the wrapping of important BHBs in TMPRSS2 is also studied using molecular dynamics. For BHBs with a large increase in wrapping groups due to these inhibitors, the radial distribution function of water revealed that certain residues involved in these BHBs, like Gln438, Asp440, and Ser441, undergo preferential desolvation. The findings offer valuable insights into the mechanisms of these inhibitors and may prove useful in the design of new inhibitors.
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Affiliation(s)
- Suraj Ugrani
- Purdue University, West Lafayette, IN, 47907, USA.
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6
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Noshay J, Walker T, Alexander W, Klingeman D, Romero J, Walker A, Prates E, Eckert C, Irle S, Kainer D, Jacobson D. Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering. Nucleic Acids Res 2023; 51:10147-10161. [PMID: 37738140 PMCID: PMC10602897 DOI: 10.1093/nar/gkad736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/07/2023] [Accepted: 08/29/2023] [Indexed: 09/24/2023] Open
Abstract
CRISPR-Cas9 tools have transformed genetic manipulation capabilities in the laboratory. Empirical rules-of-thumb have been developed for only a narrow range of model organisms, and mechanistic underpinnings for sgRNA efficiency remain poorly understood. This work establishes a novel feature set and new public resource, produced with quantum chemical tensors, for interpreting and predicting sgRNA efficiency. Feature engineering for sgRNA efficiency is performed using an explainable-artificial intelligence model: iterative Random Forest (iRF). By encoding quantitative attributes of position-specific sequences for Escherichia coli sgRNAs, we identify important traits for sgRNA design in bacterial species. Additionally, we show that expanding positional encoding to quantum descriptors of base-pair, dimer, trimer, and tetramer sequences captures intricate interactions in local and neighboring nucleotides of the target DNA. These features highlight variation in CRISPR-Cas9 sgRNA dynamics between E. coli and H. sapiens genomes. These novel encodings of sgRNAs enhance our understanding of the elaborate quantum biological processes involved in CRISPR-Cas9 machinery.
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Affiliation(s)
- Jaclyn M Noshay
- Computational and Predictive Biology, Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Tyler Walker
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - William G Alexander
- Synthetic Biology, Biosciences,Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Dawn M Klingeman
- Synthetic Biology, Biosciences,Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jonathon Romero
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Angelica M Walker
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Erica Prates
- Computational and Predictive Biology, Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Carrie Eckert
- Synthetic Biology, Biosciences,Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Stephan Irle
- Computational Sciences and Engineering, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - David Kainer
- Computational and Predictive Biology, Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Daniel A Jacobson
- Computational and Predictive Biology, Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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7
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Mishra V, Pathak AK, Bandyopadhyay T. Binding of human serum albumin with uranyl ion at various pH: an all atom molecular dynamics study. J Biomol Struct Dyn 2023; 41:7318-7328. [PMID: 36099177 DOI: 10.1080/07391102.2022.2120080] [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: 07/28/2022] [Accepted: 08/26/2022] [Indexed: 10/14/2022]
Abstract
Uranium is routinely handled in various stages of nuclear fuel cycle and its association with human serum albumin (HSA) has been reported in literature, however, their binding characteristics still remains obscure. The present study aims to understand interaction of uranium with HSA by employing all atom molecular dynamics simulation of the HSA-metal ion complex. His67, His247 and Asp249 residues constitute the major binding site of HSA, which capture the uranyl ion (UO22+). A total of six sets of initial coordinates are used for Zn2+-HSA and UO22+-HSA system at pH = 4, 7.4 and 9, respectively. Enhance sampling method, namely, well-tempered meta-dynamics (WT-MtD) is employed to study the binding and un-binding processes of UO22+ and Zn2+ ions. Potential of mean force (PMF) profiles are generated for all the six sets of complexes from the converged WT-MtD run. Various basins and barriers are observed along the (un)binding pathways. Hydrogen bond dynamics and short-range Coulomb interactions are evaluated from the equilibrium run at each basins and barriers for both the ions at all pH values. The binding of UO22+ ion with HSA is the result of the dynamical balance between UO22+-HSA and UO22+-water short range Coulomb interactions. Zn2+ ion interact more strongly than UO22+ at all pH through short range Coulomb interactions. PMF values further concludes that UO22+ cannot associate to the Zn2+ bound HSA protein but can be captured by free HSA at all pH values i.e. endosomal, alkaline and physiological pH.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vijayakriti Mishra
- Radiation Safety Systems Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Arup Kumar Pathak
- Homi Bhabha National Institute, Mumbai, India
- Chemistry Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Tusar Bandyopadhyay
- Homi Bhabha National Institute, Mumbai, India
- Chemistry Division, Bhabha Atomic Research Centre, Mumbai, India
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8
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Gardner AM, Gardner PR. Dioxygen and glucose force motion of the electron-transfer switch in the iron(III) flavohemoglobin-type nitric oxide dioxygenase. J Inorg Biochem 2023; 245:112257. [PMID: 37229820 DOI: 10.1016/j.jinorgbio.2023.112257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 04/28/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023]
Abstract
Kinetic and structural investigations of the flavohemoglobin-type NO dioxygenase have suggested critical roles for transient Fe(III)O2 complex formation and O2-forced movements affecting hydride transfer to the FAD cofactor and electron-transfer to the Fe(III)O2 complex. Stark-effect theory together with structural models and dipole and internal electrostatic field determinations provided a semi-quantitative spectroscopic method for investigating the proposed Fe(III)O2 complex and O2-forced movements. Deoxygenation of the enzyme causes Stark effects on the ferric heme Soret and charge-transfer bands revealing the Fe(III)O2 complex. Deoxygenation also elicits Stark effects on the FAD that expose forces and motions that create a more restricted NADH access to FAD for hydride transfer and switch electron-transfer off. Glucose also forces the enzyme toward an off state. Amino acid substitutions at the B10, E7, E11, G8, D5, and F7 positions influence the Stark effects of O2 on resting heme spin states and FAD consistent with the proposed roles of the side chains in the enzyme mechanism. Deoxygenation of ferric myoglobin and hemoglobin A also induces Stark effects on the hemes suggesting a common 'oxy-met' state. The ferric myoglobin and hemoglobin heme spectra are also glucose-responsive. A conserved glucose or glucose-6-phosphate binding site is found bridging the BC-corner and G-helix in flavohemoglobin and myoglobin suggesting novel allosteric effector roles for glucose or glucose-6-phosphate in the NO dioxygenase and O2 storage functions. The results support the proposed roles of a ferric O2 intermediate and protein motions in regulating electron-transfer during NO dioxygenase turnover.
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Affiliation(s)
- Anne M Gardner
- Research and Development Division, Miami Valley Biotech, Suite 2445, 1001 E. 2(nd) Street, Dayton, OH 45402, USA; Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center, R033, 3333 Burnet Avenue, Cincinnati, OH 45229, USA.
| | - Paul R Gardner
- Research and Development Division, Miami Valley Biotech, Suite 2445, 1001 E. 2(nd) Street, Dayton, OH 45402, USA; Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center, R033, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Chemistry and Biochemistry Department, University of Dayton, 300 College Park, Dayton, OH 45469, USA.
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Zhou L, Li J, Shi Y, Wu L, Zhu W, Xu Z. Preferred microenvironments of halogen bonds and hydrogen bonds revealed using statistics and QM/MM calculation studies. Phys Chem Chem Phys 2023. [PMID: 37367726 DOI: 10.1039/d3cp02096g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Hydrogen bonds (HBs) and halogen bonds (XBs) are two essential non-covalent interactions for molecular recognition and drug design. As proteins are heterogeneous in structure, the microenvironments of protein structures should have effects on the formation of HBs and XBs with ligands. However, there are no systematic studies reported on this effect to date. For quantitatively describing protein microenvironments, we defined the local hydrophobicities (LHs) and local dielectric constants (LDCs) in this study. With the defined parameters, we conducted an elaborate database survey on the basis of 22 011 ligand-protein structures to explore the microenvironmental preference of HBs (91 966 in total) and XBs (1436 in total). The statistics show that XBs prefer hydrophobic microenvironments compared to HBs. The polar residues like ASP are more likely to form HBs with ligands, while nonpolar residues such as PHE and MET prefer XBs. Both the LHs and LDCs (10.69 ± 4.36 for HBs; 8.86 ± 4.00 for XBs) demonstrate that XBs are prone to hydrophobic microenvironments compared with HBs with significant differences (p < 0.001), indicating that evaluating their strengths in the corresponding environments should be necessary. Quantum Mechanics-Molecular Mechanics (QM/MM) calculations reveal that in comparison with vacuum environments, the interaction energies of HBs and XBs are decreased to varying degrees given different microenvironments. In addition, the strengths of HBs are impaired more than those of XBs when the local dielectric constant's difference between the XB microenvironments and the HB microenvironments is large.
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Affiliation(s)
- Liping Zhou
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Jintian Li
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Yulong Shi
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Leyun Wu
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Weiliang Zhu
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Zhijian Xu
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
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Fresch E, Collini E. The Role of H-Bonds in the Excited-State Properties of Multichromophoric Systems: Static and Dynamic Aspects. Molecules 2023; 28:molecules28083553. [PMID: 37110786 PMCID: PMC10141795 DOI: 10.3390/molecules28083553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/12/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Given their importance, hydrogen bonds (H-bonds) have been the subject of intense investigation since their discovery. Indeed, H-bonds play a fundamental role in determining the structure, the electronic properties, and the dynamics of complex systems, including biologically relevant materials such as DNA and proteins. While H-bonds have been largely investigated for systems in their electronic ground state, fewer studies have focused on how the presence of H-bonds could affect the static and dynamic properties of electronic excited states. This review presents an overview of the more relevant progress in studying the role of H-bond interactions in modulating excited-state features in multichromophoric biomimetic complex systems. The most promising spectroscopic techniques that can be used for investigating the H-bond effects in excited states and for characterizing the ultrafast processes associated with their dynamics are briefly summarized. Then, experimental insights into the modulation of the electronic properties resulting from the presence of H-bond interactions are provided, and the role of the H-bond in tuning the excited-state dynamics and the related photophysical processes is discussed.
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Affiliation(s)
- Elisa Fresch
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Elisabetta Collini
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
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Kumar S, Rao NNS, Reddy KSSVP, Padole MC, Deshpande PA. Enzyme-substrate interactions in orotate-mimetic OPRT inhibitor complexes: a QM/MM analysis. Phys Chem Chem Phys 2023; 25:3472-3484. [PMID: 36637052 DOI: 10.1039/d2cp05406j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Orotate phosphoribosyltransferase (OPRT) catalyses the reversible phosphoribosyl transfer from α-D-5-phosphoribosyl-1-pyrophosphate (PRPP) to orotic acid (OA) to yield orotidine 5'-monophosphate (OMP) during the de novo synthesis of nucleotides. Numerous studies have reported the inhibition of this reaction as a strategy to check diseases like tuberculosis, malaria and cancer. Insight into the inhibition of this reaction is, therefore, of urgent interest. In this study, we implemented a QM/MM framework on OPRT derived from Saccharomyces cerevisiae to obtain insights into the competitive binding of OA and OA-mimetic inhibitors by quantifying their interactions with OPRT. 4-Hydroxy-6-methylpyridin-2(1H) one showed the best inhibiting activity among the structurally similar OA-mimetic inhibitors, as quantified from the binding energetics. Our analysis of protein-ligand interactions unveiled the association of this inhibitory ligand with a strong network of hydrogen bonds, a large contribution of hydrophobic contacts, and bridging water molecules in the binding site. The ortho-substituted CH3 group in the compound resulted in a large population of π-electrons in the aromatic ring of this inhibitor, supporting the ligand binding further.
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Affiliation(s)
- Shashi Kumar
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - N N Subrahmanyeswara Rao
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - K S S V Prasad Reddy
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Manjusha C Padole
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Parag A Deshpande
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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12
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Pal P, Chakraborty S, Jana B. Number of Hydrogen Bonds per Unit Solvent Accessible Surface Area: A Descriptor of Functional States of Proteins. J Phys Chem B 2022; 126:10822-10833. [PMID: 36524238 DOI: 10.1021/acs.jpcb.2c05367] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Proteins function close to native and near-native conformations. These states are evolutionarily selected to ensure the effect of mutations is minimized. The structural organization of a protein is hierarchical and modular, which reduces the dimensionality of the configurational space of the native states. Thus, finding appropriate descriptors that define the native state among all possible states of a protein is a problem of immense interest. The present study explores the correlation between solvent accessible surface areas (SASAs) and different intraprotein as well as protein-water hydrogen bonds of 55 single-chain globular proteins from four different structural classes (all α, all β, α+β, and α/β), 16 multichain proteins, and 4 macromolecular complexes. A systematic analysis of the solvent accessible surface area and intraprotein and protein-water hydrogen bonds suggests a linear relationship between SASAs and hydrogen bonds. The number of protein-water hydrogen bonds per unit SASA ranges from 3 to 4 for all the different structural protein classes. In contrast, the number of intramolecular hydrogen bonds per unit SASA, including the mainchain-mainchain, mainchain-sidechain, and sidechain-sidechain, varies between 0.75 to 2. The solvation free energy of a protein linearly decreases with SASA. Our study also shows that the solvation free energy/SASA varies from -75 to -105 kJ mol-1 nm-2 across all the native states studied here. The number conservancy of intraprotein hydrogen bonds per unit SASA possibly imparts structural stability to the native structure. On the other hand, 3-4 protein-water hydrogen bonds per unit SASA are possibly required to maintain a balance between the solubility and functionality of the native states. This study provides a basis for synthetic biologists to design new folds with improved functionality.
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Affiliation(s)
- Prasun Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Sandipan Chakraborty
- Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS), Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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13
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Kojasoy V, Tantillo DJ. Impacts of noncovalent interactions involving sulfur atoms on protein stability, structure, folding, and bioactivity. Org Biomol Chem 2022; 21:11-23. [PMID: 36345987 DOI: 10.1039/d2ob01602h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This review discusses the various types of noncovalent interactions in which sulfur atoms participate and their effects on protein stability, structure, folding and bioactivity. Current approaches and recommendations for modelling these noncovalent interactions (in terms of both geometries and interaction energies) are highlighted.
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Affiliation(s)
- Volga Kojasoy
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
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14
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U A, Kartha TR, Madhurima V. Hydrogen-bonded networks in alcohol-acetone binary mixtures: molecular dynamics study. J Mol Model 2022; 28:382. [DOI: 10.1007/s00894-022-05369-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/25/2022] [Indexed: 11/09/2022]
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15
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Ziada S, Diharce J, Raimbaud E, Aci-Sèche S, Ducrot P, Bonnet P. Estimation of Drug-Target Residence Time by Targeted Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:5536-5549. [PMID: 36350238 DOI: 10.1021/acs.jcim.2c00852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Drug-target residence time has emerged as a key selection factor in drug discovery since the binding duration of a drug molecule to its protein target can significantly impact its in vivo efficacy. The challenge in studying the residence time, in early drug discovery stages, lies in how to cost-effectively determine the residence time for the systematic assessment of compounds. Currently, there is still a lack of computational protocols to quickly estimate such a measure, particularly for large and flexible protein targets and drugs. Here, we report an efficient computational protocol, based on targeted molecular dynamics, to rank drug candidates by their residence time and to obtain insights into ligand-target dissociation mechanisms. The method was assessed on a dataset of 10 arylpyrazole inhibitors of CDK8, a large, flexible, and clinically important target, for which the experimental residence time of the inhibitors ranges from minutes to hours. The compounds were correctly ranked according to their estimated residence time scores compared to their experimental values. The analysis of protein-ligand interactions along the dissociation trajectories highlighted the favorable contribution of hydrophobic contacts to residence time and revealed key residues that strongly affect compound residence time.
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Affiliation(s)
- Sonia Ziada
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, Orléans Cedex 245067, France
| | - Julien Diharce
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, Orléans Cedex 245067, France
| | - Eric Raimbaud
- Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine78290, France
| | - Samia Aci-Sèche
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, Orléans Cedex 245067, France
| | - Pierre Ducrot
- Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine78290, France
| | - Pascal Bonnet
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, Orléans Cedex 245067, France
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16
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Ding T, Karlov DS, Pino-Angeles A, Tikhonova IG. Intermolecular Interactions in G Protein-Coupled Receptor Allosteric Sites at the Membrane Interface from Molecular Dynamics Simulations and Quantum Chemical Calculations. J Chem Inf Model 2022; 62:4736-4747. [PMID: 36178787 PMCID: PMC9554917 DOI: 10.1021/acs.jcim.2c00788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Allosteric modulators are called promising candidates in G protein-coupled receptor (GPCR) drug development by displaying subtype selectivity and more specific receptor modulation. Among the allosteric sites known to date, cavities at the receptor-lipid interface represent an uncharacteristic binding location that raises many questions about the ligand interactions and stability, the binding site structure, and how all of these are affected by lipid molecules. In this work, we analyze interactions in the allosteric sites of the PAR2, C5aR1, and GCGR receptors in three lipid compositions using molecular dynamics simulations. In addition, we performed quantum chemical calculations involving the symmetry-adapted perturbation theory (SAPT) and the natural population analysis to quantify the strength of intermolecular interactions. We show that besides classical hydrogen bonds, weak polar interactions such as O-HC, O-Br, and long-range electrostatics with the backbone amides contribute to the stability of allosteric modulators at the receptor-lipid interface. The allosteric cavities are detectable in various membrane compositions. The availability of polar atoms for interactions in such cavities can be assessed by water molecules from simulations. Although ligand-lipid interactions are weak, lipid tails play a role in ligand binding pose stability and the size of allosteric cavities. We discuss physicochemical aspects of ligand binding at the receptor-lipid interface and suggest a compound library enriched by weak donor groups for ligand search in such sites.
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Affiliation(s)
- Tianyi Ding
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
| | - Dmitry S Karlov
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
| | - Almudena Pino-Angeles
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
| | - Irina G Tikhonova
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
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17
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Mitchell W, Tamucci JD, Ng EL, Liu S, Birk AV, Szeto HH, May ER, Alexandrescu AT, Alder NN. Structure-activity relationships of mitochondria-targeted tetrapeptide pharmacological compounds. eLife 2022; 11:75531. [PMID: 35913044 PMCID: PMC9342957 DOI: 10.7554/elife.75531] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 07/03/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondria play a central role in metabolic homeostasis, and dysfunction of this organelle underpins the etiology of many heritable and aging-related diseases. Tetrapeptides with alternating cationic and aromatic residues such as SS-31 (elamipretide) show promise as therapeutic compounds for mitochondrial disorders. In this study, we conducted a quantitative structure-activity analysis of three alternative tetrapeptide analogs, benchmarked against SS-31, that differ with respect to aromatic side chain composition and sequence register. We present the first structural models for this class of compounds, obtained with Nuclear Magnetic Resonance (NMR) and molecular dynamics approaches, showing that all analogs except for SS-31 form compact reverse turn conformations in the membrane-bound state. All peptide analogs bound cardiolipin-containing membranes, yet they had significant differences in equilibrium binding behavior and membrane interactions. Notably, analogs had markedly different effects on membrane surface charge, supporting a mechanism in which modulation of membrane electrostatics is a key feature of their mechanism of action. The peptides had no strict requirement for side chain composition or sequence register to permeate cells and target mitochondria in mammalian cell culture assays. All four peptides were pharmacologically active in serum withdrawal cell stress models yet showed significant differences in their abilities to restore mitochondrial membrane potential, preserve ATP content, and promote cell survival. Within our peptide set, the analog containing tryptophan side chains, SPN10, had the strongest impact on most membrane properties and showed greatest efficacy in cell culture studies. Taken together, these results show that side chain composition and register influence the activity of these mitochondria-targeted peptides, helping provide a framework for the rational design of next-generation therapeutics with enhanced potency.
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Affiliation(s)
- Wayne Mitchell
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Jeffrey D Tamucci
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Emery L Ng
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Shaoyi Liu
- Social Profit Network, Menlo Park, CA, United States
| | - Alexander V Birk
- Department of Biology, York College of CUNY, New York, NY, United States
| | - Hazel H Szeto
- Social Profit Network, Menlo Park, CA, United States
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Andrei T Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Nathan N Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
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18
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Ghanbari Moheb Seraj R, Tohidfar M, Azimzadeh Irani M, Esmaeilzadeh-Salestani K, Moradian T, Ahmadikhah A, Behnamian M. Metabolomics analysis of milk thistle lipids to identify drought-tolerant genes. Sci Rep 2022; 12:12827. [PMID: 35896570 PMCID: PMC9329356 DOI: 10.1038/s41598-022-16887-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 07/18/2022] [Indexed: 11/09/2022] Open
Abstract
Milk thistle is an oil and medicinal crop known as an alternative oil crop with a high level of unsaturated fatty acids, which makes it a favorable edible oil for use in food production. To evaluate the importance of Milk thistle lipids in drought tolerance, an experiment was performed in field conditions under three different water deficit levels (Field capacity (FC), 70% FC and 40% FC). After harvesting seeds of the plant, their oily and methanolic extracts were isolated, and subsequently, types and amounts of lipids were measured using GC-MS. Genes and enzymes engaged in biosynthesizing of these lipids were identified and their expression in Arabidopsis was investigated under similar conditions. The results showed that content of almost all measured lipids of milk thistle decreased under severe drought stress, but genes (belonged to Arabidopsis), which were involved in their biosynthetic pathway showed different expression patterns. Genes biosynthesizing lipids, which had significant amounts were selected and their gene and metabolic network were established. Two networks were correlated, and for each pathway, their lipids and respective biosynthesizing genes were grouped together. Four up-regulated genes including PXG3, LOX2, CYP710A1, PAL and 4 down-regulated genes including FATA2, CYP86A1, LACS3, PLA2-ALPHA were selected. The expression of these eight genes in milk thistle was similar to Arabidopsis under drought stress. Thus, PXG3, PAL, LOX2 and CYP86A1 genes that increased expression were selected for protein analysis. Due to the lack of protein structure of these genes in the milk thistle, modeling homology was performed for them. The results of molecular docking showed that the four proteins CYP86A1, LOX2, PAL and PXG3 bind to ligands HEM, 11O, ACT and LIG, respectively. HEM ligand was involved in production of secondary metabolites and dehydration tolerance, and HEM binding site remained conserved in various plants. CA ligands were involved in synthesis of cuticles and waxes. Overall, this study confirmed the importance of lipids in drought stress tolerance in milk thistle.
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Affiliation(s)
- Rahele Ghanbari Moheb Seraj
- Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Masoud Tohidfar
- Department of Plant Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
| | | | - Keyvan Esmaeilzadeh-Salestani
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 1, 51014, Tartu, Estonia
| | - Toktam Moradian
- Department of Horticultural Sciences, Islamic Azad University, Shirvan Branch, Shirvan, Iran
| | - Asadollah Ahmadikhah
- Department of Plant Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Mahdi Behnamian
- Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
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19
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Sharma GP, Meyer AC, Habeeb S, Karbach M, Müller G. Free-energy landscapes and insertion pathways for peptides in membrane environment. Phys Rev E 2022; 106:014404. [PMID: 35974613 DOI: 10.1103/physreve.106.014404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Free-energy landscapes for short peptides-specifically for variants of the pH low insertion peptide (pHLIP)-in the heterogeneous environment of a lipid bilayer or cell membrane are constructed, taking into account a set of dominant interactions and the conformational preferences of the peptide backbone. Our methodology interprets broken internal H-bonds along the backbone of a polypeptide as statistically interacting quasiparticles, activated from the helix reference state. The favored conformation depends on the local environment (ranging from polar to nonpolar), specifically on the availability of external H-bonds (with H_{2}O molecules or lipid headgroups) to replace internal H-bonds. The dominant side-chain contribution is accounted for by residue-specific transfer free energies between polar and nonpolar environments. The free-energy landscape is sensitive to the level of pH in the aqueous environment surrounding the membrane. For high pH, we identify pathways of descending free energy that suggest a coexistence of membrane-adsorbed peptides with peptides in solution. A drop in pH raises the degree of protonation of negatively charged residues and thus increases the hydrophobicity of peptide segments near the C terminus. For low pH, we identify insertion pathways between the membrane-adsorbed state and a stable trans-membrane state with the C terminus having crossed the membrane.
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Affiliation(s)
- Ganga P Sharma
- Department of Physics, University of Rhode Island, Kingston, Rhode Island 02881, USA
| | - Aaron C Meyer
- Department of Physics, University of Rhode Island, Kingston, Rhode Island 02881, USA
| | - Suhail Habeeb
- Department of Physics, University of Rhode Island, Kingston, Rhode Island 02881, USA
| | - Michael Karbach
- Fachgruppe Physik, Bergische Universität Wuppertal, D-42097 Wuppertal, Germany
| | - Gerhard Müller
- Department of Physics, University of Rhode Island, Kingston, Rhode Island 02881, USA
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20
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Wang X, Quan M, Yao H, Pang XY, Ke H, Jiang W. Switchable bifunctional molecular recognition in water using a pH-responsive Endo-functionalized cavity. Nat Commun 2022; 13:2291. [PMID: 35484144 PMCID: PMC9051166 DOI: 10.1038/s41467-022-30012-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/08/2022] [Indexed: 11/09/2022] Open
Abstract
The construction of water-soluble synthetic hosts with a stimuli-responsive endo-functionalized cavity is challenging. These hosts feature a switchable cavity and may bring new properties to the fields of self-assembly, molecular machines, and biomedical sciences. Herein, we report a pair of water-soluble naphthotubes with a pH-responsive endo-functionalized cavity. The inward-directing secondary amine group of the hosts can be protonated and deprotonated. Thus, the hosts have different cavity features at the two states and show drastically different binding preference and selectivity in water. We reveal that the binding difference of the two host states is originated from the differences in charge repulsion, hydrogen bonding and the hydrophobic effects. Moreover, the guest binding can be easily switched in a ternary mixture with two guest molecules by adjusting the pH value of the solution. These pH-responsive hosts may be used for the construction of smart self-assembly systems and water-soluble molecular machines.
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Affiliation(s)
- Xiaoping Wang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, 518055, Shenzhen, China
| | - Mao Quan
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, 518055, Shenzhen, China
| | - Huan Yao
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, 518055, Shenzhen, China
| | - Xin-Yu Pang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, 518055, Shenzhen, China
| | - Hua Ke
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, 518055, Shenzhen, China
| | - Wei Jiang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, 518055, Shenzhen, China.
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21
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Stern KL, Dalley NA, McMurray NT, Billings WM, Loftus TJ, Jones ZB, Hadfield JR, Price JL. Prerequisites for Stabilizing Long-Range Synergistic Interactions among b-, c-, and f-Residues in Coiled Coils. Biochemistry 2022; 61:319-326. [PMID: 35129961 PMCID: PMC9202806 DOI: 10.1021/acs.biochem.1c00760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coiled coils are among the most abundant tertiary and quaternary structures found in proteins. A growing body of evidence suggests that long-range synergistic interactions among solvent-exposed residues can contribute substantially to coiled-coil conformational stability, but our understanding of the key sequence and structural prerequisites of this effect is still developing. Here, we show that the strength of synergistic interaction involving a b-position Glu (i), an f-position Tyr (i + 4), and a c-position Lys (i + 8) depends on the identity of the f-position residue, the length and stability of the coiled coil, and its oligomerization stoichiometry/surface accessibility. Combined with previous observations, these results map out predictable sequence- and structure-based criteria for enhancing coiled-coil stability by up to -0.58 kcal/mol per monomer (or -2.32 kcal/mol per coiled-coil tetramer). Our observations expand the available tools for enhancing coiled coil stability by sequence variation at solvent-exposed b-, c-, and f-positions and suggest the need to exercise care in the choice of substitutions at these positions for application-specific purposes.
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Affiliation(s)
| | | | | | | | | | | | | | - Joshua L. Price
- Corresponding Author: Joshua L. Price, C100 BNSN, Brigham Young University, Provo, UT 84602;
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22
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Luong HX, Bui HTP, Tung TT. Application of the All-Hydrocarbon Stapling Technique in the Design of Membrane-Active Peptides. J Med Chem 2022; 65:3026-3045. [PMID: 35112864 DOI: 10.1021/acs.jmedchem.1c01744] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The threats of drug resistance and new emerging pathogens have led to an urgent need to develop alternative treatment therapies. Recently, considerable research efforts have focused on membrane-active peptides (MAPs), a category of peptides in drug discovery with antimicrobial, anticancer, and cell penetration activities that have demonstrated their potential to be multifunctional agents. Nonetheless, natural MAPs have encountered various disadvantages, which mainly include poor bioavailability, the lack of a secondary structure in short peptides, and high production costs for long peptide sequences. Hence, an "all-hydrocarbon stapling system" has been applied to these peptides and proven to effectively stabilize the helical conformations, improving proteolytic resistance and increasing both the potency and the cell permeability. In this review, we summarized and categorized the advances made using this powerful technique in the development of stapled MAPs. Furthermore, outstanding issues and suggestions for future design within each subcategory were thoroughly discussed.
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Affiliation(s)
- Huy Xuan Luong
- Faculty of Pharmacy, PHENIKAA University, Hanoi 12116, Vietnam.,PHENIKAA Institute for Advanced Study (PIAS), PHENIKAA University, Hanoi 12116, Vietnam
| | | | - Truong Thanh Tung
- Faculty of Pharmacy, PHENIKAA University, Hanoi 12116, Vietnam.,PHENIKAA Institute for Advanced Study (PIAS), PHENIKAA University, Hanoi 12116, Vietnam
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23
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Li Z, Unione L, Liu L, Lang Y, de Vries RP, de Groot RJ, Boons GJ. Synthetic O-Acetylated Sialosides and their Acetamido-deoxy Analogues as Probes for Coronaviral Hemagglutinin-esterase Recognition. J Am Chem Soc 2022; 144:424-435. [PMID: 34967208 DOI: 10.1021/jacs.1c10329] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
O-Acetylation is a common modification of sialic acids that can occur at carbons 4-, 7-, 8-, and/or 9. Acetylated sialosides are employed as receptors by several betacoronaviruses and toroviruses, and by influenza C and D viruses. The molecular basis by which these viruses recognize specific O-acetylated sialosides is poorly understood, and it is unknown how viruses have evolved to recognize specific O-acetylated sialosides expressed by their host. Here, we describe a chemoenzymatic approach that can readily provide sialoglycan analogues in which acetyl esters at C4 and/or C7 are replaced by stabilizing acetamide moieties. The analogues and their natural counterparts were used to examine the ligand requirements of the lectin domain of coronaviral hemagglutinin-esterases (HEs). It revealed that HEs from viruses targeting different host species exhibit different requirements for O-acetylation. It also showed that ester-to-amide perturbation results in decreased or loss of binding. STD NMR and molecular modeling of the complexes of the HE of BCoV with the acetamido analogues and natural counterparts revealed that binding is governed by the complementarity between the acetyl moieties of the sialosides and the hydrophobic patches of the lectin. The precise spatial arrangement of these elements is important, and an ester-to-amide perturbation results in substantial loss of binding. Molecular Dynamics simulations with HEs from coronaviruses infecting other species indicate that these viruses have adapted their HE specificity by the incorporation of hydrophobic or hydrophilic elements to modulate acetyl ester recognition.
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Affiliation(s)
- Zeshi Li
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht 3584 CG, The Netherlands
| | - Luca Unione
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht 3584 CG, The Netherlands
| | - Lin Liu
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Yifei Lang
- Virology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584 CL, The Netherlands
| | - Robert P de Vries
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht 3584 CG, The Netherlands
| | - Raoul J de Groot
- Virology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584 CL, The Netherlands
| | - Geert-Jan Boons
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht 3584 CG, The Netherlands
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht 3584, The Netherlands
- Chemistry Department, University of Georgia, Athens, Georgia 30602, United States
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24
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Bernaudat F, Gustems M, Günther J, Oliva MF, Buschle A, Göbel C, Pagniez P, Lupo J, Signor L, Müller CW, Morand P, Sattler M, Hammerschmidt W, Petosa C. Structural basis of DNA methylation-dependent site selectivity of the Epstein-Barr virus lytic switch protein ZEBRA/Zta/BZLF1. Nucleic Acids Res 2021; 50:490-511. [PMID: 34893887 PMCID: PMC8754650 DOI: 10.1093/nar/gkab1183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 11/14/2021] [Accepted: 11/21/2021] [Indexed: 12/13/2022] Open
Abstract
In infected cells, Epstein-Barr virus (EBV) alternates between latency and lytic replication. The viral bZIP transcription factor ZEBRA (Zta, BZLF1) regulates this cycle by binding to two classes of ZEBRA response elements (ZREs): CpG-free motifs resembling the consensus AP-1 site recognized by cellular bZIP proteins and CpG-containing motifs that are selectively bound by ZEBRA upon cytosine methylation. We report structural and mutational analysis of ZEBRA bound to a CpG-methylated ZRE (meZRE) from a viral lytic promoter. ZEBRA recognizes the CpG methylation marks through a ZEBRA-specific serine and a methylcytosine-arginine-guanine triad resembling that found in canonical methyl-CpG binding proteins. ZEBRA preferentially binds the meZRE over the AP-1 site but mutating the ZEBRA-specific serine to alanine inverts this selectivity and abrogates viral replication. Our findings elucidate a DNA methylation-dependent switch in ZEBRA's transactivation function that enables ZEBRA to bind AP-1 sites and promote viral latency early during infection and subsequently, under appropriate conditions, to trigger EBV lytic replication by binding meZREs.
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Affiliation(s)
- Florent Bernaudat
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France.,European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38043 Grenoble, France
| | - Montse Gustems
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany and German Centre for Infection Research (DZIF), Partner site Munich, D-81377 Germany
| | - Johannes Günther
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany.,Bavarian NMR Center and Department of Chemistry, Technical University of Munich, 85748 Gaching, Germany
| | - Mizar F Oliva
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France.,Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9 Grenoble, France
| | - Alexander Buschle
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany and German Centre for Infection Research (DZIF), Partner site Munich, D-81377 Germany
| | - Christine Göbel
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany and German Centre for Infection Research (DZIF), Partner site Munich, D-81377 Germany
| | - Priscilla Pagniez
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Julien Lupo
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France.,Laboratoire de Virologie, Centre Hospitalier Universitaire Grenoble Alpes, 38000 Grenoble, France
| | - Luca Signor
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Patrice Morand
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France.,Laboratoire de Virologie, Centre Hospitalier Universitaire Grenoble Alpes, 38000 Grenoble, France
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany.,Bavarian NMR Center and Department of Chemistry, Technical University of Munich, 85748 Gaching, Germany
| | - Wolfgang Hammerschmidt
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany and German Centre for Infection Research (DZIF), Partner site Munich, D-81377 Germany
| | - Carlo Petosa
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
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25
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Durell SR, Ben-Naim A. Temperature Dependence of Hydrophobic and Hydrophilic Forces and Interactions. J Phys Chem B 2021; 125:13137-13146. [PMID: 34850632 DOI: 10.1021/acs.jpcb.1c07802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations are used to compare the forces and Gibbs free energies associated with bringing small hydrophobic and hydrophilic solutes together in an aqueous solution at different temperatures between 280 and 360 °K. For the hydrophilic solutes, different relative orientations are used to distinguish between direct, intersolute hydrogen bonds (Hbond) and solutes simultaneously hydrogen bonding to a solvent water bridge. Interestingly, the temperature dependence of the hydrophobic and directly hydrogen bonding solutes turns out to be opposite to that of the bridged hydrophilic solutes, with the ΔG becoming more negative for the former and less negative for the latter with increasing temperature. Dissection of the free energy curves into enthalpy and entropy contributions, and further separation of the enthalpy term into solute-solute, solute-solvent, and solvent-solvent components provides insight into the physical molecular causes for the distinctive thermodynamic results. Finally, it is reasoned how the opposite temperature dependencies of the two types of hydrophilic interactions provide a rationale for the cold denaturation of proteins.
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Affiliation(s)
- Stewart R Durell
- Laboratory of Cell Biology, National Cancer Institute; National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Arieh Ben-Naim
- Department of Physical Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat Ram, Jerusalem 91904, Israel
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26
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Zhou H, Pang XY, Wang X, Yao H, Yang LP, Jiang W. Biomimetic Recognition of Quinones in Water by an Endo-Functionalized Cavity with Anthracene Sidewalls. Angew Chem Int Ed Engl 2021; 60:25981-25987. [PMID: 34569134 DOI: 10.1002/anie.202112267] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Indexed: 12/27/2022]
Abstract
Selective molecular recognition in water is the foundation of numerous biological functions but is a challenge for most synthetic hosts. We employ the concept of endo-functionalized cavity and the strategy of simultaneous construction to address this issue. The concept and the strategy were demonstrated in the construction of a biomimetic host for selectively recognizing quinones in water. The host was synthesized by joining two pieces of bent anthracene dimer through amide bond formation, affording a deep hydrophobic cavity and inward-directing hydrogen bonding sites. The host can recognize quinones over their close analogues in water, and its association affinity to p-benzoquinone is the highest among all the known hosts and is even comparable to that of the bioreceptor. The binding with an anthraquinone reaches nanomolar affinity. Shielded hydrogen bonding, C-H⋅⋅⋅π, and charge transfer interactions, and the hydrophobic effect are responsible for the high binding affinity and selectivity.
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Affiliation(s)
- Hang Zhou
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China
| | - Xin-Yu Pang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China
| | - Xiaoping Wang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China
| | - Huan Yao
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China
| | - Liu-Pan Yang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China
| | - Wei Jiang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China
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27
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Khatri B, Raghunathan S, Chakraborti S, Rahisuddin R, Kumaran S, Tadala R, Wagh P, Priyakumar UD, Chatterjee J. Desolvation of Peptide Bond by O to S Substitution Impacts Protein Stability. Angew Chem Int Ed Engl 2021; 60:24870-24874. [PMID: 34519402 DOI: 10.1002/anie.202110978] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/10/2021] [Indexed: 12/31/2022]
Abstract
Amino acid side chains are key to fine-tuning the microenvironment polarity in proteins composed of polar amide bonds. Here, we report that substituting an oxygen atom of the backbone amide bond with sulfur atom desolvates the thioamide bond, thereby increasing its lipophilicity. The impact of such local desolvation by O to S substitution in proteins was tested by synthesizing thioamidated variants of Pin1 WW domain. We observe that a thioamide acts in synergy with nonpolar amino acid side chains to reduce the microenvironment polarity and increase protein stability by more than 14 °C. Through favorable van der Waals and hydrogen bonding interactions, this single atom substitution significantly stabilizes proteins without altering the amino acid sequence and structure of the native protein.
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Shampa Raghunathan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India.,Present Address: École Centrale School of Engineering, Mahindra University, Hyderabad, 500043, India
| | - Sohini Chakraborti
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - R Rahisuddin
- CSIR- Institute of Microbial Technology, Chandigarh 1, 60036, India
| | - S Kumaran
- CSIR- Institute of Microbial Technology, Chandigarh 1, 60036, India
| | | | | | - U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
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28
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Khatri B, Raghunathan S, Chakraborti S, Rahisuddin R, Kumaran S, Tadala R, Wagh P, Priyakumar UD, Chatterjee J. Desolvation of Peptide Bond by O to S Substitution Impacts Protein Stability. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit Indian Institute of Science Bangalore 560012 India
| | - Shampa Raghunathan
- Center for Computational Natural Sciences and Bioinformatics International Institute of Information Technology Hyderabad 500032 India
- Present Address: École Centrale School of Engineering Mahindra University Hyderabad 500043 India
| | - Sohini Chakraborti
- Molecular Biophysics Unit Indian Institute of Science Bangalore 560012 India
| | - R. Rahisuddin
- CSIR- Institute of Microbial Technology Chandigarh 1 60036 India
| | - S. Kumaran
- CSIR- Institute of Microbial Technology Chandigarh 1 60036 India
| | | | | | - U. Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics International Institute of Information Technology Hyderabad 500032 India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit Indian Institute of Science Bangalore 560012 India
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29
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Zhou H, Pang X, Wang X, Yao H, Yang L, Jiang W. Biomimetic Recognition of Quinones in Water by an
Endo
‐Functionalized Cavity with Anthracene Sidewalls. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202112267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Hang Zhou
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry Southern University of Science and Technology Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Xin‐Yu Pang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry Southern University of Science and Technology Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Xiaoping Wang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry Southern University of Science and Technology Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Huan Yao
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry Southern University of Science and Technology Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Liu‐Pan Yang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry Southern University of Science and Technology Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Wei Jiang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry Southern University of Science and Technology Xueyuan Blvd 1088 Shenzhen 518055 China
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30
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Morgan GJ. Transient disorder along pathways to amyloid. Biophys Chem 2021; 281:106711. [PMID: 34839162 DOI: 10.1016/j.bpc.2021.106711] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 01/15/2023]
Abstract
High-resolution structures of amyloid fibrils formed from normally-folded proteins have revealed non-native conformations of the polypeptide chains. Attaining these conformations apparently requires transition from the native state via a highly disordered conformation, in contrast to earlier models that posited a role for assembly of partially folded proteins. Modifications or interactions that extend the lifetime or constrain the conformations of these disordered states could act to enhance or suppress amyloid formation. Understanding how the properties of both the folded and transiently disordered structural ensembles influence the process of amyloid formation is a substantial challenge, but research into the properties of intrinsically disordered proteins will deliver important insights.
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Affiliation(s)
- Gareth J Morgan
- The Amyloidosis Center and Section of Hematology and Medical Oncology, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
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31
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Cho MK, Chong SH, Shin S, Ham S. Site-Specific Backbone and Side-Chain Contributions to Thermodynamic Stabilizing Forces of the WW Domain. J Phys Chem B 2021; 125:7108-7116. [PMID: 34165991 DOI: 10.1021/acs.jpcb.1c01725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The native structure of a protein is stabilized by a number of interactions such as main-chain hydrogen bonds and side-chain hydrophobic contacts. However, it has been challenging to determine how these interactions contribute to protein stability at single amino acid resolution. Here, we quantified site-specific thermodynamic stability at the molecular level to extend our understanding of the stabilizing forces in protein folding. We derived the free energy components of individual amino acid residues separately for the folding of the human Pin WW domain based on simulated structures. A further decomposition of the thermodynamic properties into contributions from backbone and side-chain groups enabled us to identify the critical residues in the secondary structure and hydrophobic core formation, without introducing physical modifications to the system as in site-directed mutagenesis methods. By relating the structural and thermodynamic changes upon folding for each residue, we find that the simultaneous formation of the backbone hydrogen bonds and side-chain contacts cooperatively stabilizes the folded structure. The identification of stabilizing interactions in a folding protein at atomic resolution will provide molecular insights into understanding the origin of the protein structure and into engineering a more stable protein.
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Affiliation(s)
- Myung Keun Cho
- Department of Chemistry, the Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-ku, Seoul 04310, Korea.,Department of Chemistry, College of Natural Sciences, Seoul National University, Gwanak-ro 1, Gwanak-ku, Seoul 08826, Korea
| | - Song-Ho Chong
- Department of Chemistry, the Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-ku, Seoul 04310, Korea
| | - Seokmin Shin
- Department of Chemistry, College of Natural Sciences, Seoul National University, Gwanak-ro 1, Gwanak-ku, Seoul 08826, Korea
| | - Sihyun Ham
- Department of Chemistry, the Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-ku, Seoul 04310, Korea
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32
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Molecular recognition of structurally disordered Pro/Ala-rich sequences (PAS) by antibodies involves an Ala residue at the hot spot of the epitope. J Mol Biol 2021; 433:167113. [PMID: 34161780 DOI: 10.1016/j.jmb.2021.167113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 11/20/2022]
Abstract
Pro/Ala-rich sequences (PAS) are polypeptides that were developed as a biological alternative to poly-ethylene glycol (PEG) to generate biopharmaceuticals with extended plasma half-life. Like PEG, PAS polypeptides are conformationally disordered and show high solubility in water. Devoid of any charged or prominent hydrophobic side chains, these biosynthetic polymers represent an extreme case of intrinsically disordered proteins. Despite lack of immunogenicity of PAS tags in numerous animal studies we now succeeded in generating monoclonal antibodies (MAbs) against three different PAS versions. To this end, mice were immunized with a PAS#1, P/A#1 or APSA 40mer peptide conjugated to keyhole limpet hemocyanin as highly immunogenic carrier protein. In each case, one MAb with high binding activity and specificity towards a particular PAS motif was obtained. The apparent affinity was strongly dependent on the avidity effect and most pronounced for the bivalent MAb when interacting with a long PAS repeat. X-ray structural analysis of four representative anti-PAS Fab fragments in complex with their cognate PAS epitope peptides revealed interactions dominated by hydrogen bond networks involving the peptide backbone as well as multiple Van der Waals contacts arising from intimate shape complementarity. Surprisingly, Ala, the L-amino acid with the smallest side chain, emerged as a crucial feature for epitope recognition, contributing specific contacts at the center of the paratope in several anti-PAS complexes. Apart from these insights into how antibodies can recognize feature-less peptides without secondary structure, the MAbs characterized in this study offer valuable reagents for the preclinical and clinical development of PASylated biologics.
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33
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Draper SRE, Jones ZB, Earl SO, Dalley NA, Ashton DS, Carter AJ, Conover BM, Price JL. PEGylation Increases the Strength of a Nearby NH-π Hydrogen Bond in the WW Domain. Biochemistry 2021; 60:2064-2070. [PMID: 34137579 DOI: 10.1021/acs.biochem.1c00132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here we show that an NH-π interaction between a highly conserved Asn and a nearby Trp stabilizes the WW domain of the human protein Pin1. The strength of this NH-π interaction depends on the structure of the arene, with NH-π interactions involving Trp or naphthylalanine being substantially more stabilizing than those involving Tyr or Phe. Calculations suggest arene size and polarizability are key structural determinants of NH-π interaction strength. Methylation or PEGylation of the Asn side-chain amide nitrogen each strengthens the associated NH-π interaction, though likely for different reasons. We hypothesize that methylation introduces steric clashes that destabilize conformations in which the NH-π interaction is not possible, whereas PEGylation strengthens the NH-π interaction via localized desolvation of the protein surface.
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Affiliation(s)
| | | | - Seth O Earl
- Brigham Young University, Provo, Utah 84602, United States
| | | | | | | | | | - Joshua L Price
- Brigham Young University, Provo, Utah 84602, United States
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34
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Aggarwal N, Eliaz D, Cohen H, Rosenhek-Goldian I, Cohen SR, Kozell A, Mason TO, Shimanovich U. Protein nanofibril design via manipulation of hydrogen bonds. Commun Chem 2021; 4:62. [PMID: 36697777 PMCID: PMC9814780 DOI: 10.1038/s42004-021-00494-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 03/16/2021] [Indexed: 02/03/2023] Open
Abstract
The process of amyloid nanofibril formation has broad implications including the generation of the strongest natural materials, namely silk fibers, and their major contribution to the progression of many degenerative diseases. The key question that remains unanswered is whether the amyloidogenic nature, which includes the characteristic H-bonded β-sheet structure and physical characteristics of protein assemblies, can be modified via controlled intervention of the molecular interactions. Here we show that tailored changes in molecular interactions, specifically in the H-bonded network, do not affect the nature of amyloidogenic fibrillation, and even have minimal effect on the initial nucleation events of self-assembly. However, they do trigger changes in networks at a higher hierarchical level, namely enhanced 2D packaging which is rationalized by the 3D hierarchy of β-sheet assembly, leading to variations in fibril morphology, structural composition and, remarkably, nanomechanical properties. These results pave the way to a better understanding of the role of molecular interactions in sculpting the structural and physical properties of protein supramolecular constructs.
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Affiliation(s)
- Nidhi Aggarwal
- grid.13992.300000 0004 0604 7563Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
| | - Dror Eliaz
- grid.13992.300000 0004 0604 7563Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
| | - Hagai Cohen
- grid.13992.300000 0004 0604 7563Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Irit Rosenhek-Goldian
- grid.13992.300000 0004 0604 7563Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Sidney R. Cohen
- grid.13992.300000 0004 0604 7563Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Kozell
- grid.13992.300000 0004 0604 7563Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
| | - Thomas O. Mason
- grid.13992.300000 0004 0604 7563Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
| | - Ulyana Shimanovich
- grid.13992.300000 0004 0604 7563Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
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35
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Christou NE, Giandoreggio-Barranco K, Ayala I, Glushonkov O, Adam V, Bourgeois D, Brutscher B. Disentangling Chromophore States in a Reversibly Switchable Green Fluorescent Protein: Mechanistic Insights from NMR Spectroscopy. J Am Chem Soc 2021; 143:7521-7530. [PMID: 33966387 DOI: 10.1021/jacs.1c02442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The photophysical properties of fluorescent proteins, including phototransformable variants used in advanced microscopy applications, are influenced by the environmental conditions in which they are expressed and used. Rational design of improved fluorescent protein markers requires a better understanding of these environmental effects. We demonstrate here that solution NMR spectroscopy can detect subtle changes in the chemical structure, conformation, and dynamics of the photoactive chromophore moiety with atomic resolution, providing such mechanistic information. Studying rsFolder, a reversibly switchable green fluorescent protein, we have identified four distinct configurations of its p-HBI chromophore, corresponding to the cis and trans isomers, with each one either protonated (neutral) or deprotonated (anionic) at the benzylidene ring. The relative populations and interconversion kinetics of these chromophore species depend on sample pH and buffer composition that alter in a complex way the strength of H-bonds that contribute in stabilizing the chromophore within the protein scaffold. We show in particular the important role of histidine-149 in stabilizing the neutral trans chromophore at intermediate pH values, leading to ground-state cis-trans isomerization with a peculiar pH dependence. We discuss the potential implications of our findings on the pH dependence of the photoswitching contrast, a critical parameter in nanoscopy applications.
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Affiliation(s)
- Nina Eleni Christou
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | | | - Isabel Ayala
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Oleksandr Glushonkov
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Virgile Adam
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Dominique Bourgeois
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Bernhard Brutscher
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
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36
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Ardejani MS, Noodleman L, Powers ET, Kelly JW. Stereoelectronic effects in stabilizing protein-N-glycan interactions revealed by experiment and machine learning. Nat Chem 2021. [PMID: 33723379 DOI: 10.1038/s41557-41021-00646-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The energetics of protein-carbohydrate interactions, central to many life processes, cannot yet be manipulated predictably. This is mostly due to an incomplete quantitative understanding of the enthalpic and entropic basis of these interactions in aqueous solution. Here, we show that stereoelectronic effects contribute to stabilizing protein-N-glycan interactions in the context of a cooperatively folding protein. Double-mutant cycle analyses of the folding data from 52 electronically varied N-glycoproteins demonstrate an enthalpy-entropy compensation depending on the electronics of the interacting side chains. Linear and nonlinear models obtained using quantum mechanical calculations and machine learning explain up to 79% and 97% of the experimental interaction energy variability, as inferred from the R2 value of the respective models. Notably, the protein-carbohydrate interaction energies strongly correlate with the molecular orbital energy gaps of the interacting substructures. This suggests that stereoelectronic effects must be given a greater weight than previously thought for accurately modelling the short-range dispersive van der Waals interactions between the N-glycan and the protein.
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Affiliation(s)
- Maziar S Ardejani
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Evan T Powers
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Jeffery W Kelly
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
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37
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Ardejani MS, Noodleman L, Powers ET, Kelly JW. Stereoelectronic effects in stabilizing protein-N-glycan interactions revealed by experiment and machine learning. Nat Chem 2021; 13:480-487. [PMID: 33723379 PMCID: PMC8102341 DOI: 10.1038/s41557-021-00646-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
The energetics of protein-carbohydrate interactions, central to many life processes, cannot yet be manipulated predictably. This is mostly due to an incomplete quantitative understanding of the enthalpic and entropic basis of these interactions in aqueous solution. Here, we show that stereoelectronic effects contribute to stabilizing protein-N-glycan interactions in the context of a cooperatively folding protein. Double-mutant cycle analyses of the folding data from 52 electronically varied N-glycoproteins demonstrate an enthalpy-entropy compensation depending on the electronics of the interacting side chains. Linear and nonlinear models obtained using quantum mechanical calculations and machine learning explain up to 79% and 97% of the experimental interaction energy variability, as inferred from the R2 value of the respective models. Notably, the protein-carbohydrate interaction energies strongly correlate with the molecular orbital energy gaps of the interacting substructures. This suggests that stereoelectronic effects must be given a greater weight than previously thought for accurately modelling the short-range dispersive van der Waals interactions between the N-glycan and the protein.
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Affiliation(s)
- Maziar S. Ardejani
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Evan T. Powers
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jeffery W. Kelly
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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38
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Lim KS, Lee DY, Han S, Bull DA, Won YW. Targeted delivery of heat shock protein 90 inhibitors prevents growth of HER2-positive tumor. Biomaterials 2021; 273:120817. [PMID: 33894402 DOI: 10.1016/j.biomaterials.2021.120817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/29/2021] [Accepted: 04/06/2021] [Indexed: 12/30/2022]
Abstract
Heat shock protein 90 (HSP90) plays a crucial role in the survival of cancer cells. When an inhibitor blocks the signaling pathway of HSP90, its client proteins are degraded, destabilized, and inactivated. Although HSP90 inhibitors are in various clinical trials, there are no HSP90 inhibitor-immunoconjugates due to the difficulty in chemical modification of HSP90 inhibitors. Here we show that biological affinity binding enables the incorporation of HSP90 inhibitors to an antibody without the need for chemical conjugation. We constructed a recombinant fusion protein composed of an anti-HER2 scFv and an HSP90 inhibitor-binding domain (HER2 scFv-HBD). The HBD spontaneously captures a HSP90 inhibitor, resulting in the formation of an HER2 scFv-HBD/HSP90 inhibitor complex. In an HER2-positive cancer mouse model, targeted delivery of HSP90 inhibitors was confirmed and improved anti-cancer efficacy was observed. We have proven the promise of tumor-directed HSP90 inhibition as a new form of targeted therapy.
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Affiliation(s)
- Kwang Suk Lim
- Department of Biotechnology and Bioengineering, Interdisciplinary Program in Biohealth-machinery Convergence Engineering, College of Art, Culture and Engineering, Kangwon National University, South Korea
| | - Daniel Y Lee
- Division of Cardiothoracic Surgery, Department of Surgery, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Seungmin Han
- Division of Cardiothoracic Surgery, Department of Surgery, University of Arizona College of Medicine, Tucson, AZ, USA
| | - David A Bull
- Division of Cardiothoracic Surgery, Department of Surgery, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Young-Wook Won
- Division of Cardiothoracic Surgery, Department of Surgery, University of Arizona College of Medicine, Tucson, AZ, USA.
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39
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Extremely Thermostabilizing Core Mutations in Coiled-Coil Mimetic Proteins of HIV-1 gp41 Produce Diverse Effects on Target Binding but Do Not Affect Their Inhibitory Activity. Biomolecules 2021; 11:biom11040566. [PMID: 33921495 PMCID: PMC8069472 DOI: 10.3390/biom11040566] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/05/2021] [Accepted: 04/09/2021] [Indexed: 11/16/2022] Open
Abstract
A promising strategy to neutralize HIV-1 is to target the gp41 spike subunit to block membrane fusion with the cell. We previously designed a series of single-chain proteins (named covNHR) that mimic the trimeric coiled-coil structure of the gp41 N-terminal heptad repeat (NHR) region and potently inhibit HIV-1 cell infection by avidly binding the complementary C-terminal heptad repeat (CHR) region. These proteins constitute excellent tools to understand the structural and thermodynamic features of this therapeutically important interaction. Gp41, as with many coiled-coil proteins, contains in core positions of the NHR trimer several highly conserved, buried polar residues, the role of which in gp41 structure and function is unclear. Here we produced three covNHR mutants by substituting each triad of polar residues for the canonical isoleucine. The mutants preserve their helical structure and show an extremely increased thermal stability. However, increased hydrophobicity enhances their self-association. Calorimetric analyses show a marked influence of mutations on the binding thermodynamics of CHR-derived peptides. The mutations do not affect however the in vitro HIV-1 inhibitory activity of the proteins. The results support a role of buried core polar residues in maintaining structural uniqueness and promoting an energetic coupling between conformational stability and NHR-CHR binding.
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40
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Timucin AC. Structure based peptide design, molecular dynamics and MM-PBSA studies for targeting C terminal dimerization of NFAT5 DNA binding domain. J Mol Graph Model 2020; 103:107804. [PMID: 33248341 DOI: 10.1016/j.jmgm.2020.107804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/10/2020] [Accepted: 11/10/2020] [Indexed: 11/27/2022]
Abstract
NFAT5 as a transcription factor with an established role in osmotic stress response, has also been revealed to be active under numerous settings, including pathological conditions such as diabetic microvascular complications, chronic arthritis and cancer. Despite these links, current strategies for downregulating NFAT5 activity only relies on indirect modulators, not directly targeting NFAT5, itself. With this study, through using a computational approach, an original peptide was explored to directly target C terminal dimerization of NFAT5 RHR, located in its DNA binding domain. At first, homodimeric NFAT5 RHR bound to its consensus DNA was used for prediction of a preliminary peptide sequence. Possible amino acid replacements for this preliminary peptide were predicted for optimization, which was followed by addition of a cell penetrating peptide sequence. These attempts yielded a small peptide library, which was further investigated for peptide affinities towards C terminal of NFAT5 RHR through molecular docking, 50 ns and 250 ns molecular dynamics simulations, followed by estimation of MM-PBSA based relative binding free energies. Results indicated that after receiving mutations on the preliminary peptide sequence for optimization, a unique peptide could target C terminal dimerization region of NFAT5 RHR through using its cell penetrating peptide sequence. In conclusion, this is the first study presenting computational evidence on identification of a novel peptide capable of directly targeting NFAT5 dimerization. Besides, future implications of these observations were also discussed in terms of methodology and possible applications.
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Affiliation(s)
- Ahmet Can Timucin
- Department of Chemical Engineering, Faculty of Natural Sciences and Engineering, Üsküdar University, Turkey; Neuropsychopharmacology Application and Research Center (NPARC), Üsküdar University, Turkey.
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41
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Li J, Chen J, An L, Yuan X, Yao L. Polyol and sugar osmolytes can shorten protein hydrogen bonds to modulate function. Commun Biol 2020; 3:528. [PMID: 32968183 PMCID: PMC7511342 DOI: 10.1038/s42003-020-01260-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/28/2020] [Indexed: 12/19/2022] Open
Abstract
Polyol and sugar osmolytes are commonly used in therapeutic protein formulations. How they may affect protein structure and function is an important question. In this work, through NMR measurements, we show that glycerol and sorbitol (polyols), as well as glucose (sugar), can shorten protein backbone hydrogen bonds. The hydrogen bond shortening is also captured by molecular dynamics simulations, which suggest a hydrogen bond competition mechanism. Specifically, osmolytes weaken hydrogen bonds between the protein and solvent to strengthen those within the protein. Although the hydrogen bond change is small, with the average experimental cross hydrogen bond 3hJNC' coupling of two proteins GB3 and TTHA increased by ~ 0.01 Hz by the three osmolytes (160 g/L), its effect on protein function should not be overlooked. This is exemplified by the PDZ3-peptide binding where several intermolecular hydrogen bonds are formed and osmolytes shift the equilibrium towards the bound state.
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Affiliation(s)
- Jingwen Li
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Jingfei Chen
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Liaoyuan An
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiang Yuan
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lishan Yao
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
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42
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Mishra L, Sundararajan M, Bandyopadhyay T. MD simulation reveals differential binding of Cm(III) and Th(IV) with serum transferrin at acidic pH. Proteins 2020; 89:193-206. [PMID: 32892408 DOI: 10.1002/prot.26006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 07/13/2020] [Accepted: 08/27/2020] [Indexed: 01/21/2023]
Abstract
The iron carrier human serum transferrin (sTf) is known to transport other metals, including some actinides (An). Radiotoxic An are routinely involved in the nuclear fuel cycle and the possibility of their accidental exposure cannot be ruled out. Understanding An interaction with sTf assumes a greater significance for the development of safe and efficacious chelators for their removal from the blood stream. Here we report several 100 ns equilibrium MD simulations of Cm(III)- and Th(IV)-loaded sTf at various protonation states of the protein to explore the possibility of the two An ions release and speciation. The results demonstrate variation in protonation state of dilysine pair (K206 and K296) and the tyrosine (Y188) residue is necessary for the opening of Cm(III)-bound protein and the release of the ion. For the tetravalent thorium, protonation of dilysine pair suffices to cause conformational changes of protein. However, in none of the protonation states, Th(IV) releases from sTf because of its strong electrostatic interaction with D63 in the first shell of the sTf binding cleft. Analysis of hydrogen bond, water bridge, and the evaluation of potential of mean forces of the An ions' release from sTf, substantiate the differential behavior of Cm(III) and Th(IV) at endosomal pH. The results provide insight in the regulation of Cm(III) and Th(IV) bioavailability that may prove useful for effective design of their decorporating agents and as well may help the future design of radiotherapy based on tetravalent ions.
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Affiliation(s)
- Lokpati Mishra
- Radiation Safety Systems Division, Bhabha Atomic Research Centre, Mumbai, India.,Department of Chemical Sciences, Homi Bhabha National Institute, Mumbai, India
| | | | - Tusar Bandyopadhyay
- Department of Chemical Sciences, Homi Bhabha National Institute, Mumbai, India.,Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai, India
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43
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Pham TK, Kim YW. Helix stabilization by stapled N-capping box. Bioorg Chem 2020; 101:104024. [PMID: 32629279 DOI: 10.1016/j.bioorg.2020.104024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 10/24/2022]
Abstract
The N-capping box is a distinct helix-stabilizing motif frequently found in proteins. In this study, we examined a ruthenium-mediated intramolecular backbone to side chain macrocyclization as a rigidified mimicry of the N-capping box. Experimental data indicate that the 15-membered macrocycle formed by a hept-4-enoyl staple, which directly tethers the α-amino group of N1 residue and the α-carbon of N3 residue, is highly effective in stabilizing helical structures of short peptides.
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Affiliation(s)
- Thanh K Pham
- College of Pharmacy, Dongguk University, Seoul, Republic of Korea
| | - Young-Woo Kim
- College of Pharmacy, Dongguk University, Seoul, Republic of Korea.
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44
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Shahzadi Z, Abbas G, Azam SS. Relational dynamics obtained through simulation studies of thioredoxin reductase: From a multi-drug resistant Entamoeba histolytica. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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45
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Mazmanian K, Sargsyan K, Lim C. How the Local Environment of Functional Sites Regulates Protein Function. J Am Chem Soc 2020; 142:9861-9871. [PMID: 32407086 DOI: 10.1021/jacs.0c02430] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteins form complex biological machineries whose functions in the cell are highly regulated at both the cellular and molecular levels. Cellular regulation of protein functions involves differential gene expressions, post-translation modifications, and signaling cascades. Molecular regulation, on the other hand, involves tuning an optimal local protein environment for the functional site. Precisely how a protein achieves such an optimal environment around a given functional site is not well understood. Herein, by surveying the literature, we first summarize the various reported strategies used by certain proteins to ensure their correct functioning. We then formulate three key physicochemical factors for regulating a protein's functional site, namely, (i) its immediate interactions, (ii) its solvent accessibility, and (iii) its conformational flexibility. We illustrate how these factors are applied to regulate the functions of free/metal-bound Cys and Zn sites in proteins.
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Affiliation(s)
- Karine Mazmanian
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Karen Sargsyan
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
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Urbanek A, Popovic M, Morató A, Estaña A, Elena-Real CA, Mier P, Fournet A, Allemand F, Delbecq S, Andrade-Navarro MA, Cortés J, Sibille N, Bernadó P. Flanking Regions Determine the Structure of the Poly-Glutamine in Huntingtin through Mechanisms Common among Glutamine-Rich Human Proteins. Structure 2020; 28:733-746.e5. [PMID: 32402249 DOI: 10.1016/j.str.2020.04.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/18/2020] [Accepted: 04/11/2020] [Indexed: 10/24/2022]
Abstract
The causative agent of Huntington's disease, the poly-Q homo-repeat in the N-terminal region of huntingtin (httex1), is flanked by a 17-residue-long fragment (N17) and a proline-rich region (PRR), which promote and inhibit the aggregation propensity of the protein, respectively, by poorly understood mechanisms. Based on experimental data obtained from site-specifically labeled NMR samples, we derived an ensemble model of httex1 that identified both flanking regions as opposing poly-Q secondary structure promoters. While N17 triggers helicity through a promiscuous hydrogen bond network involving the side chains of the first glutamines in the poly-Q tract, the PRR promotes extended conformations in neighboring glutamines. Furthermore, a bioinformatics analysis of the human proteome showed that these structural traits are present in many human glutamine-rich proteins and that they are more prevalent in proteins with longer poly-Q tracts. Taken together, these observations provide the structural bases to understand previous biophysical and functional data on httex1.
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Affiliation(s)
- Annika Urbanek
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 34090 Montpellier, France
| | - Matija Popovic
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 34090 Montpellier, France
| | - Anna Morató
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 34090 Montpellier, France
| | - Alejandro Estaña
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 34090 Montpellier, France; LAAS-CNRS, Université de Toulouse, CNRS, 31400 Toulouse, France
| | - Carlos A Elena-Real
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 34090 Montpellier, France
| | - Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Aurélie Fournet
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 34090 Montpellier, France
| | - Frédéric Allemand
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 34090 Montpellier, France
| | - Stephane Delbecq
- Laboratoire de Biologie Cellulaire et Moléculaire (LBCM-EA4558 Vaccination Antiparasitaire), UFR Pharmacie, Université de Montpellier, 34090 Montpellier, France
| | - Miguel A Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, 31400 Toulouse, France
| | - Nathalie Sibille
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 34090 Montpellier, France
| | - Pau Bernadó
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 34090 Montpellier, France.
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47
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Methanolic Bark Extract of Abroma augusta (L.) Induces Apoptosis in EAC Cells through Altered Expression of Apoptosis Regulatory Genes. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2020; 2020:9145626. [PMID: 32351610 PMCID: PMC7178513 DOI: 10.1155/2020/9145626] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/18/2020] [Accepted: 03/21/2020] [Indexed: 12/24/2022]
Abstract
Abroma augusta (L.), one of the herbal medicinal plants, is widely used for treatment of various maladies. The present study was initiated to determine the antioxidant, hemolytic, cytotoxicity, and anticancer activities of methanolic extract from the bark of the plant. The phytochemical screening was done by analyzing different phytochemicals present in the extract. We observed the presence of alkaloids, steroids, terpenoids, flavonoids, reducing sugars, and glycosides in the bark extract which showed the highest antioxidant capacity. Antioxidant potential of the methanolic extract was evaluated in vitro by DPPH (2,2-diphenyl-1-picrylhydrazyl) scavenging assay method. This extract showed prominent scavenging activity with IC50 value of 38.65 μg/ml. The hemolytic activity of the extract was evaluated at concentrations ranging from 250 to 1000 μg/ml. It was observed that the extract induced hemolysis percentage of 9.41% to 4.1%, which implies that the extract has no potent hemolytic activity. Cytotoxicity and anticancer activities were observed on Ehrlich ascites carcinoma (EAC) cells. In addition, the bark showed promising cytotoxicity with IC50 value of 329.41 μg/ml, and the study indicated that the extract was capable of inhibiting EAC cell growth by 75.5% when administered at 100 mg/kg/day body weight intraperitoneally for five consecutive days to Swiss albino mice. Morphological change of apoptotic cell was determined by fluorescence and optical microscopy. DNA fragmentation is another marker for apoptosis, and the bark extract-treated EAC cells showed smeared and fragmented DNA bands. Apoptosis correlated well with the upregulation of p53 and Bax and also with the downregulation of NF-κB and Bcl-2. Furthermore, activity and interaction of two A. augusta compounds were tested through molecular docking simulation study. In conclusion, our results suggest that A. augusta bark has the potential to be considered as an anticancer agent.
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48
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López-Chávez E, Pérez-Hernández G, Aparicio F, Alas SJ. On the Thermal Stability of O 6-Methylguanine-DNA Methyltransferase from Archaeon Pyrococcus kodakaraensis by Molecular Dynamics Simulations. J Chem Inf Model 2020; 60:2138-2154. [PMID: 32250621 DOI: 10.1021/acs.jcim.0c00012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have employed molecular dynamics simulations to analyze the thermal stability of the O6-methylguanine-DNA methyltransferase (MGMT) protein, both hyperthermophilic archaeon Pyrococcus kodakaraensis (Pk-MGMT) and its mesophilic homologue pair, obtained from enterobacterium Escherichia coli (AdaC). This theoretical study was done at three different temperatures: 302, 371, and 450 K. The molecular dynamics has been performed in explicit aqueous solvent during a period of time of 95 ns, including periodic boundary conditions and constant pressure. The same procedure has been used for both proteins, and each simulation has been carried out by triplicate. Hence, we performed 18 simulations. In this way, we have done different analyses to explore the factors that may affect the thermal stability of Pk-MGMT. The structural behavior was analyzed using indicators such as root-mean-square deviation, radius of gyration, solvent-accessible surface area, hydrogen bonds, native contacts, secondary structure, and salt bridge formation. The results showed that when the temperature increases, the global atomic fluctuations increase too, which suggests that both proteins lose thermal stability, but as expected, this fact is highlighted in AdaC. Moreover, the contacts of the native state in AdaC are considerably lower than those found in Pk-MGMT at 450 K. Also, the structural studies showed that conserved and nonconserved salt bridges kept close contacts with the Pk-MGMT protein at high temperatures. These interaction types act as molecular staples and are mainly responsible to provide thermostability to the hyperthermophilic protein.
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Affiliation(s)
- Erick López-Chávez
- Posgrado en Ciencias Naturales e Ingeniería, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México 05300, Mexico
| | - Gerardo Pérez-Hernández
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México 05300, Mexico
| | - Felipe Aparicio
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México 05300, Mexico
| | - Salomón J Alas
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México 05300, Mexico.,Departamento de Química, Unidad Iztapalapa, Universidad Autónoma Metropolitana, Ciudad de México 09340, Mexico
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49
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Inuki S. [Elucidation of Biological Mechanisms Using Synthetic Natural Products and Their Derivatives]. YAKUGAKU ZASSHI 2020; 140:455-470. [PMID: 32238625 DOI: 10.1248/yakushi.19-00206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Natural products are useful sources in the search for biochemical probes and drug leads because of their unique biological activities. However, synthetic studies or functional analyses of polycyclic complex natural products or conjugated lipids (e.g., glycolipids) are often hampered because of their synthesis and handling are challenging. On the basis of rational designs, synthetic studies, and chemical modifications, natural products need to be optimized to more potent compounds with improved activities, selectivities and/or physical properties. We have been synthesizing natural products and their derivatives for the elucidation of their biological mechanisms and discovery of drug leads. This review describes three topics for developing functional compounds derived from natural products for prospective involvement in pharmaceutical research: 1) direct construction of the ergot alkaloid scaffold by palladium catalyzed domino cyclization of amino allenes; 2) identification of novel sphingosine kinase inhibitors through a structure-activity relationship study of jaspine B; and 3) design, synthesis and biological evaluation of novel CD1d glycolipid ligands containing modified lipid moieties.
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Affiliation(s)
- Shinsuke Inuki
- Graduate School of Pharmaceutical Sciences, Kyoto University
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50
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Lessen HJ, Majumdar A, Fleming KG. Backbone Hydrogen Bond Energies in Membrane Proteins Are Insensitive to Large Changes in Local Water Concentration. J Am Chem Soc 2020; 142:6227-6235. [PMID: 32134659 PMCID: PMC7610216 DOI: 10.1021/jacs.0c00290] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A hallmark feature of biological lipid bilayer structure is a depth-dependent polarity gradient largely resulting from the change in water concentration over the angstrom length scale. This gradient is particularly steep as it crosses the membrane interfacial regions where the water concentration drops at least a million-fold along the direction of the bilayer normal. Although local water content is often assumed to be a major determinant of membrane protein stability, the effect of the water-induced polarity gradient upon backbone hydrogen bond strength has not been systematically investigated. We addressed this question by measuring the free energy change for a number of backbone hydrogen bonds in the transmembrane protein OmpW. These values were obtained at 33 backbone amides from hydrogen/deuterium fractionation factors by nuclear magnetic resonance spectroscopy. We surprisingly found that OmpW backbone hydrogen bond energies do not vary over a wide range of water concentrations that are characteristic of the solvation environment in the bilayer interfacial region. We validated the interpretation of our results by determining the hydrodynamic and solvation properties of our OmpW-micelle complex using analytical ultracentrifugation and molecular dynamics simulations. The magnitudes of the backbone hydrogen bond free energy changes in our study are comparable to those observed in water-soluble proteins, the H-segment of the leader peptidase helix used in the von Heijne and White biological scale experiments, and several interfacial peptides. Our results agree with those reported for the transmembrane α-helical portion of the amyloid precursor protein after the latter values were adjusted for kinetic isotope effects. Overall, our work suggests that backbone hydrogen bonds provide modest thermodynamic stability to membrane protein structures and that many amides are unaffected by dehydration within the bilayer.
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Affiliation(s)
- Henry J Lessen
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ananya Majumdar
- The Johns Hopkins University Biomolecular NMR Center, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Karen G Fleming
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
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