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Shitov DA, Krutin DV, Tupikina EY. Mutual influence of non-covalent interactions formed by imidazole: A systematic quantum-chemical study. J Comput Chem 2024; 45:1046-1060. [PMID: 38216334 DOI: 10.1002/jcc.27309] [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: 11/13/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/14/2024]
Abstract
Imidazole is a five-membered heterocycle that is part of a number of biologically important molecules such as the amino acid histidine and the hormone histamine. Imidazole has a unique ability to participate in a variety of non-covalent interactions involving the NH group, the pyridine-like nitrogen atom or the π-system. For many biologically active compounds containing the imidazole moiety, its participation in formation of hydrogen bond NH⋯O/N and following proton transfer is the key step of mechanism of their action. In this work a systematic study of the mutual influence of various paired combinations of non-covalent interactions (e.g., hydrogen bonds and π-interactions) involving the imidazole moiety was performed by means of quantum chemistry (PW6B95-GD3/def2-QZVPD) for a series of model systems constructed based on analysis of available x-ray data. It is shown that for considered complexes formation of additional non-covalent interactions can only enhance the proton-donating ability of imidazole. At the same time, its proton-accepting ability can be both enhanced and weakened, depending on what additional interactions are added to a given system. The mutual influence of non-covalent interactions involving imidazole can be classified as weak geometric and strong energetic cooperativity-a small change in the length of non-covalent interaction formed by imidazole can strongly influence its strength. The latter can be used to develop methods for controlling the rate and selectivity of chemical reactions involving the imidazole fragment in larger systems. It is shown that the strong mutual influence of non-covalent interactions involving imidazole is due to the unique ability of the imidazole ring to effectively redistribute electron density in non-covalently bound systems with its participation.
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Affiliation(s)
- Daniil A Shitov
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - Danil V Krutin
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - Elena Yu Tupikina
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
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2
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Raghuraman P, Ramireddy S, Raman G, Park S, Sudandiradoss C. Understanding a point mutation signature D54K in the caspase activation recruitment domain of NOD1 capitulating concerted immunity via atomistic simulation. J Biomol Struct Dyn 2024:1-17. [PMID: 38415678 DOI: 10.1080/07391102.2024.2322618] [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: 07/27/2023] [Accepted: 12/11/2023] [Indexed: 02/29/2024]
Abstract
Point mutation D54K in the human N-terminal caspase recruitment domain (CARD) of nucleotide-binding oligomerization domain -1 (NOD1) abrogates an imperative downstream interaction with receptor-interacting protein kinase (RIPK2) that entails combating bacterial infections and inflammatory dysfunction. Here, we addressed the molecular details concerning conformational changes and interaction patterns (monomeric-dimeric states) of D54K by signature-based molecular dynamics simulation. Initially, the sequence analysis prioritized D54K as a pathogenic mutation, among other variants, based on a sequence signature. Since the mutation is highly conserved, we derived the distant ortholog to predict the sequence and structural similarity between native and mutant. This analysis showed the utility of 33 communal core residues associated with structural-functional preservation and variations, concurrently served to infer the cryptic hotspots Cys39, Glu53, Asp54, Glu56, Ile57, Leu74, and Lys78 determining the inter helical fold forming homodimers for putative receptor interaction. Subsequently, the atomistic simulations with free energy (MM/PB(GB)SA) calculations predicted structural alteration that takes place in the N-terminal mutant CARD where coils changed to helices (45 α3- L4-α4-L6- α683) in contrast to native (45T2-L4-α4-L6-T483). Likewise, the C-terminal helices 93T1-α7105 connected to the loops distorted compared to native 93α6-L7105 may result in conformational misfolding that promotes functional regulation and activation. These structural perturbations of D54K possibly destabilize the flexible adaptation of critical homotypic NOD1CARD-CARDRIPK2 interactions (α4Asp42-Arg488α5 and α6Phe86-Lys471α4) is consistent with earlier experimental reports. Altogether, our findings unveil the conformational plasticity of mutation-dependent immunomodulatory response and may aid in functional validation exploring clinical investigation on CARD-regulated immunotherapies to prevent systemic infection and inflammation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- P Raghuraman
- Department of Biotechnology, School of Bioscience and Technology, Vellore Institute of Technology, Vellore, India
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do, Republic of Korea
| | - Sriroopreddy Ramireddy
- Department of Biotechnology, School of Bioscience and Technology, Vellore Institute of Technology, Vellore, India
- Department of Genetics and Molecular Biology, School of Health Sciences, The Apollo University, Chittoor, India
| | - Gurusamy Raman
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do, Republic of Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do, Republic of Korea
| | - C Sudandiradoss
- Department of Biotechnology, School of Bioscience and Technology, Vellore Institute of Technology, Vellore, India
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Szadkowska M, Kocot AM, Sowik D, Wyrzykowski D, Jankowska E, Kozlowski LP, Makowska J, Plotka M. Molecular characterization of the PhiKo endolysin from Thermus thermophilus HB27 bacteriophage phiKo and its cryptic lytic peptide RAP-29. Front Microbiol 2024; 14:1303794. [PMID: 38312500 PMCID: PMC10836841 DOI: 10.3389/fmicb.2023.1303794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/12/2023] [Indexed: 02/06/2024] Open
Abstract
Introduction In the era of increasing bacterial resistance to antibiotics, new bactericidal substances are sought, and lysins derived from extremophilic organisms have the undoubted advantage of being stable under harsh environmental conditions. The PhiKo endolysin is derived from the phiKo bacteriophage infecting Gram-negative extremophilic bacterium Thermus thermophilus HB27. This enzyme shows similarity to two previously investigated thermostable type-2 amidases, the Ts2631 and Ph2119 from Thermus scotoductus bacteriophages, that revealed high lytic activity not only against thermophiles but also against Gram-negative mesophilic bacteria. Therefore, antibacterial potential of the PhiKo endolysin was investigated in the study presented here. Methods Enzyme activity was assessed using turbidity reduction assays (TRAs) and antibacterial tests. Differential scanning calorimetry was applied to evaluate protein stability. The Collection of Anti-Microbial Peptides (CAMP) and Antimicrobial Peptide Calculator and Predictor (APD3) were used to predict regions with antimicrobial potential in the PhiKo primary sequence. The minimum inhibitory concentration (MIC) of the RAP-29 synthetic peptide was determined against Gram-positive and Gram-negative selected strains, and mechanism of action was investigated with use of membrane potential sensitive fluorescent dye 3,3'-Dipropylthiacarbocyanine iodide (DiSC3(5)). Results and discussion The PhiKo endolysin is highly thermostable with melting temperature of 91.70°C. However, despite its lytic effect against such extremophiles as: T. thermophilus, Thermus flavus, Thermus parvatiensis, Thermus scotoductus, and Deinococcus radiodurans, PhiKo showed moderate antibacterial activity against mesophiles. Consequently, its protein sequence was searched for regions with potential antibacterial activity. A highly positively charged region was identified and synthetized (PhiKo105-133). The novel RAP-29 peptide lysed mesophilic strains of staphylococci and Gram-negative bacteria, reducing the number of cells by 3.7-7.1 log units and reaching the minimum inhibitory concentration values in the range of 2-31 μM. This peptide is unstructured in an aqueous solution but forms an α-helix in the presence of detergents. Moreover, it binds lipoteichoic acid and lipopolysaccharide, and causes depolarization of bacterial membranes. The RAP-29 peptide is a promising candidate for combating bacterial pathogens. The existence of this cryptic peptide testifies to a much wider panel of antimicrobial peptides than thought previously.
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Affiliation(s)
- Monika Szadkowska
- Laboratory of Extremophiles Biology, Department of Microbiology, University of Gdańsk, Gdańsk, Poland
| | - Aleksandra Maria Kocot
- Laboratory of Extremophiles Biology, Department of Microbiology, University of Gdańsk, Gdańsk, Poland
| | - Daria Sowik
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Dariusz Wyrzykowski
- Department of General and Inorganic Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Elzbieta Jankowska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Lukasz Pawel Kozlowski
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Joanna Makowska
- Department of General and Inorganic Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Magdalena Plotka
- Laboratory of Extremophiles Biology, Department of Microbiology, University of Gdańsk, Gdańsk, Poland
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Zhou Y, Jennette MR, Ma G, Kazzaz SA, Baraniak JH, Nwokonko RM, Groff ML, Velasquez-Reynel M, Huang Y, Wang Y, Gill DL. An apical Phe-His pair defines the Orai1-coupling site and its occlusion within STIM1. Nat Commun 2023; 14:6921. [PMID: 37903816 PMCID: PMC10616141 DOI: 10.1038/s41467-023-42254-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 10/04/2023] [Indexed: 11/01/2023] Open
Abstract
Ca2+ signal-generation through inter-membrane junctional coupling between endoplasmic reticulum (ER) STIM proteins and plasma membrane (PM) Orai channels, remains a vital but undefined mechanism. We identify two unusual overlapping Phe-His aromatic pairs within the STIM1 apical helix, one of which (F394-H398) mediates important control over Orai1-STIM1 coupling. In resting STIM1, this locus is deeply clamped within the folded STIM1-CC1 helices, likely near to the ER surface. The clamped environment in holo-STIM1 is critical-positive charge replacing Phe-394 constitutively unclamps STIM1, mimicking store-depletion, negative charge irreversibly locks the clamped-state. In store-activated, unclamped STIM1, Phe-394 mediates binding to the Orai1 channel, but His-398 is indispensable for transducing STIM1-binding into Orai1 channel-gating, and is spatially aligned with Phe-394 in the exposed Sα2 helical apex. Thus, the Phe-His locus traverses between ER and PM surfaces and is decisive in the two critical STIM1 functions-unclamping to activate STIM1, and conformational-coupling to gate the Orai1 channel.
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Affiliation(s)
- Yandong Zhou
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.
| | - Michelle R Jennette
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Guolin Ma
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Sarah A Kazzaz
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - James H Baraniak
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Robert M Nwokonko
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mallary L Groff
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Marcela Velasquez-Reynel
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Youjun Wang
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, PR China
| | - Donald L Gill
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.
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Li D, Ma Y, Xia W, Tao Y, Zhang Y, Zhang H, Li D, Dai B, Liu C. Creating an Amyloid 'Kaleidoscope' Using Short Iodinated Peptides. Angew Chem Int Ed Engl 2023; 62:e202310737. [PMID: 37650358 DOI: 10.1002/anie.202310737] [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: 07/26/2023] [Revised: 08/25/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
Amyloid fibrils formed by peptides with different sequences exhibit diversified morphologies, material properties and activities, making them valuable for developing functional bionanomaterials. However, the molecular understanding underlying the structural diversity of peptide fibrillar assembly at atomic level is still lacking. In this study, by using cryogenic electron microscopy, we first revealed the structural basis underlying the highly reversible assembly of 1 GFGGNDNFG9 (referred to as hnRAC1) peptide fibril. Furthermore, by installing iodine at different sites of hnRAC1, we generated a collection of peptide fibrils with distinct thermostability. By determining the atomic structures of the iodinated fibrils, we discovered that iodination at different sites of the peptide facilitates the formation of diverse halogen bonds and triggers the assembly of entirely different structures of iodinated fibrils. Finally, based on this structural knowledge, we designed an iodinated peptide that assembles into new atomic structures of fibrils, exhibiting superior thermostability, that aligned with our design. Our work provides an in-depth understanding of the atomic-level processes underlying the formation of diverse peptide fibril structures, and paves the way for creating an amyloid "kaleidoscope" by employing various modifications and peptide sequences to fine-tune the atomic structure and properties of fibrillar nanostructures.
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Affiliation(s)
- Danni Li
- School of Sensing Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yeyang Ma
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Wencheng Xia
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Youqi Tao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yiling Zhang
- School of Sensing Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hong Zhang
- School of Sensing Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bin Dai
- School of Sensing Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China
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6
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Kumar A K, Rathore RS. Categorization of hotspots into three types - weak, moderate and strong to distinguish protein-protein versus protein-peptide interactions. J Biomol Struct Dyn 2023:1-13. [PMID: 37649387 DOI: 10.1080/07391102.2023.2252077] [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: 04/15/2023] [Accepted: 08/18/2023] [Indexed: 09/01/2023]
Abstract
Protein-protein and protein-peptide interactions (PPI and PPepI) belong to a similar category of interactions, yet seemingly subtle differences exist among them. To characterize differences between protein-protein (PP) and protein-peptide (PPep) interactions, we have focussed on two important classes of residues-hotspot and anchor residues. Using implicit solvation-based free energy calculations, a very large-scale alanine scanning has been performed on benchmark datasets, consisting of over 5700 interface residues. The differences in the two categories are more pronounced, if the data were divided into three distinct types, namely - weak hotspots (having binding free energy loss upon Ala mutation, ΔΔG, ∼2-10 kcal/mol), moderate hotspots (ΔΔG, ∼10-20 kcal/mol) and strong hotspots (ΔΔG ≥ ∼20 kcal/mol). The analysis suggests that for PPI, weak hotspots are predominantly populated by polar and hydrophobic residues. The distribution shifts towards charged and polar residues for moderate hotspot and charged residues (principally Arg) are overwhelmingly present in the strong hotspot. On the other hand, in the PPepI dataset, the distribution shifts from predominantly hydrophobic and polar (in the weak type) to almost similar preference for polar, hydrophobic and charged residues (in moderate type) and finally the charged residue (Arg) and Trp are mostly occupied in the strong type. The preferred anchor residues in both categories are Arg, Tyr and Leu, possessing bulky side chain and which also strike a delicate balance between side chain flexibility and rigidity. The present knowledge should aid in effective design of biologics, by augmentation or disruption of PPIs with peptides or peptidomimetics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kiran Kumar A
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, India
| | - R S Rathore
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, India
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7
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Antonio JJ, Kraka E. Noncovalent π Interactions in Mutated Aquomet-Myoglobin Proteins: A QM/MM and Local Vibrational Mode Study. Biochemistry 2023; 62:2325-2337. [PMID: 37458402 DOI: 10.1021/acs.biochem.3c00192] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Protein dynamics and function is strongly connected to the energy flow taking place. Myoglobin (Mb) and its mutations are ideal systems to study the process of vibrational energy transfer (VET) at the molecular level. Anti-Stokes ultraviolet resonance Raman studies using a tryptophan (Trp) probe, introduced at different Mb positions by amino acid replacement, have suggested that the amount of VET depends on the position of the Trp probe relative to the heme group. Inspired by this experimental work, we explored the strength of noncovalent π interactions, as well as covalent interactions for both the axial and distal ligands bound to iron in aquomet-Mb with the local vibrational mode analysis (LMA), originally developed by Konkoli and Cremer. Two sets of noncovalent interactions were investigated: (1) the interaction between the water ligand and Trp rings and (2) the interaction between the Trp and the porphyrin rings of the heme group. We assessed the strength of these noncovalent interactions via a special local mode force constant. Various Trp-modified water-bound ferric Mb proteins in the ground state were studied (6 in total) using gas-phase and QM/MM calculations followed by LMA. Our results disclose that VET is indeed dependent on the position of the Trp probe relative to the heme group but also on the tautomeric nature of distal histidine. They provide new guidelines on how to assess noncovalent π interactions in proteins utilizing LMA and how to use these data to explore VET, and more generally protein dynamics and function.
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Affiliation(s)
- Juliana J Antonio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
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Mitani T, Tsurumaki E, Toyota S. Structures and Supramolecular Properties of Inclusion Complexes of Anthracene-Triptycene Nanocages with Fullerene Guests and Their Dynamic Motion as Molecular Gyroscopes. Chemistry 2023; 29:e202203462. [PMID: 36460616 DOI: 10.1002/chem.202203462] [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: 11/08/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/04/2022]
Abstract
Three derivatives of macrocyclic cage compounds consisting of diarylanthracene and triptycene units were synthesized. These nanocages formed host-guest complexes with C60 and other fullerene guests as confirmed by 1 H NMR and fluorescence spectroscopy. The association constant of the mesityl and 2,4,6-tributoxyphenyl derivatives with C60 was determined to be 2.2 × 104 L mol-1 , which was larger than that of the pentafluorophenyl derivative. Direct experimental evidence of the complexation was obtained by X-ray diffraction analysis: the guest C60 molecule was included in the cavity via multipoint CH⋅⋅⋅π interactions. Dynamic disorders of the included C60 molecule in variable-temperature X-ray analysis indicated uniaxial motion, such as gyroscopic motion. The unique dynamic behavior of the spherical C60 rotor anchored by the cage stator via CH⋅⋅⋅π interactions in the crystal, as well as substituent effects on the association properties, are discussed with the aid of DFT calculations.
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Affiliation(s)
- Takuji Mitani
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Eiji Tsurumaki
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Shinji Toyota
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
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Chung SC, Park JS, Jha RK, Kim J, Kim J, Kim M, Choi J, Kim H, Park DH, Gogurla N, Lee TY, Jeon H, Park JY, Choi J, Kim G, Kim S. Engineering Silk Protein to Modulate Polymorphic Transitions for Green Lithography Resists. ACS APPLIED MATERIALS & INTERFACES 2022; 14:56623-56634. [PMID: 36524808 DOI: 10.1021/acsami.2c17843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Silk protein is being increasingly introduced as a prospective material for biomedical devices. However, a limited locus to intervene in nature-oriented silk protein makes it challenging to implement on-demand functions to silk. Here, we report how polymorphic transitions are related with molecular structures of artificially synthesized silk protein and design principles to construct a green-lithographic and high-performative protein resist. The repetition number and ratio of two major building blocks in synthesized silk protein are essential to determine the size and content of β-sheet crystallites, and radicals resulting from tyrosine cleavages by the 193 nm laser irradiation induce the β-sheet to α-helix transition. Synthesized silk is designed to exclusively comprise homogeneous building blocks and exhibit high crystallization and tyrosine-richness, thus constituting an excellent basis for developing a high-performance deep-UV photoresist. Additionally, our findings can be conjugated to design an electron-beam resist governed by the different irradiation-protein interaction mechanisms. All synthesis and lithography processes are fully water-based, promising green lithography. Using the engineered silk, a nanopatterned planar color filter showing the reduced angle dependence can be obtained. Our study provides insights into the industrial scale production of silk protein with on-demand functions.
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Affiliation(s)
- Soon-Chun Chung
- Material Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., Suwon 16678, Korea
| | - Joon-Song Park
- Material Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., Suwon 16678, Korea
| | - Rakesh Kumar Jha
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Korea
| | - Jieun Kim
- Material Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., Suwon 16678, Korea
| | - Jinha Kim
- Material Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., Suwon 16678, Korea
| | - Muyoung Kim
- Department of Plasma Engineering, Korea Institute of Machinery and Materials, Daejeon 34103, Korea
| | - Juwan Choi
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Korea
| | - Hongdeok Kim
- Department of Mechanical Engineering, BK21 FOUR ERICA-ACE Center, Hanyang University, Ansan 15588, Korea
| | - Da-Hye Park
- Material Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., Suwon 16678, Korea
| | - Narendar Gogurla
- Department of Energy Systems Research, Ajou University, Suwon 16499, Korea
| | - Tae-Yun Lee
- Department of Physics and Astronomy, Seoul National University, Seoul 08826, Korea
| | - Heonsu Jeon
- Department of Physics and Astronomy, Seoul National University, Seoul 08826, Korea
| | - Ji-Yong Park
- Department of Energy Systems Research, Ajou University, Suwon 16499, Korea
| | - Joonmyung Choi
- Department of Mechanical Engineering, BK21 FOUR ERICA-ACE Center, Hanyang University, Ansan 15588, Korea
| | - Ginam Kim
- Material Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., Suwon 16678, Korea
| | - Sunghwan Kim
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Korea
- Department of Biomedical Engineering, Hanyang University, Seoul 04763, Korea
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10
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Asghar S, Hameed S, Tahir MN, Naseer MM. Molecular duplexes featuring NH···N, CH···O and CH···π interactions in solid-state self-assembly of triazine-based compounds. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220603. [PMID: 36397969 PMCID: PMC9626258 DOI: 10.1098/rsos.220603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Synthetic supramolecular structures constructed through the cooperative action of numerous non-covalent forces are highly desirable as models to unravel and understand the complexity of systems created in nature via self-assembly. Taking advantage of the low cost of 2,4,6-trichloro-1,3,5-triazine (cyanuric chloride) and the sequential nucleophilic substitution reactions with almost all types of nucleophiles, a series of six structurally related novel s-triazine derivatives 1-6 were synthesized and structurally characterized based on their physical, spectral and crystallographic data. The solid-state structures of all the six compounds showed intriguing and unique molecular duplexes featuring NH···N, CH···O and CH···π interactions. Careful analysis of different geometric parameters of the involved H-bonds indicates that they are linear, significant and are therefore responsible for guiding the three-dimensional structure of these compounds in the solid state. The prevalence of sextuple hydrogen bond array-driven molecular duplexes and the possibility of structural modifications on the s-triazine ring render these novel triazine derivatives 1-6 attractive as a platform to create heteroduplex constructs and their subsequent utility in the field of supramolecular chemistry and crystal engineering.
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Affiliation(s)
- Shazia Asghar
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Shahid Hameed
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
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11
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Simionesie D, O’Callaghan G, Manning JRH, Düren T, Preece JA, Evans R, Zhang ZJ. Combined Experimental and Computational Study of Polycyclic Aromatic Compound Aggregation: The Impact of Solvent Composition. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2077777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Dorin Simionesie
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, UK
| | | | - Joseph R. H. Manning
- Centre for Advanced Separations Engineering, Department of Chemical Engineering, University of Bath, Claverton Down, Bath, UK
| | - Tina Düren
- Centre for Advanced Separations Engineering, Department of Chemical Engineering, University of Bath, Claverton Down, Bath, UK
| | - Jon A. Preece
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, UK
| | - Robert Evans
- Aston Institute of Materials Research, Aston University, Birmingham, UK
| | - Zhenyu J. Zhang
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, UK
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12
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O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding. Proteins 2022; 90:1159-1169. [DOI: 10.1002/prot.26298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 11/07/2022]
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13
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Chakrabarti P, Chakravarty D. Intrinsically disordered proteins/regions and insight into their biomolecular interactions. Biophys Chem 2022; 283:106769. [DOI: 10.1016/j.bpc.2022.106769] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 12/20/2022]
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14
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Kuzniak-Glanowska E, Glanowski M, Kurczab R, Bojarski AJ, Podgajny R. Mining anion-aromatic interactions in the Protein Data Bank. Chem Sci 2022; 13:3984-3998. [PMID: 35440982 PMCID: PMC8985504 DOI: 10.1039/d2sc00763k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 02/28/2022] [Indexed: 12/01/2022] Open
Abstract
Mutual positioning and non-covalent interactions in anion–aromatic motifs are crucial for functional performance of biological systems. In this context, regular, comprehensive Protein Data Bank (PDB) screening that involves various scientific points of view and individual critical analysis is of utmost importance. Analysis of anions in spheres with radii of 5 Å around all 5- and 6-membered aromatic rings allowed us to distinguish 555 259 unique anion–aromatic motifs, including 92 660 structures out of the 171 588 structural files in the PDB. The use of a scarcely exploited (x, h) coordinate system led to (i) identification of three separate areas of motif accumulation: A – over the ring, B – over the ring-substituent bonds, and C – roughly in the plane of the aromatic ring, and (ii) unprecedented simultaneous comparative description of various anion–aromatic motifs located in these areas. Of the various residues considered, i.e. aminoacids, nucleotides, and ligands, the latter two exhibited a considerable tendency to locate in region Avia archetypal anion–π contacts. The applied model not only enabled statistical quantitative analysis of space around the ring, but also enabled discussion of local intermolecular arrangements, as well as detailed sequence and secondary structure analysis, e.g. anion–π interactions in the GNRA tetraloop in RNA and protein helical structures. As a purely practical issue of this work, the new code source for the PDB research was produced, tested and made freely available at https://github.com/chemiczny/PDB_supramolecular_search. The comprehensive analysis of non-redundant PDB macromolecular structures investigating anion distributions around all aromatic molecules in available biosystems is presented.![]()
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Affiliation(s)
| | - Michał Glanowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences Niezapominajek 8 30-239 Kraków Poland
| | - Rafał Kurczab
- Maj Institute of Pharmacology, Polish Academy of Sciences Smętna 12 31-343 Kraków Poland
| | - Andrzej J Bojarski
- Maj Institute of Pharmacology, Polish Academy of Sciences Smętna 12 31-343 Kraków Poland
| | - Robert Podgajny
- Faculty of Chemistry, Jagiellonian University Gronostajowa 2 30-387 Kraków Poland
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15
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Tesmar A, Kogut MM, Żamojć K, Grabowska O, Chmur K, Samsonov SA, Makowska J, Wyrzykowski D, Chmurzyński L. Physicochemical nature of sodium dodecyl sulfate interactions with bovine serum albumin revealed by interdisciplinary approaches. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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16
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Emmerling ST, Schuldt R, Bette S, Yao L, Dinnebier RE, Kästner J, Lotsch BV. Interlayer Interactions as Design Tool for Large-Pore COFs. J Am Chem Soc 2021; 143:15711-15722. [PMID: 34495671 PMCID: PMC8485322 DOI: 10.1021/jacs.1c06518] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
Covalent organic
frameworks (COFs) with a pore size beyond 5 nm
are still rarely seen in this emerging field. Besides obvious complications
such as the elaborated synthesis of large linkers with sufficient
solubility, more subtle challenges regarding large-pore COF synthesis,
including pore occlusion and collapse, prevail. Here we present two
isoreticular series of large-pore imine COFs with pore sizes up to
5.8 nm and correlate the interlayer interactions with the structure
and thermal behavior of the COFs. By adjusting interlayer interactions
through the incorporation of methoxy groups acting as pore-directing
“anchors”, different stacking modes can be accessed,
resulting in modified stacking polytypes and, hence, effective pore
sizes. A strong correlation between stacking energy toward highly
ordered, nearly eclipsed structures, higher structural integrity during
thermal stress, and a novel, thermally induced phase transition of
stacking modes in COFs was found, which sheds light on viable design
strategies for increased structural control and stability in large-pore
COFs.
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Affiliation(s)
- Sebastian T Emmerling
- Nanochemistry Department, Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany.,Department of Chemistry, University of Munich (LMU), Butenandtstraße 5-13, 81377 Munich, Germany
| | - Robin Schuldt
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Sebastian Bette
- Nanochemistry Department, Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany.,Institute for Inorganic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Liang Yao
- Nanochemistry Department, Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Robert E Dinnebier
- Nanochemistry Department, Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Bettina V Lotsch
- Nanochemistry Department, Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany.,Department of Chemistry, University of Munich (LMU), Butenandtstraße 5-13, 81377 Munich, Germany.,E-conversion and Center for Nanoscience, Lichtenbergstraße 4a, 85748 Garching, Germany
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17
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Paul S, Paul S. Controlling the self-assembly of human calcitonin: a theoretical approach using molecular dynamics simulations. Phys Chem Chem Phys 2021; 23:14496-14510. [PMID: 34184696 DOI: 10.1039/d1cp00825k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human calcitonin (hCT) is a 32-residue amino acid poly-peptide hormone which is secreted by the C-cells (also known as parafollicular cells) of thyroid glands. It acts to inhibit osteoclast cell hormones by reducing the cell function and regulating calcium and phosphate in blood. hCT has a high tendency to assemble into protofilaments with β-sheet conformations. Amyloid fibril formation of hCT reduces its bio-activity and limits its application as a therapeutic drug. Salmon calcitonin (sCT), which also carries the same disulfide bridge at the N and C-terminus, but differs at the 16 residue position from hCT, has less propensity to aggregate than hCT. Human calcitonin has much higher bio-activity than sCT if its aggregation propensity is reduced. Substituting the key residues which are responsible for the aggregation of hCT, is one of the ways to reduce its aggregation and fibril formation. hCT analogues with less aggregation tendency can be exploited as therapeutic drugs. In this work, we study the amyloidogenic behavior of hCT and its peptide based derivatives i.e., sCT, phCT, N17H hCT, Y12L hCT and DM hCT, through classical molecular dynamics (MD) simulations. Our study reveals that sCT is the least aggregation prone derivative, and the double mutation at position 12 and 17 can reduce the aggregation propensity of this peptide. Also, we have applied these mutant variants of hCT as peptide inhibitors in the self-aggregation of hCT. This study could help in understanding and preparing peptide-based inhibitors for hCT fibrillation and their applications as therapeutic drugs.
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Affiliation(s)
- Srijita Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.
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18
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Chatterjee KS, Das R. An "up" oriented methionine-aromatic structural motif in SUMO is critical for its stability and activity. J Biol Chem 2021; 297:100970. [PMID: 34274315 PMCID: PMC8353491 DOI: 10.1016/j.jbc.2021.100970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/09/2021] [Accepted: 07/14/2021] [Indexed: 11/25/2022] Open
Abstract
Protein structural bioinformatic analyses suggest preferential associations between methionine and aromatic amino acid residues in proteins. Ab initio energy calculations highlight a conformation-dependent stabilizing interaction between the interacting sulfur-aromatic molecular pair. However, the relevance of buried methionine-aromatic motifs to protein folding and function is relatively unexplored. The Small Ubiquitin-Like Modifier (SUMO) is a β-grasp fold protein and a common posttranslational modifier that affects diverse cellular processes, including transcriptional regulation, chromatin remodeling, metabolic regulation, mitosis, and meiosis. SUMO is a member of the Ubiquitin-Like (UBL) protein family. Herein, we report that a highly conserved and buried methionine-phenylalanine motif is a unique signature of SUMO proteins but absent in other homologous UBL proteins. We also detect that a specific "up" conformation between the methionine-phenylalanine pair of interacting residues in SUMO is critical to its β-grasp fold. The noncovalent interactions of SUMO with its ligands are dependent on the methionine-phenylalanine pair. MD simulations, NMR, and biophysical and biochemical studies suggest that perturbation of the methionine-aromatic motif disrupts native contacts, modulates noncovalent interactions, and attenuates SUMOylation activity. Our results highlight the importance of conserved orientations of Met-aromatic structural motifs inside a protein core for its structure and function.
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Affiliation(s)
- Kiran Sankar Chatterjee
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Ranabir Das
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India.
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19
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Al Mughram MH, Catalano C, Bowry JP, Safo MK, Scarsdale JN, Kellogg GE. 3D Interaction Homology: Hydropathic Analyses of the "π-Cation" and "π-π" Interaction Motifs in Phenylalanine, Tyrosine, and Tryptophan Residues. J Chem Inf Model 2021; 61:2937-2956. [PMID: 34101460 DOI: 10.1021/acs.jcim.1c00235] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Three-dimensional (3D) maps of the hydropathic environments of protein amino acid residues are information-rich descriptors of preferred conformations, interaction types and energetics, and solvent accessibility. The interactions made by each residue are the primary factor for rotamer selection and the secondary, tertiary, and even quaternary protein structure. Our evolving basis set of environmental data for each residue type can be used to understand the protein structure. This work focuses on the aromatic residues phenylalanine, tyrosine, and tryptophan and their structural roles. We calculated and analyzed side chain-to-environment 3D maps for over 70,000 residues of these three types that reveal, with respect to hydrophobic and polar interactions, the environment around each. After binning with backbone ϕ/ψ and side chain χ1, we clustered each bin by 3D similarities between map-map pairs. For each of the three residue types, four bins were examined in detail: one in the β-pleat, two in the right-hand α-helix, and one in the left-hand α-helix regions of the Ramachandran plot. For high degrees of side chain burial, encapsulation of the side chain by hydrophobic interactions is ubiquitous. The more solvent-exposed side chains are more likely to be involved in polar interactions with their environments. Evidence for π-π interactions was observed in about half of the residues surveyed [phenylalanine (PHE): 53.3%, tyrosine (TYR): 34.1%, and tryptophan (TRP): 55.7%], but on an energy basis, this contributed to only ∼4% of the total. Evidence for π-cation interactions was observed in 14.1% of PHE, 8.3% of TYR, and 26.8% of TRP residues, but on an energy basis, this contributed to only ∼1%. This recognition of even these subtle interactions in the 3D hydropathic environment maps is key support for our interaction homology paradigm of protein structure elucidation and possibly prediction.
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Affiliation(s)
- Mohammed H Al Mughram
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States
| | - Claudio Catalano
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States
| | - John P Bowry
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States
| | - Martin K Safo
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
| | - J Neel Scarsdale
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
| | - Glen E Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States.,Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
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20
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Jernigan R, Jia K, Ren Z, Zhou W. Large-scale multiple inference of collective dependence with applications to protein function. Ann Appl Stat 2021; 15:902-924. [DOI: 10.1214/20-aoas1431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Robert Jernigan
- Department of Biochemistry, Biophysics, and Molecular Biology, Program of Bioinformatics and Computational Biology, Iowa State University
| | - Kejue Jia
- Department of Biochemistry, Biophysics, and Molecular Biology, Program of Bioinformatics and Computational Biology, Iowa State University
| | - Zhao Ren
- Department of Statistics, University of Pittsburgh
| | - Wen Zhou
- Department of Statistics, Colorado State University
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21
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Kasatskaya SA, Ladell K, Egorov ES, Miners KL, Davydov AN, Metsger M, Staroverov DB, Matveyshina EK, Shagina IA, Mamedov IZ, Izraelson M, Shelyakin PV, Britanova OV, Price DA, Chudakov DM. Functionally specialized human CD4 + T-cell subsets express physicochemically distinct TCRs. eLife 2020; 9:57063. [PMID: 33289628 PMCID: PMC7773335 DOI: 10.7554/elife.57063] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 12/04/2020] [Indexed: 12/26/2022] Open
Abstract
The organizational integrity of the adaptive immune system is determined by functionally discrete subsets of CD4+ T cells, but it has remained unclear to what extent lineage choice is influenced by clonotypically expressed T-cell receptors (TCRs). To address this issue, we used a high-throughput approach to profile the αβ TCR repertoires of human naive and effector/memory CD4+ T-cell subsets, irrespective of antigen specificity. Highly conserved physicochemical and recombinatorial features were encoded on a subset-specific basis in the effector/memory compartment. Clonal tracking further identified forbidden and permitted transition pathways, mapping effector/memory subsets related by interconversion or ontogeny. Public sequences were largely confined to particular effector/memory subsets, including regulatory T cells (Tregs), which also displayed hardwired repertoire features in the naive compartment. Accordingly, these cumulative repertoire portraits establish a link between clonotype fate decisions in the complex world of CD4+ T cells and the intrinsic properties of somatically rearranged TCRs.
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Affiliation(s)
- Sofya A Kasatskaya
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Evgeniy S Egorov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Kelly L Miners
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Alexey N Davydov
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czech Republic
| | - Maria Metsger
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czech Republic
| | - Dmitry B Staroverov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Elena K Matveyshina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Irina A Shagina
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Ilgar Z Mamedov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Mark Izraelson
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Pavel V Shelyakin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Olga V Britanova
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.,Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Dmitriy M Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
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22
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Sridhar S, Schmitz W, Hiltunen JK, Venkatesan R, Bergmann U, Kiema TR, Wierenga RK. Crystallographic binding studies of rat peroxisomal multifunctional enzyme type 1 with 3-ketodecanoyl-CoA: capturing active and inactive states of its hydratase and dehydrogenase catalytic sites. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:1256-1269. [DOI: 10.1107/s2059798320013819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/15/2020] [Indexed: 11/11/2022]
Abstract
The peroxisomal multifunctional enzyme type 1 (MFE1) catalyzes two successive reactions in the β-oxidation cycle: the 2E-enoyl-CoA hydratase (ECH) and NAD+-dependent 3S-hydroxyacyl-CoA dehydrogenase (HAD) reactions. MFE1 is a monomeric enzyme that has five domains. The N-terminal part (domains A and B) adopts the crotonase fold and the C-terminal part (domains C, D and E) adopts the HAD fold. A new crystal form of MFE1 has captured a conformation in which both active sites are noncompetent. This structure, at 1.7 Å resolution, shows the importance of the interactions between Phe272 in domain B (the linker helix; helix H10 of the crotonase fold) and the beginning of loop 2 (of the crotonase fold) in stabilizing the competent ECH active-site geometry. In addition, protein crystallographic binding studies using optimized crystal-treatment protocols have captured a structure with both the 3-ketodecanoyl-CoA product and NAD+bound in the HAD active site, showing the interactions between 3-ketodecanoyl-CoA and residues of the C, D and E domains. Structural comparisons show the importance of domain movements, in particular of the C domain with respect to the D/E domains and of the A domain with respect to the HAD part. These comparisons suggest that the N-terminal part of the linker helix, which interacts tightly with domains A and E, functions as a hinge region for movement of the A domain with respect to the HAD part.
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23
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Alagar S, Bahadur RP. DSS1 allosterically regulates the conformation of the tower domain of BRCA2 that has dsDNA binding specificity for homologous recombination. Int J Biol Macromol 2020; 165:918-929. [PMID: 33011260 DOI: 10.1016/j.ijbiomac.2020.09.230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 09/02/2020] [Accepted: 09/25/2020] [Indexed: 11/17/2022]
Abstract
DSS1 is an evolutionary conserved, small intrinsically disordered protein that regulates various cellular functions. Although several studies have elucidated the role of DSS1 in stabilizing BRCA2 and its importance in homologous recombination repair (HRR), yet the structural mechanism behind the stability and HRR remains elusive. In this study, using molecular dynamics simulation we show that DSS1 stabilizes linearly arranged DNA/DSS1 binding domains of BRCA2 with many native contacts. These contacts are absent in the complexes with two missense DSS1 mutants associated with germline breast cancer and somatic mouth carcinoma. Most importantly, our protein energy-based network models show DSS1 allosterically regulates the conformation of the distant tower domain of BRCA2 that has dsDNA binding specificity for HRR. We further postulate that the unique conformation of the tower domain with kinked-helices might be responsible for DNA strand invasion and initiation of HRR. Induced conformation of the tower domain by the kinked-helices is absent in the unbound BRCA2, as well as in the two mutant DSS1-BRCA2 complexes. This suggests that DSS1 allosterically regulates the tower domain conformations of BRCA2 that affects dsDNA binding, essential for HRR. Our results add a new dimension to the function of DSS1 and its role in regulating HRR.
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Affiliation(s)
- Suresh Alagar
- Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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24
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Bhattacharyya R, Dhar J, Ghosh Dastidar S, Chakrabarti P, Weiss MS. The susceptibility of disulfide bonds towards radiation damage may be explained by S⋯O interactions. IUCRJ 2020; 7:825-834. [PMID: 32939274 PMCID: PMC7467163 DOI: 10.1107/s2052252520008520] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/25/2020] [Indexed: 05/30/2023]
Abstract
Radiation-induced damage to protein crystals during X-ray diffraction data collection is a major impediment to obtaining accurate structural information on macromolecules. Some of the specific impairments that are inflicted upon highly brilliant X-ray irradiation are metal-ion reduction, disulfide-bond cleavage and a loss of the integrity of the carboxyl groups of acidic residues. With respect to disulfide-bond reduction, previous results have indicated that not all disulfide bridges are equally susceptible to damage. A careful analysis of the chemical environment of disulfide bonds in the structures of elastase, lysozyme, acetylcholinesterase and other proteins suggests that S-S bonds which engage in a close contact with a carbonyl O atom along the extension of the S-S bond vector are more susceptible to reduction than the others. Such an arrangement predisposes electron transfer to occur from the O atom to the disulfide bond, leading to its reduction. The interaction between a nucleophile and an electrophile, akin to hydrogen bonding, stabilizes protein structures, but it also provides a pathway of electron transfer to the S-S bond, leading to its reduction during exposure of the protein crystal to an intense X-ray beam. An otherwise stabilizing interaction can thus be the cause of destabilization under the condition of radiation exposure.
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Affiliation(s)
- Rajasri Bhattacharyya
- Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700 054, India
| | - Jesmita Dhar
- Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700 054, India
| | - Shubhra Ghosh Dastidar
- Division of Bioinformatics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700 054, India
| | - Pinak Chakrabarti
- Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700 054, India
| | - Manfred S. Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
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25
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Relevance of Electrostatic Charges in Compactness, Aggregation, and Phase Separation of Intrinsically Disordered Proteins. Int J Mol Sci 2020; 21:ijms21176208. [PMID: 32867340 PMCID: PMC7503639 DOI: 10.3390/ijms21176208] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/22/2020] [Accepted: 08/23/2020] [Indexed: 12/20/2022] Open
Abstract
The abundance of intrinsic disorder in the protein realm and its role in a variety of physiological and pathological cellular events have strengthened the interest of the scientific community in understanding the structural and dynamical properties of intrinsically disordered proteins (IDPs) and regions (IDRs). Attempts at rationalizing the general principles underlying both conformational properties and transitions of IDPs/IDRs must consider the abundance of charged residues (Asp, Glu, Lys, and Arg) that typifies these proteins, rendering them assimilable to polyampholytes or polyelectrolytes. Their conformation strongly depends on both the charge density and distribution along the sequence (i.e., charge decoration) as highlighted by recent experimental and theoretical studies that have introduced novel descriptors. Published experimental data are revisited herein in the frame of this formalism, in a new and possibly unitary perspective. The physicochemical properties most directly affected by charge density and distribution are compaction and solubility, which can be described in a relatively simplified way by tools of polymer physics. Dissecting factors controlling such properties could contribute to better understanding complex biological phenomena, such as fibrillation and phase separation. Furthermore, this knowledge is expected to have enormous practical implications for the design, synthesis, and exploitation of bio-derived materials and the control of natural biological processes.
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26
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Lomas JS. Cooperativity in alkane-1,2- and 1,3-polyols: NMR, QTAIM, and IQA study of O─H … OH and C─H … OH bonding interactions. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:666-684. [PMID: 32201981 DOI: 10.1002/mrc.5014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/26/2020] [Accepted: 02/29/2020] [Indexed: 06/10/2023]
Abstract
Proton nuclear magnetic resonance chemical shifts and atom-atom interaction energies for alkanepolyols with 1,2-diol and 1,3-diol repeat units, and for their 1:1 pyridine complexes, are computed by density functional theory calculations. In the 1,3-polyols, based on a tG'Gg' repeat unit, the only important intramolecular hydrogen bonding interactions are O─H… OH. By quantum theory of atoms in molecules analysis of the electron density, unstable bond and ring critical points are found for such interactions in 1,2-polyols with tG'g repeat units, from butane-1,2,3,4-tetrol onwards and in their pyridine complexes from propane-1,2,3-triol onwards. Several features (OH proton shifts and charges, and interaction energies computed by the interacting quantum atoms approach) are used to monitor the dependence of cooperativity on chain length: This is much less regular in 1,2-polyols than in 1,3-polyols and by most criteria has a higher damping factor. Well defined C─H… OH interactions are found in butane-1,2,3,4-tetrol and higher members of the 1,2-polyol series, as well as in their pyridine complexes: There is no evidence for cooperativity with O─H… OH bonding. For the 1,2-polyols, there is a tenuous empirical relationship between the existence of a bond critical point for O─H… OH hydrogen bonding and the interaction energies of competing exchange channels, but the primary/secondary ratio is always less than unity.
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Affiliation(s)
- John S Lomas
- ITODYS (CNRS UMR-7086), Université de Paris, Paris, France
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Carter-Fenk K, Herbert JM. Electrostatics does not dictate the slip-stacked arrangement of aromatic π-π interactions. Chem Sci 2020; 11:6758-6765. [PMID: 34094127 PMCID: PMC8159364 DOI: 10.1039/d0sc02667k] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Benzene dimer has long been an archetype for π-stacking. According to the Hunter–Sanders model, quadrupolar electrostatics favors an edge-to-face CH⋯π geometry but competes with London dispersion that favors cofacial π-stacking, with a compromise “slip-stacked” structure emerging as the minimum-energy geometry. This model is based on classical electrostatics, however, and neglects charge penetration. A fully quantum-mechanical analysis, presented here, demonstrates that electrostatics actually exerts very little influence on the conformational landscape of (C6H6)2. Electrostatics also cannot explain the slip-stacked arrangement of C6H6⋯C6F6, where the sign of the quadrupolar interaction is reversed. Instead, the slip-stacked geometry emerges in both systems due to competition between dispersion and Pauli repulsion, with electrostatics as an ambivalent spectator. This revised interpretation helps to rationalize the persistence of offset π-stacking in larger polycyclic aromatic hydrocarbons and across the highly varied electrostatic environments that characterize π–π interactions in proteins. According to the Hunter–Sanders model, geometries in π–π systems arise from competition between quadrupolar electrostatics (favoring an edge-to-face geometry) and London dispersion (favoring stacking), but this model misrepresents the molecular physics.![]()
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Affiliation(s)
- Kevin Carter-Fenk
- Department of Chemistry & Biochemistry, The Ohio State University Columbus OH USA
| | - John M Herbert
- Department of Chemistry & Biochemistry, The Ohio State University Columbus OH USA
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28
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Sonani RR, Roszak AW, Liu H, Gross ML, Blankenship RE, Madamwar D, Cogdell RJ. Revisiting high-resolution crystal structure of Phormidium rubidum phycocyanin. PHOTOSYNTHESIS RESEARCH 2020; 144:349-360. [PMID: 32303893 PMCID: PMC7491960 DOI: 10.1007/s11120-020-00746-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
The crystal structure of phycocyanin (pr-PC) isolated from Phormidium rubidum A09DM (P. rubidum) is described at a resolution of 1.17 Å. Electron density maps derived from crystallographic data showed many clear differences in amino acid sequences when compared with the previously obtained gene-derived sequences. The differences were found in 57 positions (30 in α-subunit and 27 in β-subunit of pr-PC), in which all residues except one (β145Arg) are not interacting with the three phycocyanobilin chromophores. Highly purified pr-PC was then sequenced by mass spectrometry (MS) using LC-MS/MS. The MS data were analyzed using two independent proteomic search engines. As a result of this analysis, complete agreement between the polypeptide sequences and the electron density maps was obtained. We attribute the difference to multiple genes in the bacterium encoding the phycocyanin apoproteins and that the gene sequencing sequenced the wrong ones. We are not implying that protein sequencing by mass spectrometry is more accurate than that of gene sequencing. The final 1.17 Å structure of pr-PC allows the chromophore interactions with the protein to be described with high accuracy.
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Affiliation(s)
- Ravi R Sonani
- Post-Graduate Department of Biosciences, Sardar Patel University, Bakrol, Anand, Gujarat, 388 315, India
- Małopolska Centre of Biotechnology, Jagiellonian University, 30-387, Kraków, Poland
| | - Aleksander W Roszak
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Haijun Liu
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Robert E Blankenship
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Datta Madamwar
- Post-Graduate Department of Biosciences, Sardar Patel University, Bakrol, Anand, Gujarat, 388 315, India.
| | - Richard J Cogdell
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK.
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29
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Zhao X, Zheng W, Zhang Y, Huang W. cis alkenes stabilized by intramolecular sulphurπ interactions. Chem Commun (Camb) 2020; 56:814-817. [PMID: 31848539 DOI: 10.1039/c9cc08558k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of alkenes with bistable isomers were obtained containing a thiophene/azoheteroaryl backbone. Visible light and heat-induced reversible cis ⇌ trans isomerizations were evidenced by UV-Vis and 1H NMR spectra. The stabilization of cis alkenes was attributed to intramolecular sulphurπ (Sπ) interactions, which were further supported by theoretical calculations.
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Affiliation(s)
- Xiaolei Zhao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China.
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30
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Dhar J, Kishore R, Chakrabarti P. Delineation of a new structural motif involving NHN γ-turn. Proteins 2019; 88:431-439. [PMID: 31587358 DOI: 10.1002/prot.25820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 10/25/2022]
Abstract
Macromolecules are characterized by distinctive arrangement of hydrogen bonds. Different patterns of hydrogen bonds give rise to distinct and stable structural motifs. An analysis of 4114 non-redundant protein chains reveals the existence of a three-residue, (i - 1) to (i + 1), structural motif, having two hydrogen-bonded five-membered pseudo rings (the first, an NH···OC involving the first residue, and the second being NH∙∙∙N involving the last two residues), separated by a peptide bond. There could be an additional hydrogen bond between the side-chain at (i-1) and the main-chain NH of (i + 1). The average backbone torsion angles of -76(±21)° and - 12(±17)° at i creates a tight turn in the polypeptide chain, akin to a γ-turn. Indeed, a search of three-residue fragments with restriction on the terminal Cα ···Cα distance and the existence of the two pseudo rings on either side revealed the presence 14 846 cases of a variant, termed NHN γ-turn, distinct from the NHO γ-turn (2032 cases) that has traditionally been characterized by the presence of NHO hydrogen bond linking the terminal main-chain atoms. As in the latter, the newly identified γ-turns are also of two types-classical and inverse, occurring in the ratio of 1:6. The propensities of residues to occur in these turns and their secondary structural features have been enumerated. An understanding of these turns would be useful for structure prediction and loop modeling, and may serve as models to represent some of the unfolded state or disordered region in proteins.
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Affiliation(s)
- Jesmita Dhar
- Bioinformatics Centre, Bose Institute, Kolkata, India
| | - Raghuvansh Kishore
- Department of Zoology and Department of Biotechnology, Mizoram University, Aizawl, India
| | - Pinak Chakrabarti
- Bioinformatics Centre, Bose Institute, Kolkata, India.,Department of Biochemistry, Bose Institute, Kolkata, India
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31
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Choudhary A, Chandra A. An ab initio molecular dynamics study of benzene in water at supercritical conditions: Structure, dynamics, and polarity of hydration shell water and the solute. J Chem Phys 2019; 151:044508. [PMID: 31370512 DOI: 10.1063/1.5094570] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Anisotropic structure and dynamics of the hydration shell of a benzene solute in supercritical water are investigated by means of ab initio molecular dynamics simulations. The polarity and structural distortion of the benzene solute in supercritical water are also investigated in this study. Calculations are done at 673 K for three different densities of the solvent. The simulations are carried out using the Becke-Lee-Yang-Parr (BLYP) and also the Becke-Lee-Yang-Parr functional including dispersion corrections of Grimme (BYLP-D). The structural anisotropy is found to exist even at supercritical conditions as elucidated by the radial distribution functions of different conical regions and also by angular and spatial distribution functions. The benzene-water πH-bond and also the water-water hydrogen bonds are found to exist even at the supercritical temperature of 673 K. However, the numbers of these hydrogen bonds are reduced substantially with a decrease in water density. The water molecules in the axial region of benzene are found to be preferably oriented with one OH vector pointing toward the benzene ring, whereas the water molecules located in the equatorial region are found to orient their dipoles mostly parallel to the ring plane. The orientational distributions, however, are found to be rather broad at the supercritical temperature due to thermal fluctuations. Although the water molecules have faster dynamics at these supercritical conditions, a slight difference is observed in the dynamics of the solvation shell and bulk molecules. The conformational flexibility of the ring is found to be enhanced which causes an increase in polarity of the benzene solute in water under supercritical conditions.
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Affiliation(s)
- Ashu Choudhary
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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32
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Bao P, Boon KL, Will CL, Hartmuth K, Lührmann R. Multiple RNA-RNA tertiary interactions are dispensable for formation of a functional U2/U6 RNA catalytic core in the spliceosome. Nucleic Acids Res 2019; 46:12126-12138. [PMID: 30335160 PMCID: PMC6294511 DOI: 10.1093/nar/gky966] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/05/2018] [Indexed: 01/24/2023] Open
Abstract
The active 3D conformation of the spliceosome's catalytic U2/U6 RNA core is stabilised by a network of secondary and tertiary RNA interactions, but also depends on spliceosomal proteins for its formation. To determine the contribution towards splicing of specific RNA secondary and tertiary interactions in the U2/U6 RNA core, we introduced mutations in critical U6 nucleotides and tested their effect on splicing using a yeast in vitro U6 depletion/complementation system. Elimination of selected RNA tertiary interactions involving the U6 catalytic triad, or deletions of the bases of U6-U80 or U6-A59, had moderate to no effect on splicing, showing that the affected secondary and tertiary interactions are not required for splicing catalysis. However, removal of the base of U6-G60 of the catalytic triad completely blocked splicing, without affecting assembly of the activated spliceosome or its subsequent conversion into a B*-like complex. Our data suggest that the catalytic configuration of the RNA core that allows catalytic metal M1 binding can be maintained by Protein–RNA contacts. However, RNA stacking interactions in the U2/U6 RNA core are required for productive coordination of metal M2. The functional conformation of the U2/U6 RNA core is thus highly buffered, with overlapping contributions from RNA–RNA and Protein–RNA interactions.
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Affiliation(s)
- Penghui Bao
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Kum-Loong Boon
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Cindy L Will
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Klaus Hartmuth
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
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33
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Tan SK, Fong KP, Polizzi NF, Sternisha A, Slusky JSG, Yoon K, DeGrado WF, Bennett JS. Modulating Integrin αIIbβ3 Activity through Mutagenesis of Allosterically Regulated Intersubunit Contacts. Biochemistry 2019; 58:3251-3259. [PMID: 31264850 DOI: 10.1021/acs.biochem.9b00430] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Integrin αIIbβ3, a transmembrane heterodimer, mediates platelet aggregation when it switches from an inactive to an active ligand-binding conformation following platelet stimulation. Central to regulating αIIbβ3 activity is the interaction between the αIIb and β3 extracellular stalks, which form a tight heterodimer in the inactive state and dissociate in the active state. Here, we demonstrate that alanine replacements of sensitive positions in the heterodimer stalk interface destabilize the inactive conformation sufficiently to cause constitutive αIIbβ3 activation. To determine the structural basis for this effect, we performed a structural bioinformatics analysis and found that perturbing intersubunit contacts with favorable interaction geometry through substitutions to alanine quantitatively accounted for the degree of constitutive αIIbβ3 activation. This mutational study directly assesses the relationship between favorable interaction geometry at mutation-sensitive positions and the functional activity of those mutants, giving rise to a simple model that highlights the importance of interaction geometry in contributing to the stability between protein-protein interactions.
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Affiliation(s)
- Sophia K Tan
- Department of Pharmaceutical Chemistry , University of California, San Francisco , San Francisco , California 94158 , United States
| | - Karen P Fong
- Hematology-Oncology Division , University of Pennsylvania School of Medicine , Philadelphia , Pennsylvania 19104 , United States
| | - Nicholas F Polizzi
- Department of Pharmaceutical Chemistry , University of California, San Francisco , San Francisco , California 94158 , United States
| | - Alex Sternisha
- Hematology-Oncology Division , University of Pennsylvania School of Medicine , Philadelphia , Pennsylvania 19104 , United States
| | - Joanna S G Slusky
- Department of Molecular Biosciences and Center for Computational Biology , University of Kansas , Lawrence , Kansas 66045 , United States
| | - Kyungchul Yoon
- Hematology-Oncology Division , University of Pennsylvania School of Medicine , Philadelphia , Pennsylvania 19104 , United States
| | - William F DeGrado
- Department of Pharmaceutical Chemistry , University of California, San Francisco , San Francisco , California 94158 , United States
| | - Joel S Bennett
- Hematology-Oncology Division , University of Pennsylvania School of Medicine , Philadelphia , Pennsylvania 19104 , United States
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34
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Zhang D, He D, Pan X, Xu Y, Liu L. Structural analysis and rational design of orthogonal stacking system in an E. coli DegP PDZ1–peptide complex. CHEMICAL PAPERS 2019. [DOI: 10.1007/s11696-019-00797-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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Sriroopreddy R, Raghuraman P, Sudandiradoss C. Structural debilitation of mutation G322D associated with MSH2 and their role in triple negative breast cancer. J Biomol Struct Dyn 2019; 38:771-780. [DOI: 10.1080/07391102.2019.1587512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ramireddy Sriroopreddy
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - P. Raghuraman
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - C. Sudandiradoss
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
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36
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Nekoei AR, Vatanparast M. π-Hydrogen bonding and aromaticity: a systematic interplay study. Phys Chem Chem Phys 2019; 21:623-630. [PMID: 30540313 DOI: 10.1039/c8cp07003b] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Quantum DFT calculations, corrected for long-range interactions, have been carried out on complex models formed between HF as a proton donor and 2-methylene-2H-indene derivatives as proton acceptors. Using various exocyclic X substitutions, mutual effects of the aromaticity and the strength of the resulting π-hydrogen bond (after its evaluation by AIM methodology) have been investigated. The results show that the aromaticity of 6-membered rings and the hydrogen bond strength increase upon increasing the electron-donating character of the X-substituents. Based on some aromaticity indices (HOMA, FLU, SA and NICS(1)zz), it has been shown that the formation of a π-hydrogen bond causes an increase of aromaticity of the 6-membered ring. Also, the strength of the resulting π-hydrogen bond (with an energy of about 4.0 to 7.0 kcal mol-1) depends on the aromaticity of the 6-membered ring and increases with an increase in the aromaticity. In addition, a linear relationship was found between the most negative value of the molecular electrostatic potential (Vmin) and the HOMA, which confirms that the Vmin in the region of the studied ring could be used as a new index to estimate the amount of aromaticity. The electronic properties of the complexes have also been evaluated by means of the molecular electrostatic potential (MEP), the atoms in molecules (AIM) and the natural bond orbital (NBO) analyses.
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Affiliation(s)
- A-Reza Nekoei
- Department of Chemistry, Shiraz University of Technology, Shiraz 71555-313, Iran.
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37
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Mason TO, Buell AK. The Kinetics, Thermodynamics and Mechanisms of Short Aromatic Peptide Self-Assembly. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:61-112. [PMID: 31713197 DOI: 10.1007/978-981-13-9791-2_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The self-assembly of short aromatic peptides and peptide derivatives into a variety of different nano- and microstructures (fibrillar gels, crystals, spheres, plates) is a promising route toward the creation of bio-compatible materials with often unexpected and useful properties. Furthermore, such simple self-assembling systems have been proposed as model systems for the self-assembly of longer peptides, a process that can be linked to biological function and malfunction. Much effort has been made in the last 15 years to explore the space of peptide sequences, chemical modifications and solvent conditions in order to maximise the diversity of assembly morphologies and properties. However, quantitative studies of the corresponding mechanisms of, and driving forces for, peptide self-assembly have remained relatively scarce until recently. In this chapter we review the current state of understanding of the thermodynamic driving forces and self-assembly mechanisms of short aromatic peptides into supramolecular structures. We will focus on experimental studies of the assembly process and our perspective will be centered around diphenylalanine (FF), a key motif of the amyloid β sequence and a paradigmatic self-assembly building block. Our main focus is the basic physical chemistry and key structural aspects of such systems, and we will also compare the mechanism of dipeptide aggregation with that of longer peptide sequences into amyloid fibrils, with discussion on how these mechanisms may be revealed through detailed analysis of growth kinetics, thermodynamics and other fundamental properties of the aggregation process.
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Affiliation(s)
- Thomas O Mason
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DTU, Lyngby, Denmark.
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38
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Dhar J, Chakrabarti P. Structural motif, topi and its role in protein function and fibrillation. Mol Omics 2018; 14:247-256. [PMID: 29896602 DOI: 10.1039/c8mo00048d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A protein chain is arranged into regions in which the backbone is organized into regular patterns (of conformation and hydrogen bonding) to form the most common secondary structures, α-helix and β-sheet, which are interspersed by turns and more irregular loop regions. A structural motif, topi, is discussed in which a pair of 2-residue segments, each containing hydrogen-bonded five-membered fused-ring motifs, distant in sequence are linked to each other by a hydrogen bond. Though a small motif, it appears to be important in the context of local folding patterns of proteins and occurs near protein active sites. The motif shows quite significant residue preference, and a Cys (or Ser) occupying the second position may further stabilize the motif by forming an additional hydrogen bond across it. Remarkably, topi is found within disease causing misfolded proteins, such as the fibrilled form of Aβ42, and also across the interface between two protein chains. This motif may be an important component of fibrillation and useful for modeling loop regions.
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Affiliation(s)
- Jesmita Dhar
- Bioinformatics Centre, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India.
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39
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Mahalakshmi R. Aromatic interactions in β-hairpin scaffold stability: A historical perspective. Arch Biochem Biophys 2018; 661:39-49. [PMID: 30395808 DOI: 10.1016/j.abb.2018.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 01/21/2023]
Abstract
Non-covalent interactions between naturally occurring aromatic residues have been widely exploited as scaffold stabilizing agents in de novo designed peptides and in Nature - inspired structures. Our understanding of the factors driving aromatic interactions and their observed interaction geometries have advanced remarkably with improvements in conventional structural studies, availability of novel molecular methods and in silico studies, which have together provided atomistic information on aromatic interactions and interaction strengths. This review attempts to recapitulate the early advances in our understanding of aromatic interactions as stabilizing agents of peptide β-hairpins.
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Affiliation(s)
- Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462066, India.
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40
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Lari M, Martínez-Alonso M, Busto N, Manzano BR, Rodríguez AM, Acuña MI, Domínguez F, Albasanz JL, Leal JM, Espino G, García B. Strong Influence of Ancillary Ligands Containing Benzothiazole or Benzimidazole Rings on Cytotoxicity and Photoactivation of Ru(II) Arene Complexes. Inorg Chem 2018; 57:14322-14336. [DOI: 10.1021/acs.inorgchem.8b02299] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Matteo Lari
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Marta Martínez-Alonso
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Natalia Busto
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | | | | | - M. Isabel Acuña
- CIMUS, Universidad de Santiago de Compostela, Avenida Barcelona s/n, 15782 Santiago de Compostela, Spain
| | - Fernando Domínguez
- CIMUS, Universidad de Santiago de Compostela, Avenida Barcelona s/n, 15782 Santiago de Compostela, Spain
| | | | - José M. Leal
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Gustavo Espino
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Begoña García
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
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41
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Hwang J, Li P, Smith MD, Warden CE, Sirianni DA, Vik EC, Maier JM, Yehl CJ, Sherrill CD, Shimizu KD. Tipping the Balance between S-π and O-π Interactions. J Am Chem Soc 2018; 140:13301-13307. [PMID: 30251855 DOI: 10.1021/jacs.8b07617] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A comprehensive experimental survey consisting of 36 molecular balances was conducted to compare 18 pairs of S-π versus O-π interactions over a wide range of structural, geometric, and solvent parameters. A strong linear correlation was observed between the folding energies of the sulfur and oxygen balances across the entire library of balance pairs. The more stable interaction systematically switched from the O-π to S-π interaction. Computational studies of bimolecular PhSCH3-arene and PhOCH3-arene complexes were able to replicate the experimental trends in the molecular balances. The change in preference for the O-π to S-π interaction was due to the interplay of stabilizing (dispersion and solvophobic) and destabilizing (exchange-repulsion) terms arising from the differences in size and polarizability of the oxygen and sulfur atoms.
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Affiliation(s)
- Jungwun Hwang
- Department of Chemistry and Biochemistry , University of South Carolina , Columbia , South Carolina 29208 , United States
| | - Ping Li
- Department of Chemistry and Biochemistry , University of South Carolina , Columbia , South Carolina 29208 , United States
| | - Mark D Smith
- Department of Chemistry and Biochemistry , University of South Carolina , Columbia , South Carolina 29208 , United States
| | | | | | - Erik C Vik
- Department of Chemistry and Biochemistry , University of South Carolina , Columbia , South Carolina 29208 , United States
| | - Josef M Maier
- Department of Chemistry and Biochemistry , University of South Carolina , Columbia , South Carolina 29208 , United States
| | - Christopher J Yehl
- Department of Chemistry and Biochemistry , University of South Carolina , Columbia , South Carolina 29208 , United States
| | | | - Ken D Shimizu
- Department of Chemistry and Biochemistry , University of South Carolina , Columbia , South Carolina 29208 , United States
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The Pathways of the iRFP713 Unfolding Induced by Different Denaturants. Int J Mol Sci 2018; 19:ijms19092776. [PMID: 30223568 PMCID: PMC6163377 DOI: 10.3390/ijms19092776] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/11/2018] [Accepted: 09/13/2018] [Indexed: 02/06/2023] Open
Abstract
Near-infrared fluorescent proteins (NIR FPs) based on the complexes of bacterial phytochromes with their natural biliverdin chromophore are widely used as genetically encoded optical probes for visualization of cellular processes and deep-tissue imaging of cells and organs in living animals. In this work, we show that the steady-state and kinetic dependencies of the various spectral characteristics of iRFP713, developed from the bacterial phytochrome RpBphP2 and recorded at protein unfolding induced by guanidine hydrochloride (GdnHCl), guanidine thiocyanate (GTC), and urea, differ substantially. A study of the unfolding of three single-tryptophan mutant forms of iRFP713 expectedly revealed that protein unfolding begins with the dissociation of the native dimer, while the monomers remain compact. A further increase in the denaturant concentration leads to the formation of an intermediate state of iRFP713 having hydrophobic areas exposed on the protein surface (I). The total surface charge of iRFP713 (pI 5.86) changes from negative to positive with an increase in the concentration of GdnHCl and GTC because the negative charge of glutamic and aspartic acids is neutralized by forming salt bridges between the carboxyl groups and GdnH+ ions and because the guanidinium cations bind to amide groups of glutamines and asparagines. The coincidence of both the concentration of the denaturants at which the intermediate state of iRFP713 accumulates and the concentration of GdnH+ ions at which the neutralization of the surface charge of the protein in this state is ensured results in strong protein aggregation. This is evidently realized by iRFP713 unfolding by GTC. At the unfolding of the protein by GdnHCl, an intermediate state is populated at higher denaturant concentrations and a strong aggregation is not observed. As expected, protein aggregates are not formed in the presence of the urea. The aggregation of the protein upon neutralization of the charge on the macromolecule surface is the main indicator of the intermediate state of protein. The unfolded state of iRFP713, whose formation is accompanied by a significant decrease in the parameter A, was found to have a different residual structure in the denaturants used.
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Lomas JS. Intramolecular O-H⋯O and C-H⋯O hydrogen bond cooperativity in D-glucopyranose and D-galactopyranose-A DFT/GIAO, QTAIM/IQA, and NCI approach. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:748-766. [PMID: 29498091 DOI: 10.1002/mrc.4728] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/07/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
Density functional theory calculations are used to compute proton nuclear magnetic resonance (NMR) chemical shifts, interatomic distances, atom-atom interaction energies, and atomic charges for partial structures and conformers of α-D-glucopyranose, β-D-glucopyranose, and α-D-galactopyranose built up by introducing OH groups into 2-methyltetrahydropyran stepwisely. For the counterclockwise conformers, the most marked effects on the NMR shift and the charge on the OH1 proton are produced by OH2, those of OH3 and OH4 being somewhat smaller. This argues for a diminishing cooperative effect. The effect of OH6 depends on the configuration of the hydroxymethyl group and the position, axial or equatorial, of OH4, which controls hydrogen bonding in the 1,3-diol motif. Variations in the interaction energies reveal that a "new" hydrogen bond is sometimes formed at the expense of a preexisting one, probably due to geometrical constraints. Whereas previous work showed that complexing a conformer with pyridine affects only the nearest neighbour, successive OH groups increase the interaction energy of the N⋯H1 hydrogen bond and reduce its length. Analogous results are obtained for the clockwise conformers. The interaction energies for C-H⋯OH hydrogen bonding between axial CH protons and OH groups in certain conformers are much smaller than for O-H⋯OH bonds but they are largely covalent, whereas those of the latter are predominantly coulombic. These interactions are modified by complexation with pyridine in the same way as O-H⋯OH interactions: the computed NMR shifts of the CH protons increase, the atom-atom distances are shorter, and interaction energies are enhanced.
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Affiliation(s)
- John S Lomas
- ITODYS (CNRS UMR-7086), Paris Diderot University, Sorbonne Paris Cité, F-75205, Paris, France
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44
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Egorov ES, Kasatskaya SA, Zubov VN, Izraelson M, Nakonechnaya TO, Staroverov DB, Angius A, Cucca F, Mamedov IZ, Rosati E, Franke A, Shugay M, Pogorelyy MV, Chudakov DM, Britanova OV. The Changing Landscape of Naive T Cell Receptor Repertoire With Human Aging. Front Immunol 2018; 9:1618. [PMID: 30087674 PMCID: PMC6066563 DOI: 10.3389/fimmu.2018.01618] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/29/2018] [Indexed: 12/22/2022] Open
Abstract
Human aging is associated with a profound loss of thymus productivity, yet naïve T lymphocytes still maintain their numbers by division in the periphery for many years. The extent of such proliferation may depend on the cytokine environment, including IL-7 and T-cell receptor (TCR) “tonic” signaling mediated by self pMHCs recognition. Additionally, intrinsic properties of distinct subpopulations of naïve T cells could influence the overall dynamics of aging-related changes within the naïve T cell compartment. Here, we investigated the differences in the architecture of TCR beta repertoires for naïve CD4, naïve CD8, naïve CD4+CD25−CD31+ (enriched with recent thymic emigrants, RTE), and mature naïve CD4+CD25−CD31− peripheral blood subsets between young and middle-age/old healthy individuals. In addition to observing the accumulation of clonal expansions (as was shown previously), we reveal several notable changes in the characteristics of T cell repertoire. We observed significant decrease of CDR3 length, NDN insert, and number of non-template added N nucleotides within TCR beta CDR3 with aging, together with a prominent change of physicochemical properties of the central part of CDR3 loop. These changes were similar across CD4, CD8, RTE-enriched, and mature CD4 subsets of naïve T cells, with minimal or no difference observed between the latter two subsets for individuals of the same age group. We also observed an increase in “publicity” (fraction of shared clonotypes) of CD4, but not CD8 naïve T cell repertoires. We propose several explanations for these phenomena built upon previous studies of naïve T-cell homeostasis, and call for further studies of the mechanisms causing the observed changes and of consequences of these changes in respect of the possible holes formed in the landscape of naïve T cell TCR repertoire.
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Affiliation(s)
- Evgeny S Egorov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Sofya A Kasatskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Vasiliy N Zubov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Mark Izraelson
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | | | - Andrea Angius
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Italy
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Italy
| | - Ilgar Z Mamedov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Mikhail Shugay
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Dmitriy M Chudakov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Olga V Britanova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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45
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Choudhary A, Chandra A. Dynamics of water in conical solvation shells around a benzene solute under different thermodynamic conditions. Phys Chem Chem Phys 2018; 20:18328-18339. [PMID: 29938274 DOI: 10.1039/c7cp08109j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water molecules in different parts of the anisotropic hydration shell of an aromatic molecule experience different interactions. In the present study, we investigate the anisotropic dynamics of water molecules in different non-overlapping conical shells around a benzene solute at sub- and supercritical conditions by means of molecular dynamics simulations using both non-polarizable and polarizable models. In addition to the dynamical properties, the effects of polarizability on the hydration structure of benzene at varying thermodynamic conditions are also investigated in the current study. The presence of πH-bonding in the solvation shell is found to be an important factor that influences the anisotropic dynamics of the benzene hydration shell. The water molecules located axial to the benzene plane are found to be maximally influenced by the πH-bonding. The extent of πH-bonding is found to be somewhat reduced on inclusion of polarizability. The πH-bonded water molecules are found to reorient through large-amplitude angular jumps where the jump-angle amplitude increases at higher temperatures and lower densities. For both non-polarizable and polarizable models, it is found that the water molecules in the axial conical shells possess faster orientational and hydrogen bond dynamics compared to those in the equatorial plane. Water molecules in the axial conical shells are also found to diffuse at a faster rate than bulk molecules due to the relatively weaker benzene-water πH-bonding interactions in the axial region of the hydration shell. The residence dynamics of water molecules in different conical solvation shells around the solute is also investigated in the current study.
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Affiliation(s)
- Ashu Choudhary
- Department of Chemistry, Indian Institute of Technology Kanpur, 208016, India.
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46
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Wang H, Liu F, Dong T, Du L, Zhang D, Gao J. Charge-Transfer Knowledge Graph among Amino Acids Derived from High-Throughput Electronic Structure Calculations for Protein Database. ACS OMEGA 2018; 3:4094-4104. [PMID: 31458645 PMCID: PMC6641752 DOI: 10.1021/acsomega.8b00336] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 03/30/2018] [Indexed: 05/25/2023]
Abstract
The charge-transfer coupling is an important component in tight-binding methods. Because of the highly complex chemical structure of biomolecules, the anisotropic feature of charge-transfer couplings in realistic proteins cannot be ignored. In this work, we have performed the first large-scale quantitative assessment of charge-transfer preference by calculating the charge-transfer couplings in all 20 × 20 possible amino acid side-chain combinations, which are extracted from available high-quality structures of thousands of protein complexes. The charge-transfer database quantitatively shows distinct features of charge-transfer couplings among millions of amino acid side-chain combinations. The overall distribution of charge-transfer couplings reveals that only one average or representative structure cannot be regarded as the typical charge-transfer preference in realistic proteins. This work provides us an alternative route to comprehensively understand the charge-transfer couplings for the overall distribution of realistic proteins in the foreseen big data scenario.
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Affiliation(s)
- Hongwei Wang
- Hubei
Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Fang Liu
- Hubei
Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Tiange Dong
- Hubei
Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Likai Du
- Hubei
Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Dongju Zhang
- Institute
of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China
| | - Jun Gao
- Hubei
Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
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van Beusekom B, Touw WG, Tatineni M, Somani S, Rajagopal G, Luo J, Gilliland GL, Perrakis A, Joosten RP. Homology-based hydrogen bond information improves crystallographic structures in the PDB. Protein Sci 2018; 27:798-808. [PMID: 29168245 PMCID: PMC5818736 DOI: 10.1002/pro.3353] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 11/16/2017] [Accepted: 11/16/2017] [Indexed: 01/06/2023]
Abstract
The Protein Data Bank (PDB) is the global archive for structural information on macromolecules, and a popular resource for researchers, teachers, and students, amassing more than one million unique users each year. Crystallographic structure models in the PDB (more than 100,000 entries) are optimized against the crystal diffraction data and geometrical restraints. This process of crystallographic refinement typically ignored hydrogen bond (H-bond) distances as a source of information. However, H-bond restraints can improve structures at low resolution where diffraction data are limited. To improve low-resolution structure refinement, we present methods for deriving H-bond information either globally from well-refined high-resolution structures from the PDB-REDO databank, or specifically from on-the-fly constructed sets of homologous high-resolution structures. Refinement incorporating HOmology DErived Restraints (HODER), improves geometrical quality and the fit to the diffraction data for many low-resolution structures. To make these improvements readily available to the general public, we applied our new algorithms to all crystallographic structures in the PDB: using massively parallel computing, we constructed a new instance of the PDB-REDO databank (https://pdb-redo.eu). This resource is useful for researchers to gain insight on individual structures, on specific protein families (as we demonstrate with examples), and on general features of protein structure using data mining approaches on a uniformly treated dataset.
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Affiliation(s)
- Bart van Beusekom
- Department of BiochemistryNetherlands Cancer Institute, Plesmanlaan 121Amsterdam1066 CXThe Netherlands
| | - Wouter G. Touw
- Department of BiochemistryNetherlands Cancer Institute, Plesmanlaan 121Amsterdam1066 CXThe Netherlands
| | - Mahidhar Tatineni
- San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman DriveLa JollaCalifornia92093‐0505
| | - Sandeep Somani
- Discovery Sciences, Janssen R&D LLCSpring HousePennsylvania
| | | | - Jinquan Luo
- Janssen BioTherapeutics, Janssen R&D LLCSpring HousePennsylvania
| | | | - Anastassis Perrakis
- Department of BiochemistryNetherlands Cancer Institute, Plesmanlaan 121Amsterdam1066 CXThe Netherlands
| | - Robbie P. Joosten
- Department of BiochemistryNetherlands Cancer Institute, Plesmanlaan 121Amsterdam1066 CXThe Netherlands
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48
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Raghuraman P, Sudandiradoss C. R516Q mutation in Melanoma differentiation-associated protein 5 (MDA5) and its pathogenic role towards rare Singleton-Merten syndrome; a signature associated molecular dynamics study. J Biomol Struct Dyn 2018; 37:750-765. [DOI: 10.1080/07391102.2018.1439770] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- P. Raghuraman
- Department of Biotechnology, School of Bioscience and Technology, VIT University, Vellore 632014, India
| | - C. Sudandiradoss
- Department of Biotechnology, School of Bioscience and Technology, VIT University, Vellore 632014, India
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49
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Andrić JM, Antonijević IS, Janjić GV, Zarić SD. Influence of hydrogen bonds on edge-to-face interactions between pyridine molecules. J Mol Model 2018; 24:60. [PMID: 29464387 DOI: 10.1007/s00894-017-3570-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/14/2017] [Indexed: 11/30/2022]
Abstract
Edge-to-face interactions between two pyridine molecules and the influence of simultaneous hydrogen bonding of one or both of the pyridines to water on those interactions were studied by analyzing data from ab initio calculations. The results show that the edge-to-face interactions of pyridine dimers that are hydrogen bonded to water are generally stronger than those of non-H-bonded pyridine dimers, especially when the donor pyridine forms a hydrogen bond. The binding energy of the most stable edge-to-face interacting H-bonded pyridine dimer is -5.05 kcal/mol, while that for the most stable edge-to-face interacting non-H-bonded pyridine dimer is -3.64 kcal/mol. The interaction energy data obtained in this study cannot be explained solely by the differences in electrostatic potential between pyridine and the pyridine-water dimer. However, the calculated cooperative effect can be predicted using electrostatic potential maps.
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Affiliation(s)
- Jelena M Andrić
- Innovation Center of the Faculty of Chemistry, Studentski trg 12-16, Belgrade, Serbia
| | - Ivana S Antonijević
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, Belgrade, Serbia
| | - Goran V Janjić
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, Belgrade, Serbia
| | - Snežana D Zarić
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, Serbia. .,Department of Chemistry, Texas A & M University at Qatar, P.O. Box 23874, Doha, Qatar.
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50
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Vodyanova OS, Kochergin BA, Usoltsev SD, Marfin YS, Rumyantsev EV, Aleksakhina EL, Tomilova IK. BODIPY dyes in bio environment: Spectral characteristics and possibilities for practical application. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2017.09.049] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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