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Love O, Pacheco Lima MC, Clark C, Cornillie S, Roalstad S, Cheatham TE. Evaluating the accuracy of the AMBER protein force fields in modeling dihydrofolate reductase structures: misbalance in the conformational arrangements of the flexible loop domains. J Biomol Struct Dyn 2022:1-15. [PMID: 35838167 PMCID: PMC9840716 DOI: 10.1080/07391102.2022.2098823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Protein flexible loop regions were once thought to be simple linkers between other more functional secondary structural elements. However, as it becomes clearer that these loop domains are critical players in a plethora of biological processes, accurate conformational sampling of 3D loop structures is vital to the advancement of drug design techniques and the overall growth of knowledge surrounding molecular systems. While experimental techniques provide a wealth of structural information, the resolution of flexible loop domains is sometimes low or entirely absent due to their complex and dynamic nature. This highlights an opportunity for de novo structure prediction using in silico methods with molecular dynamics (MDs). This study evaluates some of the AMBER protein force field's (ffs) ability to accurately model dihydrofolate reductase (DHFR) conformations, a protein complex characterized by specific arrangements and interactions of multiple flexible loops whose conformations are determined by the presence or absence of bound ligands and cofactors. Although the AMBER ffs, including ff19SB, studied well model most protein structures with rich secondary structure, results obtained here suggest the inability to significantly sample the expected DHFR loop-loop conformations - of the six distinct protein-ligand systems simulated, a majority lacked consistent stabilization of experimentally derived metrics definitive the three enzyme conformations. Although under-sampling and the chosen ff parameter combinations could be the cause, given past successes with these MD approaches for many protein systems, this suggests a potential misbalance in available ff parameters required to accurately predict the structure of multiple flexible loop regions present in proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Olivia Love
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | | | - Casey Clark
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Sean Cornillie
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Shelly Roalstad
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Thomas E. Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
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2
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Ikeda A, Capellan A, Welch JT. The secondary structure of a heptapeptide containing trifluoromethyl-λ 6-tetrafluorosulfanyl substituted amino acids. Org Biomol Chem 2019; 17:8079-8082. [PMID: 31454017 DOI: 10.1039/c9ob01797f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Site specific introduction of the polar hydrophobic trifluoromethyl-λ6-tetrafluorosulfanyl (CF3SF4) group can effectively control the secondary structure of a heptapeptide, the minimum repeat unit of an α-helix. The structural influence of CF3SF4-containing amino acid on the heptapeptide was established using NMR methods.
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Affiliation(s)
- Akari Ikeda
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA.
| | - Aimée Capellan
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA.
| | - John T Welch
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA.
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4
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Krepl M, Blatter M, Cléry A, Damberger FF, Allain FH, Sponer J. Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition. Nucleic Acids Res 2017; 45:8046-8063. [PMID: 28505313 PMCID: PMC5737849 DOI: 10.1093/nar/gkx418] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/26/2017] [Accepted: 05/02/2017] [Indexed: 01/07/2023] Open
Abstract
The Fox-1 RNA recognition motif (RRM) domain is an important member of the RRM protein family. We report a 1.8 Å X-ray structure of the free Fox-1 containing six distinct monomers. We use this and the nuclear magnetic resonance (NMR) structure of the Fox-1 protein/RNA complex for molecular dynamics (MD) analyses of the structured hydration. The individual monomers of the X-ray structure show diverse hydration patterns, however, MD excellently reproduces the most occupied hydration sites. Simulations of the protein/RNA complex show hydration consistent with the isolated protein complemented by hydration sites specific to the protein/RNA interface. MD predicts intricate hydration sites with water-binding times extending up to hundreds of nanoseconds. We characterize two of them using NMR spectroscopy, RNA binding with switchSENSE and free-energy calculations of mutant proteins. Both hydration sites are experimentally confirmed and their abolishment reduces the binding free-energy. A quantitative agreement between theory and experiment is achieved for the S155A substitution but not for the S122A mutant. The S155 hydration site is evolutionarily conserved within the RRM domains. In conclusion, MD is an effective tool for predicting and interpreting the hydration patterns of protein/RNA complexes. Hydration is not easily detectable in NMR experiments but can affect stability of protein/RNA complexes.
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Affiliation(s)
- Miroslav Krepl
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Markus Blatter
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
- Present address: Global Discovery Chemistry, Novartis Institute for BioMedical Research, Basel CH-4002, Switzerland
| | - Antoine Cléry
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Fred F. Damberger
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Frédéric H.T. Allain
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Jiri Sponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
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Kohlmann J, Braun T, Laubenstein R, Herrmann R. Suzuki-Miyaura Cross-Coupling Reactions of Highly Fluorinated Arylboronic Esters: Catalytic Studies and Stoichiometric Model Reactions on the Transmetallation Step. Chemistry 2017; 23:12218-12232. [DOI: 10.1002/chem.201700549] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Johannes Kohlmann
- Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Thomas Braun
- Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Reik Laubenstein
- Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Roy Herrmann
- Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Germany
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6
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Childers MC, Daggett V. Insights from molecular dynamics simulations for computational protein design. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2017; 2:9-33. [PMID: 28239489 PMCID: PMC5321087 DOI: 10.1039/c6me00083e] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.
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Affiliation(s)
| | - Valerie Daggett
- Corresponding author: , Phone: 1.206.685.7420, Fax: 1.206.685.3300
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Abstract
As methods to incorporate noncanonical amino acid residues into proteins have become more powerful, interest in their use to modify the physical and biological properties of proteins and enzymes has increased. This chapter discusses the use of highly fluorinated analogs of hydrophobic amino acids, for example, hexafluoroleucine, in protein design. In particular, fluorinated residues have proven to be generally effective in increasing the thermodynamic stability of proteins. The chapter provides an overview of the different fluorinated amino acids that have been used in protein design and the various methods available for producing fluorinated proteins. It discusses model proteins systems into which highly fluorinated amino acids have been introduced and the reasons why fluorinated residues are generally stabilizing, with particular reference to thermodynamic and structural studies from our laboratory. Lastly, details of the methodology we have developed to measure the thermodynamic stability of oligomeric fluorinated proteins are presented, as this may be generally applicable to many proteins.
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Affiliation(s)
- E N G Marsh
- University of Michigan, Ann Arbor, MI, United States.
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Bulacu M, Sevink GJA. Erratum. Computational insight in the role of fusogenic lipopeptides at the onset of liposome fusion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1716-25. [PMID: 26273716 DOI: 10.1016/j.bbamem.2015.03.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We performed an extensive computational study to obtain insight in the molecular mechanisms that take place prior to membrane fusion. We focused on membrane-anchored hybrid macromolecules (lipid–polymer–oligopeptide) that mimic biological SNARE proteins in terms of liposome fusion characteristics [H. Robson Marsden et al., 2009]; efficient micro-second simulation was enabled by combining validated MARTINI force fields for the molecular building blocks in coarse-grained molecular dynamics (CGMD). We find that individual peptide domains in the hybrid macromolecules bind and partially integrate parallel to the membrane surface, in agreement with experimental findings. By varying several experimental design parameters, we observe that peptide domains remain in the solvent phase only in two cases: (1) for solitary lipopeptides (low concentration), below a threshold area per lipid in the membrane, and (2) when the lipopeptide concentration is high enough for the peptide domains to self-assemble into tetrameric homo-complexes. The peptide-membrane binding is not affected by solvent-induced peptide unfolding, which we mimicked by relaxing the usual MARTINI helix constraints. Remarkably, in this case, a reverse transition to a helical secondary structure is observed after binding, highlighting the role of the membrane as a template (partitioning-folding coupling). Our findings undermine the current view of the initial stages towards fusion, in which membranes are thought to be kept in close apposition via dimerization of individual complementary peptides in the solvent phase. Although we did not study actual fusion, our simulations show that the formation of homomers, which is suppressed in experimental peptide pair design and therefore believed to be insignificant for fusion, by peptides anchored to the same membrane does play a key role in this locking mechanism and potentially also in membrane destabilization that precedes fusion.
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Huhmann S, Nyakatura EK, Erdbrink H, Gerling UI, Czekelius C, Koksch B. Effects of single substitutions with hexafluoroleucine and trifluorovaline on the hydrophobic core formation of a heterodimeric coiled coil. J Fluor Chem 2015. [DOI: 10.1016/j.jfluchem.2015.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Ye S, Loll B, Berger AA, Mülow U, Alings C, Wahl MC, Koksch B. Fluorine teams up with water to restore inhibitor activity to mutant BPTI. Chem Sci 2015; 6:5246-5254. [PMID: 29449928 PMCID: PMC5669249 DOI: 10.1039/c4sc03227f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 06/11/2015] [Indexed: 11/21/2022] Open
Abstract
Fluorinated derivatives of aminobutyric acid engage in unique interactions with structural waters within the BPTI/trypsin interface and restore inhibitor activity.
Introducing fluorine into molecules has a wide range of effects on their physicochemical properties, often desirable but in most cases unpredictable. The fluorine atom imparts the C–F bond with low polarizability and high polarity, and significantly affects the behavior of neighboring functional groups, in a covalent or noncovalent manner. Here, we report that fluorine, present in the form of a single fluoroalkyl amino acid side chain in the P1 position of the well-characterized serine-protease inhibitor BPTI, can fully restore inhibitor activity to a mutant that contains the corresponding hydrocarbon side chain at the same site. High resolution crystal structures were obtained for four BPTI variants in complex with bovine β-trypsin, revealing changes in the stoichiometry and dynamics of water molecules in the S1 subsite. These results demonstrate that the introduction of fluorine into a protein environment can result in “chemical complementation” that has a significantly favorable impact on protein–protein interactions.
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Affiliation(s)
- Shijie Ye
- Department of Biology, Chemistry, and Pharmacy , Freie Universität Berlin , Institute of Chemistry and Biochemistry , Takustr. 3 , Berlin, 14195 , Germany . ; ; Tel: +49-30-83855344
| | - Bernhard Loll
- Department of Biology, Chemistry, and Pharmacy , Freie Universität Berlin , Institute of Chemistry and Biochemistry, Structural Biochemistry , Takustr. 6 , Berlin, 14195 , Germany
| | - Allison Ann Berger
- Department of Biology, Chemistry, and Pharmacy , Freie Universität Berlin , Institute of Chemistry and Biochemistry , Takustr. 3 , Berlin, 14195 , Germany . ; ; Tel: +49-30-83855344
| | - Ulrike Mülow
- Department of Biology, Chemistry, and Pharmacy , Freie Universität Berlin , Institute of Chemistry and Biochemistry , Takustr. 3 , Berlin, 14195 , Germany . ; ; Tel: +49-30-83855344
| | - Claudia Alings
- Department of Biology, Chemistry, and Pharmacy , Freie Universität Berlin , Institute of Chemistry and Biochemistry, Structural Biochemistry , Takustr. 6 , Berlin, 14195 , Germany
| | - Markus Christian Wahl
- Department of Biology, Chemistry, and Pharmacy , Freie Universität Berlin , Institute of Chemistry and Biochemistry, Structural Biochemistry , Takustr. 6 , Berlin, 14195 , Germany
| | - Beate Koksch
- Department of Biology, Chemistry, and Pharmacy , Freie Universität Berlin , Institute of Chemistry and Biochemistry , Takustr. 3 , Berlin, 14195 , Germany . ; ; Tel: +49-30-83855344
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11
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Mehta D, Anand P, Kumar V, Joshi A, Mathur D, Singh S, Tuknait A, Chaudhary K, Gautam SK, Gautam A, Varshney GC, Raghava GPS. ParaPep: a web resource for experimentally validated antiparasitic peptide sequences and their structures. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau051. [PMID: 24923818 PMCID: PMC4054663 DOI: 10.1093/database/bau051] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
ParaPep is a repository of antiparasitic peptides, which provides comprehensive information related to experimentally validated antiparasitic peptide sequences and their structures. The data were collected and compiled from published research papers, patents and from various databases. The current release of ParaPep holds 863 entries among which 519 are unique peptides. In addition to peptides having natural amino acids, ParaPep also consists of peptides having d-amino acids and chemically modified residues. In ParaPep, most of the peptides have been evaluated for growth inhibition of various species of Plasmodium, Leishmania and Trypanosoma. We have provided comprehensive information about these peptides that include peptide sequence, chemical modifications, stereochemistry, antiparasitic activity, origin, nature of peptide, assay types, type of parasite, mode of action and hemolytic activity. Structures of peptides consisting of natural, as well as modified amino acids have been determined using state-of-the-art software, PEPstr. To facilitate users, various user-friendly web tools, for data fetching, analysis and browsing, have been integrated. We hope that ParaPep will be advantageous in designing therapeutic peptides against parasitic diseases. Database URL: http://crdd.osdd.net/raghava/parapep/
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Affiliation(s)
- Divya Mehta
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Priya Anand
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Vineet Kumar
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Anshika Joshi
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Deepika Mathur
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Sandeep Singh
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Abhishek Tuknait
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Kumardeep Chaudhary
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Shailendra K Gautam
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Ankur Gautam
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Grish C Varshney
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Gajendra P S Raghava
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
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12
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Abstract
Highly fluorinated analogs of hydrophobic amino acids have proven to be generally effective in increasing the thermodynamic stability of proteins. These non-proteogenic amino acids can be incorporated into both α-helix and β-sheet structural motifs and generally enhance protein stability towards unfolding by heat and chemical denaturants, and retard their degradation by proteases. Recent detailed structural and thermodynamic studies have demonstrated that the increase in buried hydrophobic surface area that accompanies fluorination is primarily responsible for the stabilizing properties of fluorinated side chains. Fluorination appears to be a particularly useful strategy for increasing protein stability because fluorinated amino acids closely retain the shape of the side chain, and are thus minimally perturbing to protein structure and function. The first part of this chapter discusses some examples of highly fluorinated model proteins designed by our laboratory and protocols for their synthesis. In the second part, methods for determining their thermodynamic stability, along with conditions that have proven to be useful for crystallizing these proteins, are presented.
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Affiliation(s)
- Benjamin C Buer
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
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13
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Gautam A, Chaudhary K, Singh S, Joshi A, Anand P, Tuknait A, Mathur D, Varshney GC, Raghava GPS. Hemolytik: a database of experimentally determined hemolytic and non-hemolytic peptides. Nucleic Acids Res 2013; 42:D444-9. [PMID: 24174543 PMCID: PMC3964980 DOI: 10.1093/nar/gkt1008] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Hemolytik (http://crdd.osdd.net/raghava/hemolytik/) is a manually curated database of experimentally determined hemolytic and non-hemolytic peptides. Data were compiled from a large number of published research articles and various databases like Antimicrobial Peptide Database, Collection of Anti-microbial Peptides, Dragon Antimicrobial Peptide Database and Swiss-Prot. The current release of Hemolytik database contains ∼3000 entries that include ∼2000 unique peptides whose hemolytic activities were evaluated on erythrocytes isolated from as many as 17 different sources. Each entry in Hemolytik provides comprehensive information about a peptide, like its name, sequence, origin, reported function, property such as chirality, types (linear and cyclic), end modifications as well as details pertaining to its hemolytic activity. In addition, tertiary structure of each peptide has been predicted, and secondary structure states have been assigned. To facilitate the scientific community, a user-friendly interface has been developed with various tools for data searching and analysis. We hope, Hemolytik will be useful for researchers working in the field of designing therapeutic peptides.
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Affiliation(s)
- Ankur Gautam
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh 160036, India and Cell Biology and Immunology Division, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
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14
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Erdbrink H, Nyakatura EK, Huhmann S, Gerling UIM, Lentz D, Koksch B, Czekelius C. Synthesis of enantiomerically pure (2S,3S)-5,5,5-trifluoroisoleucine and (2R,3S)-5,5,5-trifluoro-allo-isoleucine. Beilstein J Org Chem 2013; 9:2009-2014. [PMID: 24204411 PMCID: PMC3817528 DOI: 10.3762/bjoc.9.236] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 09/11/2013] [Indexed: 12/26/2022] Open
Abstract
A practical route for the stereoselective synthesis of (2S,3S)-5,5,5-trifluoroisoleucine (L-5-F3Ile) and (2R,3S)-5,5,5-trifluoro-allo-isoleucine (D-5-F3-allo-Ile) was developed. The hydrophobicity of L-5-F3Ile was examined and it was incorporated into a model peptide via solid phase peptide synthesis to determine its α-helix propensity. The α-helix propensity of 5-F3Ile is significantly lower than Ile, but surprisingly high when compared with 4’-F3Ile.
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Affiliation(s)
- Holger Erdbrink
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Elisabeth K Nyakatura
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Susanne Huhmann
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Ulla I M Gerling
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Dieter Lentz
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Beate Koksch
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Constantin Czekelius
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
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15
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Zuo Z, Gandhi NS, Arndt KM, Mancera RL. Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein. Biopolymers 2012; 97:899-909. [DOI: 10.1002/bip.22099] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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16
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Lim DS, Lin JH, Welch JT. The Synthesis and Characterization of a Pentafluorosulfanylated Peptide. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200327] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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17
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Buer BC, Marsh ENG. Fluorine: a new element in protein design. Protein Sci 2012; 21:453-62. [PMID: 22274989 PMCID: PMC3375745 DOI: 10.1002/pro.2030] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 01/09/2012] [Indexed: 11/08/2022]
Abstract
Fluorocarbons are quintessentially man-made molecules, fluorine being all but absent from biology. Perfluorinated molecules exhibit novel physicochemical properties that include extreme chemical inertness, thermal stability, and an unusual propensity for phase segregation. The question we and others have sought to answer is to what extent can these properties be engineered into proteins? Here, we review recent studies in which proteins have been designed that incorporate highly fluorinated analogs of hydrophobic amino acids with the aim of creating proteins with novel chemical and biological properties. Fluorination seems to be a general and effective strategy to enhance the stability of proteins, both soluble and membrane bound, against chemical and thermal denaturation, although retaining structure and biological activity. Most studies have focused on small proteins that can be produced by peptide synthesis as synthesis of large proteins containing specifically fluorinated residues remains challenging. However, the development of various biosynthetic methods for introducing noncanonical amino acids into proteins promises to expand the utility of fluorinated amino acids in protein design.
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Affiliation(s)
- Benjamin C Buer
- Department of Chemistry, University of MichiganAnn Arbor, Michigan 48109
| | - E Neil G Marsh
- Department of Chemistry, University of MichiganAnn Arbor, Michigan 48109
- Department of Biological Chemistry, University of Michigan Medical SchoolAnn Arbor, Michigan 48109
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18
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Salwiczek M, Nyakatura EK, Gerling UIM, Ye S, Koksch B. Fluorinated amino acids: compatibility with native protein structures and effects on protein-protein interactions. Chem Soc Rev 2011; 41:2135-71. [PMID: 22130572 DOI: 10.1039/c1cs15241f] [Citation(s) in RCA: 321] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fluorinated analogues of the canonical α-L-amino acids have gained widespread attention as building blocks that may endow peptides and proteins with advantageous biophysical, chemical and biological properties. This critical review covers the literature dealing with investigations of peptides and proteins containing fluorinated analogues of the canonical amino acids published over the course of the past decade including the late nineties. It focuses on side-chain fluorinated amino acids, the carbon backbone of which is identical to their natural analogues. Each class of amino acids--aliphatic, aromatic, charged and polar as well as proline--is presented in a separate section. General effects of fluorine on essential properties such as hydrophobicity, acidity/basicity and conformation of the specific side chains and the impact of these altered properties on stability, folding kinetics and activity of peptides and proteins are discussed (245 references).
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Affiliation(s)
- Mario Salwiczek
- Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany.
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19
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Zuo Z, Gandhi NS, Mancera RL. Calculations of the Free Energy of Interaction of the c-Fos−c-Jun Coiled Coil: Effects of the Solvation Model and the Inclusion of Polarization Effects. J Chem Inf Model 2010; 50:2201-12. [DOI: 10.1021/ci100321h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhili Zuo
- Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Biomedical Sciences and School of Pharmacy, Curtin University, GPO Box U1987, Perth WA 6845, Australia
| | - Neha S. Gandhi
- Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Biomedical Sciences and School of Pharmacy, Curtin University, GPO Box U1987, Perth WA 6845, Australia
| | - Ricardo L. Mancera
- Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Biomedical Sciences and School of Pharmacy, Curtin University, GPO Box U1987, Perth WA 6845, Australia
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Samsonov SA, Salwiczek M, Anders G, Koksch B, Pisabarro MT. Fluorine in protein environments: a QM and MD study. J Phys Chem B 2010; 113:16400-8. [PMID: 19947631 DOI: 10.1021/jp906402b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Noncanonical amino acids with newly designed side-chain functionalities represent powerful tools to improve structural, biological, and pharmacological properties of peptides and proteins. In this context, fluorinated amino acids have increasingly gained importance. Despite the current wide use of fluorination in protein engineering, the basic properties of fluorine in protein environments are still not completely understood. Our aim has been to characterize the physicochemical properties of fluorinated amino acids by using quantum mechanics (QM) and molecular dynamics (MD) approaches. We have analyzed geometry, charges, and hydrogen bonding abilities of several ethane fluorinated derivatives at different QM theory levels and have used them as simplified models for fluorinated amino acid side chains. We have parametrized four fluorinated L-amino acids for the AMBER ff94/99 force field: 4-monofluoroethylglycine (MfeGly), 4,4-difluoroethylglycine (DfeGly), 4,4,4-trifluoroethylglycine (TfeGly), and 4,4-difluoropropylglycine (DfpGly). We have characterized them in terms of molecular volumes, conformational preferences, and hydration properties. The obtained results illustrate that fluorine and hydrogen atoms of fluoromethyl groups could be potential acceptors or donors of weak hydrogen bonds in protein environments. Hydration of the studied fluorinated amino acids was found to be more favorable than for their nonfluorinated analogues, and hydrophobicity was observed to increase with the number of fluorine atoms, which is in accordance with the experimental retention times we obtain for these amino acids. This study broadens our understanding of the properties of fluorine within protein environments, which is important to exploit the full potential of fluorine's unique properties for applications in the field of protein engineering.
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Affiliation(s)
- Sergey A Samsonov
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg 47-51, 01307 Dresden, Germany
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Salwiczek M, Samsonov S, Vagt T, Nyakatura E, Fleige E, Numata J, Cölfen H, Pisabarro M, Koksch B. Position-Dependent Effects of Fluorinated Amino Acids on the Hydrophobic Core Formation of a Heterodimeric Coiled Coil. Chemistry 2009; 15:7628-36. [DOI: 10.1002/chem.200802136] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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