1
|
Castro TG, Melle-Franco M, Sousa CEA, Cavaco-Paulo A, Marcos JC. Non-Canonical Amino Acids as Building Blocks for Peptidomimetics: Structure, Function, and Applications. Biomolecules 2023; 13:981. [PMID: 37371561 DOI: 10.3390/biom13060981] [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: 04/19/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
This review provides a fresh overview of non-canonical amino acids and their applications in the design of peptidomimetics. Non-canonical amino acids appear widely distributed in nature and are known to enhance the stability of specific secondary structures and/or biological function. Contrary to the ubiquitous DNA-encoded amino acids, the structure and function of these residues are not fully understood. Here, results from experimental and molecular modelling approaches are gathered to classify several classes of non-canonical amino acids according to their ability to induce specific secondary structures yielding different biological functions and improved stability. Regarding side-chain modifications, symmetrical and asymmetrical α,α-dialkyl glycines, Cα to Cα cyclized amino acids, proline analogues, β-substituted amino acids, and α,β-dehydro amino acids are some of the non-canonical representatives addressed. Backbone modifications were also examined, especially those that result in retro-inverso peptidomimetics and depsipeptides. All this knowledge has an important application in the field of peptidomimetics, which is in continuous progress and promises to deliver new biologically active molecules and new materials in the near future.
Collapse
Affiliation(s)
- Tarsila G Castro
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
| | - Manuel Melle-Franco
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Cristina E A Sousa
- BioMark Sensor Research-School of Engineering of the Polytechnic Institute of Porto, 4249-015 Porto, Portugal
| | - Artur Cavaco-Paulo
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
| | - João C Marcos
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| |
Collapse
|
2
|
Pyasi S, Gupta A, Hegde NR, Nayak D. Complete genome sequencing and assessment of mutation-associated protein dynamics of the first Indian bovine ephemeral fever virus (BEFV) isolate. Vet Q 2021; 41:308-319. [PMID: 34663182 PMCID: PMC8567923 DOI: 10.1080/01652176.2021.1995909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Background Bovine ephemeral fever (BEF) is a re-emerging disease caused by bovine ephemeral fever virus (BEFV). Although it poses a huge economic threat to the livestock sector, complete viral genome information from any South Asian country, including India, lacks. Aim Genome characterization of the first Indian BEFV isolate and to evaluate its genetic diversity by characterizing genomic mutations and their associated protein dynamics. Materials and Methods Of the nineteen positive blood samples collected from BEF symptomatic animals during the 2018-19 outbreaks in India, one random sample was used to amplify the entire viral genome by RT-PCR. Utilizing Sanger sequencing and NGS technology, a complete genome was determined. Genome characterization, genetic diversity and phylogenetic analyses were explored by comparing the results with available global isolates. Additionally, unique genomic mutations within the Indian isolate were investigated, followed by in-silico assessment of non-synonymous (NS) mutations impacts on corresponding proteins’ secondary structure, solvent accessibility and dynamics. Results The complete genome of Indian BEFV has 14,903 nucleotides with 33% GC with considerable genetic diversity. Its sequence comparison and phylogenetic analysis revealed a close relatedness to the Middle Eastern lineage. Genome-wide scanning elucidated 30 unique mutations, including 10 NS mutations in the P, L and GNS proteins. The mutational impact evaluation confirmed alterations in protein structure and dynamics, with minimal effect on solvent accessibility. Additionally, alteration in the interatomic interactions was compared against the wild type. Conclusion These findings extend our understanding of the BEFV epidemiological and pathogenic potential, aiding in developing better therapeutic and preventive interventions.
Collapse
Affiliation(s)
- Shruti Pyasi
- Discipline of Bioscience and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Advika Gupta
- Discipline of Bioscience and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Nagendra R Hegde
- Department of Biotechnology, National Institute of Animal Biotechnology, Hyderabad, India
| | - Debasis Nayak
- Discipline of Bioscience and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| |
Collapse
|
3
|
Alabbas AB, Alamri MA. Analyzing the Effect of Mutations in SARS-CoV2 Papain-Like Protease from Saudi Isolates on Protein Structure and Drug-Protein Binding: Molecular Modelling and Dynamics Studies. Saudi J Biol Sci 2021; 29:526-533. [PMID: 34548835 PMCID: PMC8447498 DOI: 10.1016/j.sjbs.2021.09.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 08/31/2021] [Accepted: 09/09/2021] [Indexed: 02/09/2023] Open
Abstract
The continuous and rapid development of the severe acute
respiratory syndrome coronavirus-2 (SARS-CoV-2) virus remains a health concern
especially with the emergence of numerous variants and mutations worldwide. As
with other RNA viruses, SARS-CoV-2 has a genetically high mutation rate. These
mutations have an impact on the virus characteristics, including
transmissibility, antigenicity and development of drug and vaccine resistance.
This work was pursued to identify the differences that exist in the papain-like
protease (PLPro) from 58 Saudi isolates in comparison to the
first reported sequence from Wuhan, China and determine their implications on
protein structure and the inhibitor binding. PLpro is a key
protease enzyme for the host cells invasion and viral proteolytic cleavage,
hence, it emerges as a valuable antiviral therapeutic target. Two mutations were
identified including D108G and A249V and shown to increase the molecular
flexibility of PLPro protein and alter the protein stability,
particularly with D108G mutation. The effect of these mutations on the stability
and dynamic behavior of PLPro structures as well as their
effect on the binding of a known inhibitor; GRL0617 were further investigated by
molecular docking and dynamic simulation.
Collapse
Affiliation(s)
- Alhumaidi B Alabbas
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| |
Collapse
|
4
|
A virus that has gone viral: amino acid mutation in S protein of Indian isolate of Coronavirus COVID-19 might impact receptor binding, and thus, infectivity. Biosci Rep 2020; 40:223851. [PMID: 32378705 PMCID: PMC7225408 DOI: 10.1042/bsr20201312] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 12/05/2022] Open
Abstract
Since 2002, β coronaviruses (CoVs) have caused three zoonotic outbreaks, SARS-CoV in 2002, MERS-CoV in 2012, and the recent outbreak of SARS-CoV-2 late in 2019 (also named as COVID-19 or novel coronavirus 2019 or nCoV2019). Spike (S) protein, one of the structural proteins of this virus plays key role in receptor (ACE2) binding and thus virus entry. Thus, this protein has attracted scientists for detailed study and therapeutic targeting. As the nCoV2019 takes its course throughout the world, more and more sequence analyses are being done and genome sequences are being deposited in various databases. From India, two clinical isolates have been sequenced and the full genome has been deposited in GenBank. We have performed sequence analyses of the Spike protein of the Indian isolates and compared with that of the Wuhan, China (where the outbreak was first reported). While all the sequences of Wuhan isolates are identical, we found point mutations in the Indian isolates. Out of the two isolates, one was found to harbor a mutation in its receptor-binding domain (RBD) at position 407. At this site, arginine (a positively charged amino acid) was replaced by isoleucine (a hydrophobic amino acid that is also a C-β branched amino acid). This mutation has been seen to change the secondary structure of the protein at that region and this can potentially alter receptor binding of the virus. Although this finding needs further validation and more sequencing, the information might be useful in rational drug designing and vaccine engineering.
Collapse
|
5
|
Tian C, Kasavajhala K, Belfon KAA, Raguette L, Huang H, Migues AN, Bickel J, Wang Y, Pincay J, Wu Q, Simmerling C. ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution. J Chem Theory Comput 2019; 16:528-552. [PMID: 31714766 DOI: 10.1021/acs.jctc.9b00591] [Citation(s) in RCA: 753] [Impact Index Per Article: 150.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular dynamics (MD) simulations have become increasingly popular in studying the motions and functions of biomolecules. The accuracy of the simulation, however, is highly determined by the molecular mechanics (MM) force field (FF), a set of functions with adjustable parameters to compute the potential energies from atomic positions. However, the overall quality of the FF, such as our previously published ff99SB and ff14SB, can be limited by assumptions that were made years ago. In the updated model presented here (ff19SB), we have significantly improved the backbone profiles for all 20 amino acids. We fit coupled φ/ψ parameters using 2D φ/ψ conformational scans for multiple amino acids, using as reference data the entire 2D quantum mechanics (QM) energy surface. We address the polarization inconsistency during dihedral parameter fitting by using both QM and MM in aqueous solution. Finally, we examine possible dependency of the backbone fitting on side chain rotamer. To extensively validate ff19SB parameters, and to compare to results using other Amber models, we have performed a total of ∼5 ms MD simulations in explicit solvent. Our results show that after amino-acid-specific training against QM data with solvent polarization, ff19SB not only reproduces the differences in amino-acid-specific Protein Data Bank (PDB) Ramachandran maps better but also shows significantly improved capability to differentiate amino-acid-dependent properties such as helical propensities. We also conclude that an inherent underestimation of helicity is present in ff14SB, which is (inexactly) compensated for by an increase in helical content driven by the TIP3P bias toward overly compact structures. In summary, ff19SB, when combined with a more accurate water model such as OPC, should have better predictive power for modeling sequence-specific behavior, protein mutations, and also rational protein design. Of the explicit water models tested here, we recommend use of OPC with ff19SB.
Collapse
Affiliation(s)
- Chuan Tian
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Koushik Kasavajhala
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Kellon A A Belfon
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Lauren Raguette
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - He Huang
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Angela N Migues
- Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - John Bickel
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Yuzhang Wang
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Jorge Pincay
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Qin Wu
- Center for Functional Nanomaterials , Brookhaven National Laboratory , Upton , New York 11973 , United States
| | - Carlos Simmerling
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| |
Collapse
|
6
|
Vincenzi M, Mercurio FA, Leone M. About TFE: Old and New Findings. Curr Protein Pept Sci 2019; 20:425-451. [PMID: 30767740 DOI: 10.2174/1389203720666190214152439] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 01/28/2023]
Abstract
The fluorinated alcohol 2,2,2-Trifluoroethanol (TFE) has been implemented for many decades now in conformational studies of proteins and peptides. In peptides, which are often disordered in aqueous solutions, TFE acts as secondary structure stabilizer and primarily induces an α -helical conformation. The exact mechanism through which TFE plays its stabilizing roles is still debated and direct and indirect routes, relying either on straight interaction between TFE and molecules or indirect pathways based on perturbation of solvation sphere, have been proposed. Another still unanswered question is the capacity of TFE to favor in peptides a bioactive or a native-like conformation rather than simply stimulate the raise of secondary structure elements that reflect only the inherent propensity of a specific amino-acid sequence. In protein studies, TFE destroys unique protein tertiary structure and often leads to the formation of non-native secondary structure elements, but, interestingly, gives some hints about early folding intermediates. In this review, we will summarize proposed mechanisms of TFE actions. We will also describe several examples, in which TFE has been successfully used to reveal structural properties of different molecular systems, including antimicrobial and aggregation-prone peptides, as well as globular folded and intrinsically disordered proteins.
Collapse
Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia A Mercurio
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy.,Cirpeb, InterUniversity Research Centre on Bioactive Peptides, University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy.,Cirpeb, InterUniversity Research Centre on Bioactive Peptides, University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| |
Collapse
|
7
|
Chabert V, Lebrun V, Lebrun C, Latour JM, Sénèque O. Model peptide for anti-sigma factor domain HHCC zinc fingers: high reactivity toward 1O 2 leads to domain unfolding. Chem Sci 2019; 10:3608-3615. [PMID: 30996953 PMCID: PMC6432622 DOI: 10.1039/c9sc00341j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 02/14/2019] [Indexed: 11/25/2022] Open
Abstract
All organisms have to cope with the deleterious effects of reactive oxygen species. Some of them are able to mount a transcriptional response to various oxidative stresses, which involves sensor proteins capable of assessing the redox status of the cell or to detect reactive oxygen species. In this article, we describe the design, synthesis and characterization of Zn·LASD(HHCC), a model for the Zn(Cys)2(His)2 zinc finger site of ChrR, a sensor protein involved in the bacterial defence against singlet oxygen that belongs to the family of zinc-binding anti-sigma factors possessing a characteristic H/C-X24/25-H-X3-C-X2-C motif. The 46-amino acid model peptide LASD(HHCC) was synthetized by solid phase peptide synthesis and its Zn2+-binding properties were investigated using electronic absorption, circular dichroism and NMR. LASD(HHCC) forms a 1 : 1 complex with Zn2+, namely Zn·LASD(HHCC), that adopts a well-defined conformation with the Zn2+ ion capping a 3-helix core that reproduces almost perfectly the fold of the ChrR in the vicinity of its zinc site. H2O2 reacts with Zn·LASD(HHCC) to yield a disulfide with a second order rate constant of 0.030 ± 0.002 M-1 s-1. Zn·LASD(HHCC) reacts rapidly with singlet oxygen to yield sulfinates and sulfonates. A lower limit of the chemical reaction rate constant between Zn·LASD(HHCC) and 1O2 was determined to be 3.9 × 106 M-1 s-1. Therefore, the Zn(Cys)2(His)2 site of Zn·LASD(HHCC) appears to be at least 5 times more reactive toward these two oxidants than that of a classical ββα zinc finger. Consequences for the activation mechanism of ChrR are discussed.
Collapse
Affiliation(s)
- Valentin Chabert
- Univ. Grenoble Alpes , CNRS , CEA , BIG , LCBM (UMR 5249) , F-38000 Grenoble , France .
| | - Vincent Lebrun
- Univ. Grenoble Alpes , CNRS , CEA , BIG , LCBM (UMR 5249) , F-38000 Grenoble , France .
| | - Colette Lebrun
- Univ. Grenoble Alpes , CEA , CNRS , INAC-SyMMES , F-38000 Grenoble , France
| | - Jean-Marc Latour
- Univ. Grenoble Alpes , CNRS , CEA , BIG , LCBM (UMR 5249) , F-38000 Grenoble , France .
| | - Olivier Sénèque
- Univ. Grenoble Alpes , CNRS , CEA , BIG , LCBM (UMR 5249) , F-38000 Grenoble , France .
| |
Collapse
|
8
|
Boville CE, Scheele RA, Koch P, Brinkmann-Chen S, Buller AR, Arnold FH. Engineered Biosynthesis of β-Alkyl Tryptophan Analogues. Angew Chem Int Ed Engl 2018; 57:14764-14768. [PMID: 30215880 DOI: 10.1002/anie.201807998] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Indexed: 11/12/2022]
Abstract
Noncanonical amino acids (ncAAs) with dual stereocenters at the α and β positions are valuable precursors to natural products and therapeutics. Despite the potential applications of such bioactive β-branched ncAAs, their availability is limited due to the inefficiency of the multistep methods used to prepare them. Herein we report a stereoselective biocatalytic synthesis of β-branched tryptophan analogues using an engineered variant of Pyrococcus furiosus tryptophan synthase (PfTrpB), PfTrpB7E6 . PfTrpB7E6 is the first biocatalyst to synthesize bulky β-branched tryptophan analogues in a single step, with demonstrated access to 27 ncAAs. The molecular basis for the efficient catalysis and broad substrate tolerance of PfTrpB7E6 was explored through X-ray crystallography and UV/Vis spectroscopy, which revealed that a combination of active-site and remote mutations increase the abundance and persistence of a key reactive intermediate. PfTrpB7E6 provides an operationally simple and environmentally benign platform for the preparation of β-branched tryptophan building blocks.
Collapse
Affiliation(s)
- Christina E Boville
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California, 91125, USA
| | - Remkes A Scheele
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California, 91125, USA
| | - Philipp Koch
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California, 91125, USA
| | - Sabine Brinkmann-Chen
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California, 91125, USA
| | - Andrew R Buller
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California, 91125, USA
| |
Collapse
|
9
|
Boville CE, Scheele RA, Koch P, Brinkmann-Chen S, Buller AR, Arnold FH. Engineered Biosynthesis of β-Alkyl Tryptophan Analogues. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807998] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Christina E. Boville
- Division of Chemistry and Chemical Engineering 210-41; California Institute of Technology; 1200 East California Boulevard Pasadena California 91125 USA
| | - Remkes A. Scheele
- Division of Chemistry and Chemical Engineering 210-41; California Institute of Technology; 1200 East California Boulevard Pasadena California 91125 USA
| | - Philipp Koch
- Division of Chemistry and Chemical Engineering 210-41; California Institute of Technology; 1200 East California Boulevard Pasadena California 91125 USA
| | - Sabine Brinkmann-Chen
- Division of Chemistry and Chemical Engineering 210-41; California Institute of Technology; 1200 East California Boulevard Pasadena California 91125 USA
| | - Andrew R. Buller
- Department of Chemistry; University of Wisconsin; 1101 University Avenue Madison WI 53706 USA
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering 210-41; California Institute of Technology; 1200 East California Boulevard Pasadena California 91125 USA
| |
Collapse
|
10
|
Honda K, Inoue M, Ono T, Okano K, Dekishima Y, Kawabata H. Improvement of operational stability of Ogataea minuta carbonyl reductase for chiral alcohol production. J Biosci Bioeng 2017; 123:673-678. [PMID: 28214241 DOI: 10.1016/j.jbiosc.2017.01.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/17/2017] [Accepted: 01/23/2017] [Indexed: 11/24/2022]
Abstract
Directed evolution of enantio-selective carbonyl reductase from Ogataea minuta was conducted to improve the operational stability of the enzyme. A mutant library was constructed by an error-prone PCR and screened using a newly developed colorimetric assay. The stability of a mutant with two amino acid substitutions was significantly higher than that of the wild type at 50°C in the presence of dimethyl sulfoxide. Site-directed mutagenesis analysis showed that the improved stability of the enzyme can be attributed to the amino acid substitution of V166A. The half-lives of the V166A mutant were 11- and 6.1-times longer than those of the wild type at 50°C in the presence and absence, respectively, of 20% (v/v) dimethyl sulfoxide. No significant differences in the substrate specificity and enantio-selectivity of the enzyme were observed. The mutant enzyme converted 60 mM 2,2,2-trifluoroacetophenone to (R)-(-)-α-(trifluoromethyl)benzyl alcohol in a molar yield of 71% whereas the conversion yield with an equivalent concentration of the wild-type enzyme was 27%.
Collapse
Affiliation(s)
- Kohsuke Honda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Mizuha Inoue
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tomohiro Ono
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kenji Okano
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yasumasa Dekishima
- Mitsubishi Chemical Group Science and Technology Research Center, Inc., 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-8502, Japan
| | - Hiroshi Kawabata
- Mitsubishi Chemical Group Science and Technology Research Center, Inc., 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-8502, Japan
| |
Collapse
|
11
|
Francis D, Winn M, Latham J, Greaney MF, Micklefield J. An Engineered Tryptophan Synthase Opens New Enzymatic Pathways to β-Methyltryptophan and Derivatives. Chembiochem 2017; 18:382-386. [PMID: 28005309 DOI: 10.1002/cbic.201600471] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Indexed: 01/23/2023]
Abstract
β-Methyltryptophans (β-mTrp) are precursors in the biosynthesis of bioactive natural products and are used in the synthesis of peptidomimetic-based therapeutics. Currently β-mTrp is produced by inefficient multistep synthetic methods. Here we demonstrate how an engineered variant of tryptophan synthase from Salmonella (StTrpS) can catalyse the efficient condensation of l-threonine and various indoles to generate β-mTrp and derivatives in a single step. Although l-serine is the natural substrate for TrpS, targeted mutagenesis of the StTrpS active site provided a variant (βL166V) that can better accommodate l-Thr as a substrate. The condensation of l-Thr and indole proceeds with retention of configuration at both α- and β-positions to give (2S,3S)-β-mTrp. The integration of StTrpS (βL166V) with l-amino acid oxidase, halogenase enzymes and palladium chemocatalysts provides access to further d-configured and regioselectively halogenated or arylated β-mTrp derivatives.
Collapse
Affiliation(s)
- Daniel Francis
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Michael Winn
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Jonathan Latham
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Michael F Greaney
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Jason Micklefield
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| |
Collapse
|
12
|
Boyken SE, Chopra N, Xie Q, Joseph RE, Wales TE, Fulton DB, Engen JR, Jernigan RL, Andreotti AH. A conserved isoleucine maintains the inactive state of Bruton's tyrosine kinase. J Mol Biol 2014; 426:3656-69. [PMID: 25193673 DOI: 10.1016/j.jmb.2014.08.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 08/22/2014] [Accepted: 08/23/2014] [Indexed: 12/22/2022]
Abstract
Despite high level of homology among non-receptor tyrosine kinases, different kinase families employ a diverse array of regulatory mechanisms. For example, the catalytic kinase domains of the Tec family kinases are inactive without assembly of the adjacent regulatory domains, whereas the Src kinase domains are autoinhibited by the assembly of similar adjacent regulatory domains. Using molecular dynamics simulations, biochemical assays, and biophysical approaches, we have uncovered an isoleucine residue in the kinase domain of the Tec family member Btk that, when mutated to the closely related leucine, leads to a shift in the conformational equilibrium of the kinase domain toward the active state. The single amino acid mutation results in measureable catalytic activity for the Btk kinase domain in the absence of the regulatory domains. We suggest that this isoleucine side chain in the Tec family kinases acts as a "wedge" that restricts the conformational space available to key regions in the kinase domain, preventing activation until the kinase domain associates with its regulatory subunits and overcomes the energetic barrier to activation imposed by the isoleucine side chain.
Collapse
Affiliation(s)
- Scott E Boyken
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Nikita Chopra
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Qian Xie
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Raji E Joseph
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - D Bruce Fulton
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Robert L Jernigan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Amy H Andreotti
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| |
Collapse
|
13
|
Minakuchi K, Murata D, Okubo Y, Nakano Y, Yoshida S. Remarkable alkaline stability of an engineered protein A as immunoglobulin affinity ligand: C domain having only one amino acid substitution. Protein Sci 2013; 22:1230-8. [PMID: 23868198 DOI: 10.1002/pro.2310] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 07/04/2013] [Accepted: 07/05/2013] [Indexed: 01/19/2023]
Abstract
Protein A affinity chromatography is the standard purification process for the capture of therapeutic antibodies. The individual IgG-binding domains of protein A (E, D, A, B, C) have highly homologous amino acid sequences. From a previous report, it has been assumed that the C domain has superior resistance to alkaline conditions compared to the other domains. We investigated several properties of the C domain as an IgG-Fc capture ligand. Based on cleavage site analysis of a recombinant protein A using a protein sequencer, the C domain was found to be the only domain to have neither of the potential alkaline cleavage sites. Circular dichroism (CD) analysis also indicated that the C domain has good physicochemical stability. Additionally, we evaluated the amino acid substitutions at the Gly-29 position of the C domain, as the Z domain (an artificial B domain) acquired alkaline resistance through a G29A mutation. The G29A mutation proved to increase the alkaline resistance of the C domain, based on BIACORE analysis, although the improvement was significantly smaller than that observed for the B domain. Interestingly, a number of other amino acid mutations at the same position increased alkaline resistance more than did the G29A mutation. This result supports the notion that even a single mutation on the originally alkali-stable C domain would improve its alkaline stability. An engineered protein A based on this C domain is expected to show remarkable performance as an affinity ligand for immunoglobulin.
Collapse
Affiliation(s)
- Kazunobu Minakuchi
- Frontier Biochemical and Medical Research Laboratories, Kaneka Corp., 1-8 Miyamae-cho, Takasago-cho, Takasago, Hyogo, 676-8688, Japan
| | | | | | | | | |
Collapse
|
14
|
Pandey AK, Naduthambi D, Thomas KM, Zondlo NJ. Proline editing: a general and practical approach to the synthesis of functionally and structurally diverse peptides. Analysis of steric versus stereoelectronic effects of 4-substituted prolines on conformation within peptides. J Am Chem Soc 2013; 135:4333-63. [PMID: 23402492 PMCID: PMC4209921 DOI: 10.1021/ja3109664] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Functionalized proline residues have diverse applications. Herein we describe a practical approach, proline editing, for the synthesis of peptides with stereospecifically modified proline residues. Peptides are synthesized by standard solid-phase peptide synthesis to incorporate Fmoc-hydroxyproline (4R-Hyp). In an automated manner, the Hyp hydroxyl is protected and the remainder of the peptide synthesized. After peptide synthesis, the Hyp protecting group is orthogonally removed and Hyp selectively modified to generate substituted proline amino acids, with the peptide main chain functioning to "protect" the proline amino and carboxyl groups. In a model tetrapeptide (Ac-TYPN-NH2), 4R-Hyp was stereospecifically converted to 122 different 4-substituted prolyl amino acids, with 4R or 4S stereochemistry, via Mitsunobu, oxidation, reduction, acylation, and substitution reactions. 4-Substituted prolines synthesized via proline editing include incorporated structured amino acid mimetics (Cys, Asp/Glu, Phe, Lys, Arg, pSer/pThr), recognition motifs (biotin, RGD), electron-withdrawing groups to induce stereoelectronic effects (fluoro, nitrobenzoate), handles for heteronuclear NMR ((19)F:fluoro; pentafluorophenyl or perfluoro-tert-butyl ether; 4,4-difluoro; (77)SePh) and other spectroscopies (fluorescence, IR: cyanophenyl ether), leaving groups (sulfonate, halide, NHS, bromoacetate), and other reactive handles (amine, thiol, thioester, ketone, hydroxylamine, maleimide, acrylate, azide, alkene, alkyne, aryl halide, tetrazine, 1,2-aminothiol). Proline editing provides access to these proline derivatives with no solution-phase synthesis. All peptides were analyzed by NMR to identify stereoelectronic and steric effects on conformation. Proline derivatives were synthesized to permit bioorthogonal conjugation reactions, including azide-alkyne, tetrazine-trans-cyclooctene, oxime, reductive amination, native chemical ligation, Suzuki, Sonogashira, cross-metathesis, and Diels-Alder reactions. These proline derivatives allowed three parallel bioorthogonal reactions to be conducted in one solution.
Collapse
Affiliation(s)
- Anil K. Pandey
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
| | - Devan Naduthambi
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
| | - Krista M. Thomas
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
| |
Collapse
|
15
|
Brown AM, Zondlo NJ. A propensity scale for type II polyproline helices (PPII): aromatic amino acids in proline-rich sequences strongly disfavor PPII due to proline-aromatic interactions. Biochemistry 2012; 51:5041-51. [PMID: 22667692 DOI: 10.1021/bi3002924] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Type II polyproline helices (PPII) are a fundamental secondary structure of proteins, common in globular and nonglobular regions and important in cellular signaling. We developed a propensity scale for PPII using a host-guest system with sequence Ac-GPPXPPGY-NH(2), where X represents any amino acid. We found that proline has the highest PPII propensity, but most other amino acids display significant PPII propensities. The PPII propensity of leucine was the highest of all propensities of non-proline residues. Alanine and residues with linear side chains displayed the next highest PPII propensities. Three classes of residues displayed lower PPII propensities: β-branched amino acids (Thr, Val, and Ile), short amino acids with polar side chains (Asn, protonated Asp, Ser, Thr, and Cys), and aromatic amino acids (Phe, Tyr, and Trp). tert-Leucine particularly disfavored PPII. The basis of the low PPII propensities of aromatic amino acids in this context was significant cis-trans isomerism, with proline-rich peptides containing aromatic residues exhibiting 45-60% cis amide bonds, due to Pro-cis-Pro-aromatic and aromatic-cis-Pro amide bonds.
Collapse
Affiliation(s)
- Alaina M Brown
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | | |
Collapse
|
16
|
Ding H, Portilla-Arias J, Patil R, Black KL, Ljubimova JY, Holler E. The optimization of polymalic acid peptide copolymers for endosomolytic drug delivery. Biomaterials 2011; 32:5269-78. [PMID: 21514661 PMCID: PMC4110056 DOI: 10.1016/j.biomaterials.2011.03.073] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 03/29/2011] [Indexed: 11/29/2022]
Abstract
Membranolytic macromolecules are promising vehicles for cytoplasmic drug delivery, but their efficiency and safety remains primary concerns. To address those concerns, membranolytic properties of various poly(β-L-malic acid) (PMLA) copolymers were extensively investigated as a function of concentration and pH. PMLA, a naturally occurring biodegradable polymer, acquires membranolytic activities after substitution of pendent carboxylates with hydrophobic amino acid derivatives. Ruled by hydrophobization and charge neutralization, membranolysis of PMLA copolymers increased as a function of polymer molecular weight and demonstrated a maximum with 50% substitution of carboxylates. Charge neutralization was achieved either conditionally by pH-dependent protonation or permanently by masking carboxylates. Membranolysis of PMLA copolymers containing tripeptides of leucine, tryptophan and phenylalanine were pH-dependent in contrast to pH-independent copolymers of Leucine ethyl ester and Leu-Leu-Leu-NH(2) with permanent charge neutralization. PMLA and tripeptides seemed a unique combination for pH-dependent membranolysis. In contrast to nontoxic pH-dependent PMLA copolymers, pH-independent copolymers were found toxic at high concentration, which is ascribed to their nonspecific disruption of plasma membrane at physiological pH. pH-Dependent copolymers were membranolytically active only at acidic pH typical of maturating endosomes, and are thus devoid of cytotoxicity. The PMLA tripeptide copolymers are useful for safe and efficient cytoplasmic delivery routed through endosome.
Collapse
Affiliation(s)
- Hui Ding
- Department of Neurosurgery, Cedars-Sinai Medical Center, 110 N. George Burns Rd, Davis 2094A, Los Angeles, CA 90048, USA.
| | | | | | | | | | | |
Collapse
|
17
|
Hawwa R, Aikens J, Turner RJ, Santarsiero BD, Mesecar AD. Structural basis for thermostability revealed through the identification and characterization of a highly thermostable phosphotriesterase-like lactonase from Geobacillus stearothermophilus. Arch Biochem Biophys 2009; 488:109-20. [PMID: 19615330 DOI: 10.1016/j.abb.2009.06.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 06/05/2009] [Accepted: 06/09/2009] [Indexed: 11/18/2022]
Abstract
A new enzyme homologous to phosphotriesterase was identified from the bacterium Geobacillus stearothermophilus (GsP). This enzyme belongs to the amidohydrolase family and possesses the ability to hydrolyze both lactone and organophosphate (OP) compounds, making it a phosphotriesterase-like lactonase (PLL). GsP possesses higher OP-degrading activity than recently characterized PLLs, and it is extremely thermostable. GsP is active up to 100 degrees C with an energy of activation of 8.0 kcal/mol towards ethyl paraoxon, and it can withstand an incubation temperature of 60 degrees C for two days. In an attempt to understand the thermostability of PLLs, the X-ray structure of GsP was determined and compared to those of existing PLLs. Based upon a comparative analysis, a new thermal advantage score and plot was developed and reveals that a number of different factors contribute to the thermostability of PLLs.
Collapse
Affiliation(s)
- Renda Hawwa
- Department of Medicinal Chemistry and Pharmacognosy and the Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, USA
| | | | | | | | | |
Collapse
|
18
|
Katritzky AR, Haase DN, Johnson JV, Chung A. Benzotriazole-Assisted Solid-Phase Assembly of Leu-Enkephalin, Amyloid β segment 34−42, and other “Difficult” Peptide Sequences. J Org Chem 2009; 74:2028-32. [DOI: 10.1021/jo8026214] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alan R. Katritzky
- Center for Heterocyclic Compounds and Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, and PROTEOMICS, Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida, Gainesville, Florida 32611-1376
| | - Danniebelle N. Haase
- Center for Heterocyclic Compounds and Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, and PROTEOMICS, Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida, Gainesville, Florida 32611-1376
| | - Jodie V. Johnson
- Center for Heterocyclic Compounds and Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, and PROTEOMICS, Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida, Gainesville, Florida 32611-1376
| | - Alfred Chung
- Center for Heterocyclic Compounds and Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, and PROTEOMICS, Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida, Gainesville, Florida 32611-1376
| |
Collapse
|
19
|
Ihm Y, Sparks WO, Lee JH, Cao H, Carpenter S, Wang CZ, Ho KM, Dobbs D. Structural model of the Rev regulatory protein from equine infectious anemia virus. PLoS One 2009; 4:e4178. [PMID: 19137065 PMCID: PMC2613556 DOI: 10.1371/journal.pone.0004178] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Accepted: 12/03/2008] [Indexed: 11/23/2022] Open
Abstract
Rev is an essential regulatory protein in the equine infectious anemia virus (EIAV) and other lentiviruses, including HIV-1. It binds incompletely spliced viral mRNAs and shuttles them from the nucleus to the cytoplasm, a critical prerequisite for the production of viral structural proteins and genomic RNA. Despite its important role in production of infectious virus, the development of antiviral therapies directed against Rev has been hampered by the lack of an experimentally-determined structure of the full length protein. We have used a combined computational and biochemical approach to generate and evaluate a structural model of the Rev protein. The modeled EIAV Rev (ERev) structure includes a total of 6 helices, four of which form an anti-parallel four-helix bundle. The first helix contains the leucine-rich nuclear export signal (NES). An arginine-rich RNA binding motif, RRDRW, is located in a solvent-exposed loop region. An ERLE motif required for Rev activity is predicted to be buried in the core of modeled structure where it plays an essential role in stabilization of the Rev fold. This structural model is supported by existing genetic and functional data as well as by targeted mutagenesis of residues predicted to be essential for overall structural integrity. Our predicted structure should increase understanding of structure-function relationships in Rev and may provide a basis for the design of new therapies for lentiviral diseases.
Collapse
Affiliation(s)
- Yungok Ihm
- Department of Physics and Astronomy, Iowa State University, Ames, IA, USA.
| | | | | | | | | | | | | | | |
Collapse
|
20
|
Oyedotun KS, Sit CS, Lemire BD. The Saccharomyces cerevisiae succinate dehydrogenase does not require heme for ubiquinone reduction. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:1436-45. [PMID: 18028869 DOI: 10.1016/j.bbabio.2007.09.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Revised: 08/09/2007] [Accepted: 09/10/2007] [Indexed: 11/26/2022]
Abstract
The coupling of succinate oxidation to the reduction of ubiquinone by succinate dehydrogenase (SDH) constitutes a pivotal reaction in the aerobic generation of energy. In Saccharomyces cerevisiae, SDH is a tetramer composed of a catalytic dimer comprising a flavoprotein subunit, Sdh1p and an iron-sulfur protein, Sdh2p and a heme b-containing membrane-anchoring dimer comprising the Sdh3p and Sdh4p subunits. In order to investigate the role of heme in SDH catalysis, we constructed an S. cerevisiae strain expressing a mutant enzyme lacking the two heme axial ligands, Sdh3p His-106 and Sdh4p Cys-78. The mutant enzyme was characterized for growth on a non-fermentable carbon source, for enzyme assembly, for succinate-dependent quinone reduction and for its heme b content. Replacement of both Sdh3p His-106 and Sdh4p Cys-78 with alanine residues leads to an undetectable level of cytochrome b(562). Although enzyme assembly is slightly impaired, the apocytochrome SDH retains a significant ability to reduce quinone. The enzyme has a reduced affinity for quinone and its catalytic efficiency is reduced by an order of magnitude. To better understand the effects of the mutations, we employed atomistic molecular dynamic simulations to investigate the enzyme's structure and stability in the absence of heme. Our results strongly suggest that heme is not required for electron transport from succinate to quinone nor is it necessary for assembly of the S. cerevisiae SDH.
Collapse
Affiliation(s)
- Kayode S Oyedotun
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | | | | |
Collapse
|
21
|
Formaggio F, Baldini C, Moretto V, Crisma M, Kaptein B, Broxterman QB, Toniolo C. Preferred Conformations of Peptides Containingtert-Leucine, a Sterically Demanding, Lipophilic ?-Amino Acid with a Quaternary Side-Chain C? Atom. Chemistry 2005; 11:2395-404. [PMID: 15669065 DOI: 10.1002/chem.200400892] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Terminally protected homopeptides of tert-leucine, from the dimer to the hexamer, co-oligopeptides of tert-leucine in combination with alpha-aminoisobutyric acid or glycine residues up to the hexamer level, and simple dipeptides representing known scaffolds for catalysts in asymmetric organic reactions were prepared by solution methods and fully characterized. The results of conformation analysis, performed by use of FT-IR absorption, NMR, CD, and X-ray diffraction techniques, indicate that this hydrophobic alpha-amino acid with tetrasubstitution at the Cbeta atom is structurally versatile. We show that it prefers extended or semiextended conformations, but can also be accommodated in folded structures, provided that these are biased by the presence of helicogenic residues. The current large-scale production of Tle, combined with its conformational preferences unravelled in this work, should make this bulky, hydrophobic, Calpha-trisubstituted alpha-amino acid a regular building block of any strategy seeking to tailor peptides with improved catalytic and pharmacological properties.
Collapse
Affiliation(s)
- Fernando Formaggio
- Institute of Biomolecular Chemistry, CNR, and Department of Chemistry, University of Padova, via Marzolo 1, 35131 Padova, Italy.
| | | | | | | | | | | | | |
Collapse
|
22
|
Abstract
We describe the NMR structure of a deletion mutant of the B1 IgG-binding domain from Group G Streptococcus. The deletion occurs within the last beta-strand of the protein, where it may potentially have a deleterious effect on the stability of the protein if the protein were not able to conformationally adjust to the perturbation. In particular, the deletion changes the registry of the final three residues in the sheet, forcing a polar Thr to be buried in the interior of the protein and exposing a hydrophobic Val to solvent. The deletion could also potentially create a large cavity in the beta-sheet and force the alpha- and gamma-carboxylates of the C-terminal Glu residue into a partially buried region of the sheet. The structure of the mutant illustrates how the conformation of the protein adjusts to the deletion, thereby mitigating some of the potentially deleterious consequences. Although the elements of secondary structure are retained between the mutant and the wt domain, there are multiple small adjustments in the segments connecting secondary structure elements. In particular, a hydrogen bond between the Glu57 carboxylates and two main chain amides is introduced that alters the conformation in the loop connecting the helix to strand 3. In addition, to minimize hydrophobic surface exposure, the turn connecting strands 1 and 2 folds toward the core so that the molecular volume is decreased.
Collapse
Affiliation(s)
- K T O'Neil
- Department of Biochemistry and Biophysics, The University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania, USA
| | | | | |
Collapse
|
23
|
Kono H, Saito M, Sarai A. Stability analysis for the cavity-filling mutations of the Myb DNA-binding domain utilizing free-energy calculations. Proteins 2000; 38:197-209. [PMID: 10656266 DOI: 10.1002/(sici)1097-0134(20000201)38:2<197::aid-prot8>3.0.co;2-b] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We have analyzed the effect of cavity-filling mutations on protein stability by means of free-energy calculations based on molecular dynamics simulations to identify the factors contributing to stability changes caused by the mutations. We have studied the DNA-binding domain of Myb, which has a cavity in one of three homologous repeat units, and analyzed a series of mutations with nonnatural and natural amino acids at a single site, which change the size of the cavity. We found that the calculated free-energy changes caused by the mutations are in excellent agreement with experimental data (correlation coefficient 0.98). The free-energy changes in the native and denatured states were independently compared with the unfolding free-energy change (deltadeltaG) and cavity-volume changes (deltaV), and it was found that deltadeltaG and deltaV correlate with the native-state free-energy changes but not with the denatured-state free-energy changes. Further analyses in terms of enthalpy and entropy show that compensation between entropy and enthalpy occurs in the denatured state but not in the native state. The main contribution to the native-state free energy was found to be van der Waals interactions associated with the cavity. We estimate that the decrease in free energy per methylene group, which results from filling the cavity, is about 2 to 3 kcal/mol. These results suggest that the stabilization of a protein by cavity-filling mutations be determined primarily by the free energy associated with the cavity volume in the native state.
Collapse
Affiliation(s)
- H Kono
- Tsukuba Life Science Center, The Institute of Physical & Chemical Research (RIKEN), Ibaraki, Japan
| | | | | |
Collapse
|
24
|
|
25
|
|
26
|
Sisido M, Hohsaka T. Extension of Protein Functions by the Incorporation of Nonnatural Amino Acids. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1999. [DOI: 10.1246/bcsj.72.1409] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
27
|
|
28
|
Affiliation(s)
- N R Kallenbach
- Department of Chemistry, New York University, New York 10003, USA
| | | |
Collapse
|
29
|
Rao SN, Chan MF, Balaji VN. Conformational Studies Using Molecular Mechanics on Model Peptides with 1-Aminocycloalkane 1-Carboxylic Acid Residues. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1997. [DOI: 10.1246/bcsj.70.293] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
30
|
Cornish VW, Mendel D, Schultz PG. Untersuchungen von Struktur und Funktion von Proteinen mit einem erweiterten genetischen Code. Angew Chem Int Ed Engl 1995. [DOI: 10.1002/ange.19951070604] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|