1
|
John EA, Riel AMS, Wieske LHE, Ray D, Decato DA, Boller M, Takacs Z, Erdélyi M, Bryantsev VS, Berryman OB. Taming Molecular Folding: Anion-Templated Foldamers with Tunable Quaternary Structures. J Am Chem Soc 2024. [PMID: 38842125 DOI: 10.1021/jacs.3c14820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Higher-order foldamers represent a unique class of supramolecules at the forefront of molecular design. Herein we control quaternary folding using a novel approach that combines halogen bonding (XBing) and hydrogen bonding (HBing). We present the first anion-templated double helices induced by halogen bonds (XBs) and stabilized by "hydrogen bond enhanced halogen bonds" (HBeXBs). Our findings demonstrate that the number and orientation of hydrogen bond (HB) and XB donors significantly affect the quaternary structure and guest selectivity of two similar oligomers. This research offers new design elements to engineer foldamers and tailor their quaternary structure for specific guest binding.
Collapse
Affiliation(s)
- Eric A John
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
| | - Asia Marie S Riel
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
| | - Lianne H E Wieske
- Department of Chemistry─BMC, Organic Chemistry, Uppsala University, Husargatan 3, 752 37 Uppsala, Sweden
| | - Debmalya Ray
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Daniel A Decato
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
| | - Madeleine Boller
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
| | - Zoltan Takacs
- Swedish NMR Center, University of Gothenburg, Gothenburg SE-405 30, Sweden
| | - Máté Erdélyi
- Department of Chemistry─BMC, Organic Chemistry, Uppsala University, Husargatan 3, 752 37 Uppsala, Sweden
| | - Vyacheslav S Bryantsev
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Orion B Berryman
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
| |
Collapse
|
2
|
Olgenblum GI, Hutcheson BO, Pielak GJ, Harries D. Protecting Proteins from Desiccation Stress Using Molecular Glasses and Gels. Chem Rev 2024; 124:5668-5694. [PMID: 38635951 PMCID: PMC11082905 DOI: 10.1021/acs.chemrev.3c00752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 04/20/2024]
Abstract
Faced with desiccation stress, many organisms deploy strategies to maintain the integrity of their cellular components. Amorphous glassy media composed of small molecular solutes or protein gels present general strategies for protecting against drying. We review these strategies and the proposed molecular mechanisms to explain protein protection in a vitreous matrix under conditions of low hydration. We also describe efforts to exploit similar strategies in technological applications for protecting proteins in dry or highly desiccated states. Finally, we outline open questions and possibilities for future explorations.
Collapse
Affiliation(s)
- Gil I. Olgenblum
- Institute
of Chemistry, Fritz Haber Research Center, and The Harvey M. Krueger
Family Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
| | - Brent O. Hutcheson
- Department
of Chemistry, University of North Carolina
at Chapel Hill (UNC-CH), Chapel
Hill, North Carolina 27599, United States
| | - Gary J. Pielak
- Department
of Chemistry, University of North Carolina
at Chapel Hill (UNC-CH), Chapel
Hill, North Carolina 27599, United States
- Department
of Chemistry, Department of Biochemistry & Biophysics, Integrated
Program for Biological & Genome Sciences, Lineberger Comprehensive
Cancer Center, University of North Carolina
at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Daniel Harries
- Institute
of Chemistry, Fritz Haber Research Center, and The Harvey M. Krueger
Family Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
| |
Collapse
|
3
|
Wang G. Cold unfolding of heat-responsive TRPV3. RESEARCH SQUARE 2024:rs.3.rs-4285061. [PMID: 38746116 PMCID: PMC11092857 DOI: 10.21203/rs.3.rs-4285061/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The homotetrameric thermosensitive transient receptor potential vanilloid 1-4 (TRPV1-4) channels in sensory neurons are strongly responsive to heat stimuli. However, their cold activations have not been reported in line with the nonzero heat capacity difference during heat or cold unfolding transitions. Here, along with the experimental examinations of the predicted ring size changes in different domains against the central pore during channel gating at various temperatures, the K169A mutant of reduced human TRPV3 was first found to be activated and inactivated by cold below 42°C. Further thermoring analyses revealed distinct heat and cold unfolding pathways, which resulted in different protein thermostabilities. Thus, both cold and heat unfolding transitions of thermosensitive TRPV1-4 channels may exist once a mutation destabilizes the closed state.
Collapse
|
4
|
Zhou Q, Huang D, Yang H, Hong Z, Wang C. Improvement of Carotenoids' Production by Increasing the Activity of Beta-Carotene Ketolase with Different Strategies. Microorganisms 2024; 12:377. [PMID: 38399781 PMCID: PMC10891602 DOI: 10.3390/microorganisms12020377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Canthaxanthin is an important antioxidant with wide application prospects, and β-carotene ketolase is the key enzyme involved in the biosynthesis of canthaxanthin. However, the challenge for the soluble expression of β-carotene ketolase is that it hinders the large-scale production of carotenoids such as canthaxanthin and astaxanthin. Hence, this study employed several strategies aiming to improve the soluble expression of β-carotene ketolase and its activity, including selecting optimal expression vectors, screening induction temperatures, adding soluble expression tags, and adding a molecular chaperone. Results showed that all these strategies can improve the soluble expression and activity of β-carotene ketolase in Escherichia coli. In particular, the production of soluble β-carotene ketolase was increased 8 times, with a commercial molecular chaperon of pG-KJE8, leading to a 1.16-fold enhancement in the canthaxanthin production from β-carotene. Interestingly, pG-KJE8 could also enhance the soluble expression of β-carotene ketolase derived from eukaryotic microalgae. Further research showed that the production of canthaxanthin and echinenone was significantly improved by as many as 30.77 times when the pG-KJE8 was added, indicating the molecular chaperone performed differently among different β-carotene ketolase. This study not only laid a foundation for further research on the improvement of β-carotene ketolase activity but also provided new ideas for the improvement of carotenoid production.
Collapse
Affiliation(s)
- Qiaomian Zhou
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (Q.Z.); (D.H.)
| | - Danqiong Huang
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (Q.Z.); (D.H.)
- Shenzhen Engineering Laboratory for Marine Algal Biological Development and Application, Shenzhen 518060, China
| | - Haihong Yang
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (Q.Z.); (D.H.)
| | - Zeyu Hong
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (Q.Z.); (D.H.)
| | - Chaogang Wang
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (Q.Z.); (D.H.)
- Shenzhen Engineering Laboratory for Marine Algal Biological Development and Application, Shenzhen 518060, China
| |
Collapse
|
5
|
Burra VLSP, Sahoo PS, Dhankhar A, Jhajj J, Kasamuthu PS, K SSVK, Macha SKR. Understanding the structural basis of the binding specificity of c-di-AMP to M. smegmatis RecA using computational biology approach. J Biomol Struct Dyn 2024; 42:2043-2057. [PMID: 38093709 DOI: 10.1080/07391102.2023.2227709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/09/2023] [Indexed: 02/21/2024]
Abstract
Mycobacterium tuberculosis RecA (MtRecA), a protein involved in DNA repair, homologous recombination and SOS pathway, contributes to the development of multidrug resistance. ATP binding-site in RecA has been a drug target to disable RecA dependent DNA repair. For the first time, experiments have shown the existence and binding of c-di-AMP to a novel allosteric site in the C-terminal-Domain (CTD) of Mycobacterium smegmatis RecA (MsRecA), a close homolog of MtRecA. In addition, it was observed that the c-di-AMP was not binding to Escherichia coli RecA (EcRecA). This article analyses the possible interactions of the three RecA homologs with the various c-di-AMP conformations to gain insights into the structural basis of the natural preference of c-di-AMP to MsRecA and not to EcRecA, using the structural biology tools. The comparative analysis, based on amino acid composition, homology, motifs, residue types, docking, molecular dynamics simulations and binding free energy calculations, indeed, conclusively indicates strong binding of c-di-AMP to MsRecA. Having very similar results as MsRecA, it is highly plausible for c-di-AMP to strongly bind MtRecA as well. These insights from the in-silico studies adds a new therapeutic approach against TB through design and development of novel allosteric inhibitors for the first time against MtRecA.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- V L S Prasad Burra
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
| | - Partha Sarathi Sahoo
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
| | - Amit Dhankhar
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
| | - Jatinder Jhajj
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
| | - Prasanna Sudharson Kasamuthu
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
| | - S S V Kiran K
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
| | - Samuel Krupa Rakshan Macha
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
| |
Collapse
|
6
|
Majou D, Dermenghem AL. Effects of DHA (omega-3 fatty acid) and estradiol on amyloid β-peptide regulation in the brain. Brain Res 2024; 1823:148681. [PMID: 37992797 DOI: 10.1016/j.brainres.2023.148681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/24/2023]
Abstract
In the early stages of sporadic Alzheimer's disease (SAD), there is a strong correlation between memory impairment and cortical levels of soluble amyloid-β peptide oligomers (Aβ). It has become clear that Aβ disrupt glutamatergic synaptic function, which can in turn lead to the characteristic cognitive deficits of SAD, but the actual pathways are still not well understood. This opinion article describes the pathogenic mechanisms underlying cerebral amyloidosis. These mechanisms are dependent on the amyloid precursor protein and concern the synthesis of Aβ peptides with competition between the non-amyloidogenic pathway and the amyloidogenic pathway (i.e. a competition between the ADAM10 and BACE1 enzymes), on the one hand, and the various processes of Aβ residue clearance, on the other hand. This clearance mobilizes both endopeptidases (NEP, and IDE) and removal transporters across the blood-brain barrier (LRP1, ABCB1, and RAGE). Lipidated ApoE also plays a major role in all processes. The disturbance of these pathways induces an accumulation of Aβ. The description of the mechanisms reveals two key molecules in particular: (i) free estradiol, which has genomic and non-genomic action, and (ii) free DHA as a preferential ligand of PPARα-RXRα and PPARɣ-RXRα heterodimers. DHA and free estradiol are also self-regulating, and act in synergy. When a certain level of chronic DHA and free estradiol deficiency is reached, a permanent imbalance is established in the central nervous system. The consequences of these deficits are revealed in particular by the presence of Aβ peptide deposits, as well as other markers of the etiology of SAD.
Collapse
Affiliation(s)
- Didier Majou
- ACTIA, 149, rue de Bercy, 75595 Paris Cedex 12, France.
| | | |
Collapse
|
7
|
Lee J, Sim KM, Kang M, Oh HJ, Choi HJ, Kim YE, Pack CG, Kim K, Kim KM, Oh SH, Kim I, Chang I. Understanding the molecular mechanism of pathogenic variants of BIR2 domain in XIAP-deficient inflammatory bowel disease. Sci Rep 2024; 14:853. [PMID: 38191507 PMCID: PMC10774423 DOI: 10.1038/s41598-023-50932-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/28/2023] [Indexed: 01/10/2024] Open
Abstract
X-linked inhibitor of apoptosis protein (XIAP) deficiency causes refractory inflammatory bowel disease. The XIAP protein plays a pivotal role in the pro-inflammatory response through the nucleotide-binding oligomerization domain-containing signaling pathway that is important in mucosal homeostasis. We analyzed the molecular mechanism of non-synonymous pathogenic variants (PVs) of XIAP BIR2 domain. We generated N-terminally green fluorescent protein-tagged XIAP constructs of representative non-synonymous PVs. Co-immunoprecipitation and fluorescence cross-correlation spectroscopy showed that wild-type XIAP and RIP2 preferentially interacted in live cells, whereas all non-synonymous PV XIAPs failed to interact properly with RIP2. Structural analysis showed that various structural changes by mutations, such as hydrophobic core collapse, Zn-finger loss, and spatial rearrangement, destabilized the two loop structures (174-182 and 205-215) that critically interact with RIP2. Subsequently, it caused a failure of RIP2 ubiquitination and loss of protein deficiency by the auto-ubiquitination of all XIAP mutants. These findings could enhance our understanding of the role of XIAP mutations in XIAP-deficient inflammatory bowel disease and may benefit future therapeutic strategies.
Collapse
Affiliation(s)
- Juhwan Lee
- iProtein Therapeutics Inc., Munji-ro 281-9, Yuseong-gu, Daejeon, Korea
| | - Kyoung Mi Sim
- Department of Convergence Medicine, Asan Medical Center, Asan Institutes for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea
| | - Mooseok Kang
- iProtein Therapeutics Inc., Munji-ro 281-9, Yuseong-gu, Daejeon, Korea
| | - Hyun Ju Oh
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-Gu, Seoul, 05505, Korea
| | - Ho Jung Choi
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-Gu, Seoul, 05505, Korea
| | - Yeong Eun Kim
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-Gu, Seoul, 05505, Korea
| | - Chan-Gi Pack
- Department of Convergence Medicine, Asan Medical Center, Asan Institutes for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyunggon Kim
- Department of Convergence Medicine, Asan Medical Center, Asan Institutes for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyung Mo Kim
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-Gu, Seoul, 05505, Korea
| | - Seak Hee Oh
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-Gu, Seoul, 05505, Korea.
| | - Inki Kim
- Department of Convergence Medicine, Asan Medical Center, Asan Institutes for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea.
- Department of Pharmacology, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-Gu, Seoul, 05505, Korea.
| | - Iksoo Chang
- Creative Research Initiatives Center for Proteome Biophysics, Department of Brain Sciences and Supercomputing Bigdata Center, DGIST, Daegu, 42988, Korea.
- Department of Brain Sciences and Supercomputing Big Data Center, DGIST, Daegu, 42988, Korea.
| |
Collapse
|
8
|
Rudolph A, Nyerges A, Chiappino-Pepe A, Landon M, Baas-Thomas M, Church G. Strategies to identify and edit improvements in synthetic genome segments episomally. Nucleic Acids Res 2023; 51:10094-10106. [PMID: 37615546 PMCID: PMC10570025 DOI: 10.1093/nar/gkad692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/30/2023] [Accepted: 08/16/2023] [Indexed: 08/25/2023] Open
Abstract
Genome engineering projects often utilize bacterial artificial chromosomes (BACs) to carry multi-kilobase DNA segments at low copy number. However, all stages of whole-genome engineering have the potential to impose mutations on the synthetic genome that can reduce or eliminate the fitness of the final strain. Here, we describe improvements to a multiplex automated genome engineering (MAGE) protocol to improve recombineering frequency and multiplexability. This protocol was applied to recoding an Escherichia coli strain to replace seven codons with synonymous alternatives genome wide. Ten 44 402-47 179 bp de novo synthesized DNA segments contained in a BAC from the recoded strain were unable to complement deletion of the corresponding 33-61 wild-type genes using a single antibiotic resistance marker. Next-generation sequencing (NGS) was used to identify 1-7 non-recoding mutations in essential genes per segment, and MAGE in turn proved a useful strategy to repair these mutations on the recoded segment contained in the BAC when both the recoded and wild-type copies of the mutated genes had to exist by necessity during the repair process. Finally, two web-based tools were used to predict the impact of a subset of non-recoding missense mutations on strain fitness using protein structure and function calls.
Collapse
Affiliation(s)
- Alexandra Rudolph
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Akos Nyerges
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Anush Chiappino-Pepe
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
| | - Matthieu Landon
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - George Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
| |
Collapse
|
9
|
Agarwal A, Kant S, Bahadur RP. Efficient mapping of RNA-binding residues in RNA-binding proteins using local sequence features of binding site residues in protein-RNA complexes. Proteins 2023; 91:1361-1379. [PMID: 37254800 DOI: 10.1002/prot.26528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 04/13/2023] [Accepted: 05/02/2023] [Indexed: 06/01/2023]
Abstract
Protein-RNA interactions play vital roles in plethora of biological processes such as regulation of gene expression, protein synthesis, mRNA processing and biogenesis. Identification of RNA-binding residues (RBRs) in proteins is essential to understand RNA-mediated protein functioning, to perform site-directed mutagenesis and to develop novel targeted drug therapies. Moreover, the extensive gap between sequence and structural data restricts the identification of binding sites in unsolved structures. However, efficient use of computational methods demanding only sequence to identify binding residues can bridge this huge sequence-structure gap. In this study, we have extensively studied protein-RNA interface in known RNA-binding proteins (RBPs). We find that the interface is highly enriched in basic and polar residues with Gly being the most common interface neighbor. We investigated several amino acid features and developed a method to predict putative RBRs from amino acid sequence. We have implemented balanced random forest (BRF) classifier with local residue features of protein sequences for prediction. With 5-fold cross-validations, the sequence pattern derived dipeptide composition based BRF model (DCP-BRF) resulted in an accuracy of 87.9%, specificity of 88.8%, sensitivity of 82.2%, Mathew's correlation coefficient of 0.60 and AUC of 0.93, performing better than few existing methods. We further validated our prediction model on known human RBPs through RBR prediction and could map ~54% of them. Further, knowledge of binding site preferences obtained from computational predictions combined with experimental validations of potential RNA binding sites can enhance our understanding of protein-RNA interactions. This may serve to accelerate investigations on functional roles of many novel RBPs.
Collapse
Affiliation(s)
- Ankita Agarwal
- School of Bio Science, Indian Institute of Technology Kharagpur, Kharagpur, India
- Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Shri Kant
- Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| |
Collapse
|
10
|
Barroso M, Gertzen M, Puchwein-Schwepcke AF, Preisler H, Sturm A, Reiss DD, Danecka MK, Muntau AC, Gersting SW. Glutaryl-CoA Dehydrogenase Misfolding in Glutaric Acidemia Type 1. Int J Mol Sci 2023; 24:13158. [PMID: 37685964 PMCID: PMC10487539 DOI: 10.3390/ijms241713158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/11/2023] [Accepted: 08/19/2023] [Indexed: 09/10/2023] Open
Abstract
Glutaric acidemia type 1 (GA1) is a neurotoxic metabolic disorder due to glutaryl-CoA dehydrogenase (GCDH) deficiency. The high number of missense variants associated with the disease and their impact on GCDH activity suggest that disturbed protein conformation can affect the biochemical phenotype. We aimed to elucidate the molecular basis of protein loss of function in GA1 by performing a parallel analysis in a large panel of GCDH missense variants using different biochemical and biophysical methodologies. Thirteen GCDH variants were investigated in regard to protein stability, hydrophobicity, oligomerization, aggregation, and activity. An altered oligomerization, loss of protein stability and solubility, as well as an augmented susceptibility to aggregation were observed. GA1 variants led to a loss of enzymatic activity, particularly when present at the N-terminal domain. The reduced cellular activity was associated with loss of tetramerization. Our results also suggest a correlation between variant sequence location and cellular protein stability (p < 0.05), with a more pronounced loss of protein observed with variant proximity to the N-terminus. The broad panel of variant-mediated conformational changes of the GCDH protein supports the classification of GA1 as a protein-misfolding disorder. This work supports research toward new therapeutic strategies that target this molecular disease phenotype.
Collapse
Affiliation(s)
- Madalena Barroso
- University Children’s Research, UCR@Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.B.); (M.K.D.); (A.C.M.)
| | - Marcus Gertzen
- Department of Molecular Pediatrics, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany; (M.G.); (A.F.P.-S.); (H.P.); (A.S.); (D.D.R.)
- Psychiatry and Psychotherapy, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
| | - Alexandra F. Puchwein-Schwepcke
- Department of Molecular Pediatrics, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany; (M.G.); (A.F.P.-S.); (H.P.); (A.S.); (D.D.R.)
- Department of Pediatric Neurology and Developmental Medicine, University of Basel Children’s Hospital, 4056 Basel, Switzerland
| | - Heike Preisler
- Department of Molecular Pediatrics, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany; (M.G.); (A.F.P.-S.); (H.P.); (A.S.); (D.D.R.)
| | - Andreas Sturm
- Department of Molecular Pediatrics, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany; (M.G.); (A.F.P.-S.); (H.P.); (A.S.); (D.D.R.)
| | - Dunja D. Reiss
- Department of Molecular Pediatrics, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany; (M.G.); (A.F.P.-S.); (H.P.); (A.S.); (D.D.R.)
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, 81377 Munich, Germany
| | - Marta K. Danecka
- University Children’s Research, UCR@Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.B.); (M.K.D.); (A.C.M.)
| | - Ania C. Muntau
- University Children’s Research, UCR@Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.B.); (M.K.D.); (A.C.M.)
- University Children’s Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Søren W. Gersting
- University Children’s Research, UCR@Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.B.); (M.K.D.); (A.C.M.)
| |
Collapse
|
11
|
Szpotkowski K, Wójcik K, Kurzyńska-Kokorniak A. Structural studies of protein-nucleic acid complexes: A brief overview of the selected techniques. Comput Struct Biotechnol J 2023; 21:2858-2872. [PMID: 37216015 PMCID: PMC10195699 DOI: 10.1016/j.csbj.2023.04.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
Protein-nucleic acid complexes are involved in all vital processes, including replication, transcription, translation, regulation of gene expression and cell metabolism. Knowledge of the biological functions and molecular mechanisms beyond the activity of the macromolecular complexes can be determined from their tertiary structures. Undoubtably, performing structural studies of protein-nucleic acid complexes is challenging, mainly because these types of complexes are often unstable. In addition, their individual components may display extremely different surface charges, causing the complexes to precipitate at higher concentrations used in many structural studies. Due to the variety of protein-nucleic acid complexes and their different biophysical properties, no simple and universal guideline exists that helps scientists chose a method to successfully determine the structure of a specific protein-nucleic acid complex. In this review, we provide a summary of the following experimental methods, which can be applied to study the structures of protein-nucleic acid complexes: X-ray and neutron crystallography, nuclear magnetic resonance (NMR) spectroscopy, cryogenic electron microscopy (cryo-EM), atomic force microscopy (AFM), small angle scattering (SAS) methods, circular dichroism (CD) and infrared (IR) spectroscopy. Each method is discussed regarding its historical context, advancements over the past decades and recent years, and weaknesses and strengths. When a single method does not provide satisfactory data on the selected protein-nucleic acid complex, a combination of several methods should be considered as a hybrid approach; thus, specific structural problems can be solved when studying protein-nucleic acid complexes.
Collapse
|
12
|
Pinto MBC, Schmidt FL, Rappsilber J, Gibson B, Wietstock PC. Addition of Hop ( Humulus Lupulus L.) Bitter Acids Yields Modification of Malt Protein Aggregate Profiles during Wort Boiling. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5700-5711. [PMID: 36989404 DOI: 10.1021/acs.jafc.3c00185] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Hop bitter acids are used in the brewing industry to give beer bitterness. However, much of this bitterness is lost during processing, specifically during the wort boiling step. One of the major causes might be the interaction with protein-protein complexes. Therefore, the aim of this study was to clarify the role of hop bitter acids in protein aggregate formation using a proteomic approach. The effect of hop addition on protein composition was analyzed by liquid chromatography-mass spectrometry/MS (LC-MS/MS), and further analyses were performed to characterize the wort before and after boiling. Addition of hop bitter acids yielded a change in wort protein profiles, and hop bitter acids were found to bind primarily to less abundant proteins which are not related to beer quality traits, such as foam or haze. Wort protein aggregate profiles were revealed, and findings from this study suggested the precipitation of particular proteins in the aggregates during boiling when hops were added.
Collapse
Affiliation(s)
- Mariana B C Pinto
- Fruit, Vegetable and Confectionery Products Laboratory, Department of Food Engineering and Technology, School of Food Engineering, Universidade Estadual de Campinas, Rua Monteiro Lobato 80, 13083-862 Campinas, São Paulo, Brazil
- Chair of Brewing and Beverage Technology, Department of Food Technology and Food Chemistry, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
| | - Flavio L Schmidt
- Fruit, Vegetable and Confectionery Products Laboratory, Department of Food Engineering and Technology, School of Food Engineering, Universidade Estadual de Campinas, Rua Monteiro Lobato 80, 13083-862 Campinas, São Paulo, Brazil
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Brian Gibson
- Chair of Brewing and Beverage Technology, Department of Food Technology and Food Chemistry, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
| | - Philip C Wietstock
- Chair of Brewing and Beverage Technology, Department of Food Technology and Food Chemistry, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
| |
Collapse
|
13
|
Dutta P, Roy P, Sengupta N. Effects of External Perturbations on Protein Systems: A Microscopic View. ACS OMEGA 2022; 7:44556-44572. [PMID: 36530249 PMCID: PMC9753117 DOI: 10.1021/acsomega.2c06199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.
Collapse
Affiliation(s)
- Pallab Dutta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
| | - Priti Roy
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma74078, United States
| | - Neelanjana Sengupta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
| |
Collapse
|
14
|
Abdel-Mageed HM, Nada D, Radwan RA, Mohamed SA, Gohary NAEL. Optimization of catalytic properties of Mucor racemosus lipase through immobilization in a biocompatible alginate gelatin hydrogel matrix for free fatty acid production: a sustainable robust biocatalyst for ultrasound-assisted olive oil hydrolysis. 3 Biotech 2022; 12:285. [PMID: 36276456 PMCID: PMC9485409 DOI: 10.1007/s13205-022-03319-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 08/15/2022] [Indexed: 12/22/2022] Open
Abstract
AbstractImmobilization is a key technology that improves the operational stability of enzymes. In this study, alginate-gelatin (Alg-Gel) hydrogel matrix was synthesized and used as immobilization support for Mucor racemosus lipase (Lip). Enzyme catalyzed ultrasound-assisted hydrolysis of olive oil was also investigated. Alg-Gel matrix exhibited high entrapment efficiency (94.5%) with a degradation rate of 42% after 30 days. The hydrolysis of olive oil using Alg-Gel-Lip increased significantly (P < 0.05) as compared to free Lip. Optimum pH and temperature were determined as pH 5.0 and 40 °C, respectively. The Vmax values for free and immobilized Lip were determined to be 5.5 mM and 5.8 mM oleic acid/min/ml, respectively, and the Km values were 2.2 and 2.58 mM/ml respectively. Thermal stability was highly improved for Alg-Gel-Lip (t1/2 650 min and Ed 87.96 kJ/mol) over free Lip (t1/2 150 min and Ed 23.36 kJ/mol). The enzymatic activity of Alg-Gel-Lip was preserved at 96% after four consecutive cycles and 90% of the initial activity after storage for 60 days at 4 °C. Alg-Gel-Lip catalyzed olive oil hydrolysis using ultrasound showed a significant (P < 0.05) increase in hydrolysis rate compared to free Lip (from 0.0 to 58.2%, within the first 2 h). In contrast to traditional methodology, using ultrasonic improved temperature-dependent enzymatic catalyzed reactions and delivered greater reaction yields. Results suggest that Alg-Gel-Lip biocatalyst has great industrial application potential, particularly for free fatty acid production. In addition, the combined use of enzyme and ultrasound has the potential of eco-friendly technology.
Collapse
Affiliation(s)
| | - Dina Nada
- Pharmacology and Biochemistry Department, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt
| | - Rasha Ali Radwan
- Center for Drug Research and Development (CDRD), The British University in Egypt (BUE), Cairo, Egypt
| | - Saleh Ahmed Mohamed
- Molecular Biology Department, National Research Centre (NRC), El Behoth St Dokki, Cairo, Egypt
| | | |
Collapse
|
15
|
Sarkar D, Maity NC, Shome G, Varnava KG, Sarojini V, Vivekanandan S, Sahoo N, Kumar S, Mandal AK, Biswas R, Bhunia A. Mechanistic insight into functionally different human islet polypeptide (hIAPP) amyloid: the intrinsic role of the C-terminal structural motifs. Phys Chem Chem Phys 2022; 24:22250-22262. [PMID: 36098073 DOI: 10.1039/d2cp01650h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Targeting amyloidosis requires high-resolution insight into the underlying mechanisms of amyloid aggregation. The sequence-specific intrinsic properties of a peptide or protein largely govern the amyloidogenic propensity. Thus, it is essential to delineate the structural motifs that define the subsequent downstream amyloidogenic cascade of events. Additionally, it is important to understand the role played by extrinsic factors, such as temperature or sample agitation, in modulating the overall energy barrier that prompts divergent nucleation events. Consequently, these changes can affect the fibrillation kinetics, resulting in structurally and functionally distinct amyloidogenic conformers associated with disease pathogenesis. Here, we have focused on human Islet Polypeptide (hIAPP) amyloidogenesis for the full-length peptide along with its N- and C-terminal fragments, under different temperatures and sample agitation conditions. This helped us to gain a comprehensive understanding of the intrinsic role of specific functional epitopes in the primary structure of the peptide that regulates amyloidogenesis and subsequent cytotoxicity. Intriguingly, our study involving an array of biophysical experiments and ex vivo data suggests a direct influence of external changes on the C-terminal fibrillating sequence. Furthermore, the observations indicate a possible collaborative role of this segment in nucleating hIAPP amyloidogenesis in a physiological scenario, thus making it a potential target for future therapeutic interventions.
Collapse
Affiliation(s)
- Dibakar Sarkar
- Department of Biophysics, Bose Institute, EN 80, Sector V, Kolkata 700 091, India.
| | - Narayan Chandra Maity
- Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector-III, Salt Lake, Kolkata 700106, India
| | - Gourav Shome
- Division of Molecular Medicine, Bose Institute, EN 80, Sector V, Kolkata 700 091, India
| | - Kyriakos Gabriel Varnava
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | | | - Nirakar Sahoo
- Department of Biology, University of Texas Rio Grande Valley, Edinburg, Texas, 78539, USA
| | - Sourav Kumar
- Department of Biophysics, Bose Institute, EN 80, Sector V, Kolkata 700 091, India.
| | - Atin Kumar Mandal
- Division of Molecular Medicine, Bose Institute, EN 80, Sector V, Kolkata 700 091, India
| | - Ranjit Biswas
- Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector-III, Salt Lake, Kolkata 700106, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, EN 80, Sector V, Kolkata 700 091, India.
| |
Collapse
|
16
|
Jaswandkar SV, Katti KS, Katti DR. Molecular and structural basis of actin filament severing by ADF/cofilin. Comput Struct Biotechnol J 2022; 20:4157-4171. [PMID: 36016710 PMCID: PMC9379983 DOI: 10.1016/j.csbj.2022.07.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/30/2022] [Accepted: 07/31/2022] [Indexed: 12/04/2022] Open
Abstract
ADF/cofilin’s cooperative binding to actin filament modifies the conformation and alignment of G-actin subunits locally, causing the filament to sever at “boundaries” formed among bare and ADF/cofilin-occupied regions. Analysis of the impact of the ADF/cofilin cluster boundary on the deformation behavior of actin filaments in a mechanically strained environment is critical for understanding the biophysics of their severing. The present investigation uses molecular dynamics simulations to generate atomic resolution models of bare, partially, and fully cofilin decorated actin filaments. Steered molecular dynamics simulations are utilized to determine the mechanical properties of three filament models when subjected to axial stretching, axial compression, and bending forces. We highlight differences in strain distribution, failure mechanisms in the three filament models, and biomechanical effects of cofilin cluster boundaries in overall filament rupture. Based on the influence of ADF/cofilin binding on intrastrand and interstrand G-actin interfaces, the cofilin-mediated actin filament severing model proposed here can help understand cofilin mediated actin dynamics.
Collapse
|
17
|
Nanavare P, Choudhury AR, Sarkar S, Maity A, Chakrabarti R. Structure and Orientation of Water and Choline Chloride Molecules Around a Methane Hydrophobe: A Computer Simulation Study. Chemphyschem 2022; 23:e202200446. [DOI: 10.1002/cphc.202200446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/18/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Pooja Nanavare
- IIT Bombay: Indian Institute of Technology Bombay Department of Chemistry INDIA
| | - Asha Rani Choudhury
- IIT Bombay: Indian Institute of Technology Bombay Department of Chemistry INDIA
| | - Soham Sarkar
- TU Darmstadt: Technische Universitat Darmstadt Eduard-Zintl-Institute für Anorganische und Physikalische Chemie INDIA
| | - Atanu Maity
- IIT Bombay: Indian Institute of Technology Bombay Department of Chemistry INDIA
| | - Rajarshi Chakrabarti
- Indian Institute of Technology Bombay Chemistry Indian Institute of Technology BombayPowaiIndia 400076 Mumbai INDIA
| |
Collapse
|
18
|
Nezhad NG, Rahman RNZRA, Normi YM, Oslan SN, Shariff FM, Leow TC. Thermostability engineering of industrial enzymes through structure modification. Appl Microbiol Biotechnol 2022; 106:4845-4866. [PMID: 35804158 DOI: 10.1007/s00253-022-12067-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/25/2022] [Accepted: 07/02/2022] [Indexed: 01/14/2023]
Abstract
Thermostability is an essential requirement of enzymes in the industrial processes to catalyze the reactions at high temperatures; thus, enzyme engineering through directed evolution, semi-rational design and rational design are commonly employed to construct desired thermostable mutants. Several strategies are implemented to fulfill enzymes' thermostability demand including decreasing the entropy of the unfolded state through substitutions Gly → Xxx or Xxx → Pro, hydrogen bond, salt bridge, introducing two different simultaneous interactions through single mutant, hydrophobic interaction, filling the hydrophobic cavity core, decreasing surface hydrophobicity, truncating loop, aromatic-aromatic interaction and introducing positively charged residues to enzyme surface. In the current review, horizons about compatibility between secondary structures and substitutions at preferable structural positions to generate the most desirable thermostability in industrial enzymes are broadened. KEY POINTS: • Protein engineering is a powerful tool for generating thermostable industrial enzymes. • Directed evolution and rational design are practical approaches in enzyme engineering. • Substitutions in preferable structural positions can increase thermostability.
Collapse
Affiliation(s)
- Nima Ghahremani Nezhad
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Yahaya M Normi
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Fairolniza Mohd Shariff
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia. .,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia. .,Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
| |
Collapse
|
19
|
Bychkova VE, Dolgikh DA, Balobanov VA, Finkelstein AV. The Molten Globule State of a Globular Protein in a Cell Is More or Less Frequent Case Rather than an Exception. Molecules 2022; 27:molecules27144361. [PMID: 35889244 PMCID: PMC9319461 DOI: 10.3390/molecules27144361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 02/01/2023] Open
Abstract
Quite a long time ago, Oleg B. Ptitsyn put forward a hypothesis about the possible functional significance of the molten globule (MG) state for the functioning of proteins. MG is an intermediate between the unfolded and the native state of a protein. Its experimental detection and investigation in a cell are extremely difficult. In the last decades, intensive studies have demonstrated that the MG-like state of some globular proteins arises from either their modifications or interactions with protein partners or other cell components. This review summarizes such reports. In many cases, MG was evidenced to be functionally important. Thus, the MG state is quite common for functional cellular proteins. This supports Ptitsyn’s hypothesis that some globular proteins may switch between two active states, rigid (N) and soft (MG), to work in solution or interact with partners.
Collapse
Affiliation(s)
- Valentina E. Bychkova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (V.E.B.); (A.V.F.)
| | - Dmitry A. Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117871 Moscow, Russia;
| | - Vitalii A. Balobanov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (V.E.B.); (A.V.F.)
- Correspondence:
| | - Alexei V. Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (V.E.B.); (A.V.F.)
| |
Collapse
|
20
|
Sun Q, Fu Y, Wang W. Temperature effects on hydrophobic interactions: Implications for protein unfolding. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
21
|
Qu Y, Davey K, Sun Y, Middelberg A, Bi J. Engineered Design of the E-Helix Structure on Ferritin Nanoparticles. ACS APPLIED BIO MATERIALS 2022; 5:3167-3179. [PMID: 35770389 DOI: 10.1021/acsabm.2c00154] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Insertion of an immunogenic epitope at the C-terminus of ferritin has shown the potential to produce a stable and efficacious vaccine. There is however limited understanding of how C-terminus insertion affects ferritin protein stability. The E-helix at the C-terminus has attracted interest because there are contradictory reports as to whether it has a role in protein stabilization. Here, we report, for the first time, combining molecular dynamics simulation (MDS) with experiment to engineer the design of the E-helix at the C-terminus of engineered human ferritin heavy chain (F1) inserted with Epstein-Barr nuclear antigen 1 (EBNA1, E1) and flexible linker (L3) residues (to afford F1L3E1). Hot spots on the E-helix of the C-terminus were predicted by MDS at aa 167 (Glu) and aa 171 (Asp). Five (5) variants of F1L3E1 were constructed by considering hot spots and alteration of electrostatic or hydrophobic interfaces, namely, (1) C1, hot spots substituted with noncharged residue Gln; (2) C2, hot spots substituted with positively charged residue Arg; (3) C3, hydrophobic residues substituted with the most hydrophobic residues Val and Ile; (4) C4, hydrophobic residues substituted with the most hydrophilic residues Gln and Asn; and (5) C5, a heptad repeat structure in the E-helix disrupted by substituting "a" and "d" heptad residues with noncharged polar residue Gln. It was found that the E-helix is essential to maintain integrated protein stability and that changing the hydrophobic interface (C3 and C4) had more significant effects on protein folding and stability than changing the electrostatic interface (C1 and C2). It was confirmed by both MDS and experiment that variants C1, C2, and C5 were able to fold to form stable conformational structures with protein surface hydrophobicity similar to that of F1L3E1. However, they are less thermally stable than F1L3E1. Significant changes in hydrophobicity drove significant protein aggregation for variants C3 and C4. It is concluded that the molecular design of the C-terminus in engineered ferritin, especially the E-helix, is important to ensure the epitope-based chimeric vaccine is safe (aggregate free) and efficacious.
Collapse
Affiliation(s)
- Yiran Qu
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Kenneth Davey
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Anton Middelberg
- Division of Research and Innovation, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Jingxiu Bi
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, SA 5005, Australia
| |
Collapse
|
22
|
Norgate EL, Upton R, Hansen K, Bellina B, Brookes C, Politis A, Barran PE. Cold Denaturation of Proteins in the Absence of Solvent: Implications for Protein Storage. Angew Chem Int Ed Engl 2022; 61:e202115047. [PMID: 35313047 PMCID: PMC9325448 DOI: 10.1002/anie.202115047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Indexed: 12/12/2022]
Abstract
The effect of temperature on the stability of proteins is well explored above 298 K, but harder to track experimentally below 273 K. Variable-temperature ion mobility mass spectrometry (VT IM-MS) allows us to measure the structure of molecules at sub-ambient temperatures. Here we monitor conformational changes that occur to two isotypes of monoclonal antibodies (mAbs) on cooling by measuring their collision cross sections (CCS) at discrete drift gas temperatures from 295 to 160 K. The CCS at 250 K is larger than predicted from collisional theory and experimental data at 295 K. This restructure is attributed to change in the strength of stabilizing intermolecular interactions. Below 250 K the CCS of the mAbs increases in line with prediction implying no rearrangement. Comparing data from isotypes suggest disulfide bridging influences thermal structural rearrangement. These findings indicate that in vacuo deep-freezing minimizes denaturation and maintains the native fold and VT IM-MS measurements at sub ambient temperatures provide new insights to the phenomenon of cold denaturation.
Collapse
Affiliation(s)
- Emma L Norgate
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK
| | - Rosie Upton
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK
| | - Kjetil Hansen
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK
| | - Bruno Bellina
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK
| | - C Brookes
- Bristol-Myers Squibb, Moreton, Wirral, CH46 1QW, UK
| | - Argyris Politis
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK
| | - Perdita E Barran
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK
| |
Collapse
|
23
|
Norgate EL, Upton R, Hansen K, Bellina B, Brookes C, Politis A, Barran PE. Cold Denaturation of Proteins in the Absence of Solvent: Implications for Protein Storage. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202115047. [PMID: 38505418 PMCID: PMC10947158 DOI: 10.1002/ange.202115047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Indexed: 11/07/2022]
Abstract
The effect of temperature on the stability of proteins is well explored above 298 K, but harder to track experimentally below 273 K. Variable-temperature ion mobility mass spectrometry (VT IM-MS) allows us to measure the structure of molecules at sub-ambient temperatures. Here we monitor conformational changes that occur to two isotypes of monoclonal antibodies (mAbs) on cooling by measuring their collision cross sections (CCS) at discrete drift gas temperatures from 295 to 160 K. The CCS at 250 K is larger than predicted from collisional theory and experimental data at 295 K. This restructure is attributed to change in the strength of stabilizing intermolecular interactions. Below 250 K the CCS of the mAbs increases in line with prediction implying no rearrangement. Comparing data from isotypes suggest disulfide bridging influences thermal structural rearrangement. These findings indicate that in vacuo deep-freezing minimizes denaturation and maintains the native fold and VT IM-MS measurements at sub ambient temperatures provide new insights to the phenomenon of cold denaturation.
Collapse
Affiliation(s)
- Emma L. Norgate
- Manchester Institute of BiotechnologyUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| | - Rosie Upton
- Manchester Institute of BiotechnologyUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| | - Kjetil Hansen
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
| | - Bruno Bellina
- Manchester Institute of BiotechnologyUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| | - C. Brookes
- Bristol-Myers SquibbMoretonWirralCH46 1QWUK
| | - Argyris Politis
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
| | - Perdita E. Barran
- Manchester Institute of BiotechnologyUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| |
Collapse
|
24
|
Screening of OTULIN gene mutation with targeted next generation sequencing in Turkish populations and in silico analysis of these mutations. Mol Biol Rep 2022; 49:4643-4652. [PMID: 35294702 DOI: 10.1007/s11033-022-07312-5] [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: 12/21/2021] [Accepted: 03/01/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND OTULIN-related autoinflammatory syndrome (ORAS) is an autosomal recessive disease characterized by systemic inflammation, recurrent fever. Due to limited knowledge about the OTULIN DNA variants that cause ORAS, the diagnosis and treatment of this disease is difficult. In this study, we aim to identify OTULIN DNA variants responsible for the genetic pathology of ORAS and observe the effects of these variants on the OTULIN protein structure and the function with different bioinformatics approaches. METHODS The present study included 3230 individuals with the suspicion of an autoinflammatory disease who were referred to Ege University Children's Hospital Molecular Medicine Laboratory. OTULIN variants were detected using a panel consisting of 37 different autoinflammatory diseases (AID) genes via targeted Next-Generation Sequencing. RESULTS As a result of the study, DNA variants associated with various AID were detected in 65% of the individuals to whom the panel was applied. Among these variants, only three different OTULIN variants (p.Val82Ile, p.Gln115His and p.Leu131_Arg132insLeuCysThrGlu) were detected. The pathogenic effects of the variants detected in the OTULIN gene were determined by using Polyphen2 as "Probably Pathogenic" for the p.Val82Ile and "benign" for the p.Gln115His. At the same time, the effects of these variants on the structure and function of the OTULIN protein were investigated by in silico approaches. Both variants reduce protein stability and binding affinity. CONCLUSION The results of the current study suggest that the evaluation of OTULIN variants with in silico approaches will contribute to the development of personalized treatments by diagnosing the disease specific to the variant.
Collapse
|
25
|
Wang Y, Wang J, Zhang Z, Yang J, Turunen O, Xiong H. High-temperature behavior of hyperthermostable Thermotoga maritima xylanase XYN10B after designed and evolved mutations. Appl Microbiol Biotechnol 2022; 106:2017-2027. [PMID: 35171339 DOI: 10.1007/s00253-022-11823-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/29/2022] [Accepted: 02/05/2022] [Indexed: 11/24/2022]
Abstract
A hyperthermostable xylanase XYN10B from Thermotoga maritima (PDB code 1VBR, GenBank accession number KR078269) was subjected to site-directed and error-prone PCR mutagenesis. From the selected five mutants, the two site-directed mutants (F806H and F806V) showed a 3.3-3.5-fold improved enzyme half-life at 100 °C. The mutant XYNA generated by error-prone PCR showed slightly improved stability at 100 °C and a lower Km. In XYNB and XYNC, the additional mutations over XYNA decreased the thermostability and temperature optimum, while elevating the Km. In XYNC, two large side-chains were introduced into the protein's interior. Micro-differential scanning calorimetry (DSC) showed that the melting temperature (Tm) dropped in XYNB and XYNC from 104.9 °C to 93.7 °C and 78.6 °C, respectively. The detrimental mutations showed that extremely thermostable enzymes can tolerate quite radical mutations in the protein's interior and still retain high thermostability. The analysis of mutations (F806H and F806V) in a hydrophobic area lining the substrate-binding region indicated that active site hydrophobicity is important for high activity at extreme temperatures. Although polar His at 806 provided higher stability, the hydrophobic Phe at 806 provided higher activity than His. This study generates an understanding of how extreme thermostability and high activity are formed in GH10 xylanases. KEY POINTS: • Characterization and molecular dynamics simulations of TmXYN10B and its mutants • Explanation of structural stability of GH10 xylanase.
Collapse
Affiliation(s)
- Yawei Wang
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430048, China
| | - Jing Wang
- College of Life Science, South-central University for Nationalities, Wuhan, 430074, China
| | - Zhongqiang Zhang
- College of Life Science, South-central University for Nationalities, Wuhan, 430074, China
| | - Jiangke Yang
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430048, China
| | - Ossi Turunen
- School of Forest Sciences, University of Eastern Finland, FI-80101, Joensuu, Finland.
| | - Hairong Xiong
- College of Life Science, South-central University for Nationalities, Wuhan, 430074, China.
| |
Collapse
|
26
|
Puglisi R. Protein Mutations and Stability, a Link with Disease: The Case Study of Frataxin. Biomedicines 2022; 10:biomedicines10020425. [PMID: 35203634 PMCID: PMC8962269 DOI: 10.3390/biomedicines10020425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/16/2022] Open
Abstract
Protein mutations may lead to pathologies by causing protein misfunction or propensity to degradation. For this reason, several studies have been performed over the years to determine the capability of proteins to retain their native conformation under stress condition as well as factors to explain protein stabilization and the mechanisms behind unfolding. In this review, we explore the paradigmatic example of frataxin, an iron binding protein involved in Fe–S cluster biogenesis, and whose impairment causes a neurodegenerative disease called Friedreich’s Ataxia (FRDA). We summarize what is known about most common point mutations identified so far in heterozygous FRDA patients, their effects on frataxin structure and function and the consequences of its binding with partners.
Collapse
Affiliation(s)
- Rita Puglisi
- UK Dementia Research Institute at the Wohl Institute of King's College London, London SE59RT, UK
| |
Collapse
|
27
|
Pulavarti SVSRK, Maguire JB, Yuen S, Harrison JS, Griffin J, Premkumar L, Esposito EA, Makhatadze GI, Garcia AE, Weiss TM, Snell EH, Kuhlman B, Szyperski T. From Protein Design to the Energy Landscape of a Cold Unfolding Protein. J Phys Chem B 2022; 126:1212-1231. [PMID: 35128921 PMCID: PMC9281400 DOI: 10.1021/acs.jpcb.1c10750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding protein folding is crucial for protein sciences. The conformational spaces and energy landscapes of cold (unfolded) protein states, as well as the associated transitions, are hardly explored. Furthermore, it is not known how structure relates to the cooperativity of cold transitions, if cold and heat unfolded states are thermodynamically similar, and if cold states play important roles for protein function. We created the cold unfolding 4-helix bundle DCUB1 with a de novo designed bipartite hydrophilic/hydrophobic core featuring a hydrogen bond network which extends across the bundle in order to study the relative importance of hydrophobic versus hydrophilic protein-water interactions for cold unfolding. Structural and thermodynamic characterization resulted in the discovery of a complex energy landscape for cold transitions, while the heat unfolded state is a random coil. Below ∼0 °C, the core of DCUB1 disintegrates in a largely cooperative manner, while a near-native helical content is retained. The resulting cold core-unfolded state is compact and features extensive internal dynamics. Below -5 °C, two additional cold transitions are seen, that is, (i) the formation of a water-mediated, compact, and highly dynamic dimer, and (ii) the onset of cold helix unfolding decoupled from cold core unfolding. Our results suggest that cold unfolding is initiated by the intrusion of water into the hydrophilic core network and that cooperativity can be tuned by varying the number of core hydrogen bond networks. Protein design has proven to be invaluable to explore the energy landscapes of cold states and to robustly test related theories.
Collapse
Affiliation(s)
- Surya V S R K Pulavarti
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Jack B Maguire
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Shirley Yuen
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Joseph S Harrison
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jermel Griffin
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Edward A Esposito
- Malvern Panalytical Inc, Northhampton, Massachsetts 01060, United States
| | - George I Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 08544, United States
| | - Angel E Garcia
- Center for Non Linear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Thomas M Weiss
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center, Stanford University, Menlo Park, California 94025, United States
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, New York 14203, United States.,Department of Materials Design and Innovation, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Thomas Szyperski
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| |
Collapse
|
28
|
Sharma N, Gadhave K, Kumar P, Giri R. Transactivation domain of Adenovirus Early Region 1A (E1A): Investigating folding dynamics and aggregation. Curr Res Struct Biol 2022; 4:29-40. [PMID: 35146445 PMCID: PMC8801969 DOI: 10.1016/j.crstbi.2022.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 12/05/2021] [Accepted: 01/04/2022] [Indexed: 02/06/2023] Open
Abstract
Transactivation domain of Adenovirus Early region 1A (E1A) oncoprotein is an intrinsically disordered molecular hub protein. It is involved in binding to different domains of human cell transcriptional co-activators such as retinoblastoma (pRb), CREB-binding protein (CBP), and its paralogue p300. The conserved region 1 (TAD) of E1A is known to undergo structural transitions and folds upon interaction with transcriptional adaptor zinc finger 2 (TAZ2). Previous reports on Taz2-E1A studies have suggested the formation of helical conformations of E1A-TAD. However, the folding behavior of the TAD region in isolation has not been studied in detail. Here, we have elucidated the folding behavior of E1A peptide at varied temperatures and solution conditions. Further, we have studied the effects of macromolecular crowding on E1A-TAD peptide. Additionally, we have also predicted the molecular recognition features of E1A using MoRF predictors. The predicted MoRFs are consistent with its structural transitions observed during TAZ2 interactions for transcriptional regulation in literature. Also, as a general rule of MoRFs, E1A undergoes helical transitions in alcohol and osmolyte solution. Finally, we studied the aggregation behavior of E1A, where we observed that the E1A could form amyloid-like aggregates that are cytotoxic to mammalian cells.
Collapse
Affiliation(s)
- Nitin Sharma
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
| | - Kundlik Gadhave
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
- BioX Center, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
| |
Collapse
|
29
|
Negron C, Fang J, McPherson MJ, Stine WB, McCluskey AJ. Separating clinical antibodies from repertoire antibodies, a path to in silico developability assessment. MAbs 2022; 14:2080628. [PMID: 35771588 PMCID: PMC9255221 DOI: 10.1080/19420862.2022.2080628] [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: 11/22/2022] Open
Abstract
Approaches for antibody discovery have seen substantial improvement and success in recent years. Yet, advancing antibodies into the clinic remains difficult because therapeutic developability concerns are challenging to predict. We developed a computational model to simplify antibody developability assessment and enable accelerated early-stage screening. To this end, we quantified the ability of hundreds of sequence- and structure-based descriptors to differentiate clinical antibodies that have undergone rigorous screening and characterization for drug-like properties from antibodies in the human repertoire that are not natively paired. This analysis identified 144 descriptors capable of distinguishing clinical from repertoire antibodies. Five descriptors were selected and combined based on performance and orthogonality into a single model referred to as the Therapeutic Antibody Developability Analysis (TA-DA). On a hold-out test set, this tool separated clinical antibodies from repertoire antibodies with an AUC = 0.8, demonstrating the ability to identify developability attributes unique to clinical antibodies. Based on our results, the TA-DA score may serve as an approach for selecting lead antibodies for further development. Abbreviations: Affinity-Capture Self-Interaction Nanoparticle Spectroscopy (AC-SINS), Area Under the Curve (AUC), Complementary-Determining Region (CDR), Clinical-Stage Therapeutics (CST), Framework (FR), Monoclonal Antibodies (mAbs), Observed Antibody Space (OAS), Receiver Operating Characteristic (ROC), Size-Exclusion Chromatography (SEC), Structural Aggregation Propensity (SAP), Therapeutic Antibody Developability Analysis (TA-DA), Therapeutic Antibody Profiler (TAP), Therapeutic Structural Antibody Database (Thera-SAbDab), Variable Heavy (VH), Variable Light (VL).
Collapse
Affiliation(s)
| | - Joyce Fang
- AbbVie Bioresearch Center, Worcester, MA, USA
| | | | | | | |
Collapse
|
30
|
Zhu Z, Zhang B, Cai Q, Cao Y, Ling J, Lee K, Chen B. A critical review on the environmental application of lipopeptide micelles. BIORESOURCE TECHNOLOGY 2021; 339:125602. [PMID: 34311406 DOI: 10.1016/j.biortech.2021.125602] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
The importance of lipopeptide micelles in environmental applications has been highlighted. These vessels exhibit various sizes, shapes, and surface properties under different environmental conditions. An in-depth understanding of the tunable assembling behavior of biosurfactant micelles is of great importance for their applications. However, a systematic review of such behaviors with assorted micro/nano micellar structures under given environmental conditions, particularly under low temperature and high salinity, remains untapped. Such impacts on their environmental applications have yet to be summarized. This review tried to fill the knowledge gaps by providing a comprehensive summary of the recent knowledge advancement in genetically regulated lipopeptides production, micelles associated decontamination mechanisms in low temperature and high salinity environments, and up-to-date environmental applications. This work is expected to deliver valuable insights to guide lipopeptide design and discovery. The mechanisms concluded in this study could inspire the forthcoming research efforts in the advanced environmental application of lipopeptide micelles.
Collapse
Affiliation(s)
- Zhiwen Zhu
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL, Canada
| | - Baiyu Zhang
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL, Canada.
| | - Qinhong Cai
- Biotechnology Research Institute of the National Research Council of Canada, Montreal, QC, Canada
| | - Yiqi Cao
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL, Canada
| | - Jingjing Ling
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL, Canada
| | - Kenneth Lee
- Ecosystem Science, Fisheries and Oceans Canada, Ottawa, ON, Canada
| | - Bing Chen
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL, Canada
| |
Collapse
|
31
|
Gorenjak M, Fijačko N, Bogomir Marko P, Živanović M, Potočnik U. De novo mutation in KITLG gene causes a variant of Familial Progressive Hyper- and Hypo-pigmentation (FPHH). Mol Genet Genomic Med 2021; 9:e1841. [PMID: 34716665 PMCID: PMC8683634 DOI: 10.1002/mgg3.1841] [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] [Received: 01/20/2021] [Revised: 09/09/2021] [Accepted: 10/17/2021] [Indexed: 11/30/2022] Open
Abstract
Familial Progressive Hyper‐ and Hypopigmentation is a pigmentary disorder characterized by a mix of hypo‐ and hyperpigmented lesions, café‐au‐lait spots and hypopigmented ash‐leaf macules. The disorder was previously linked to KITLG and various mutations have been reported to segregate in different families. Furthermore, association between KITLG mutations and malignancies was also suggested. Exome and SANGER sequencing were performed for identification of KITLG mutations. Functional in silico analyses were additionally performed to assess the findings. We identified a de novo mutation in exon 4 of KITLG gene causing NM_000899.4:c.[329A>T] (chr12:88912508A>T) leading to NP_000890.1:p.(Asp110Val) substitution in the 3rd alpha helix. It was predicted as pathogenic, located in a conserved region and causing an increase in hydrophobicity in the KITLG protein. Our findings clearly confirm an additional hot spot of KITLG mutations in the 3rd alpha helix, which very likely increases the risk of malignancies. To our knowledge the present study provides the strongest evidence of association of the KITLG mutation with both Familial Progressive Hyper‐ and Hypopigmentation and malignancy due to its’ location on somatic cancer mutation locus. Additionally we also address difficulties with classification of the unique phenotype and propose a subtype within broader diagnosis.
Collapse
Affiliation(s)
- Mario Gorenjak
- Faculty of Medicine, Centre for Human Molecular Genetics and Pharmacogenomics, University of Maribor, Maribor, Slovenia
| | - Nino Fijačko
- Faculty of Health Sciences, Department of Nursing, Maribor, Slovenia
| | - Pij Bogomir Marko
- Department of Dermatology and Venereal Diseases, University Clinical Centre Maribor, Maribor, Slovenia
| | - Milanka Živanović
- Faculty of Medicine, Institute of Pathology, University of Ljubljana, Ljubljana, Slovenia
| | - Uroš Potočnik
- Faculty of Medicine, Centre for Human Molecular Genetics and Pharmacogenomics, University of Maribor, Maribor, Slovenia.,Faculty of Chemistry and Chemical Engineering, Laboratory of Biochemistry, Molecular Biology and Genomics, University of Maribor, Maribor, Slovenia
| |
Collapse
|
32
|
Zhang C, Tang F, Chen M, Xu J, Zhang L, Qiu DY, Perdew JP, Klein ML, Wu X. Modeling Liquid Water by Climbing up Jacob's Ladder in Density Functional Theory Facilitated by Using Deep Neural Network Potentials. J Phys Chem B 2021; 125:11444-11456. [PMID: 34533960 DOI: 10.1021/acs.jpcb.1c03884] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Within the framework of Kohn-Sham density functional theory (DFT), the ability to provide good predictions of water properties by employing a strongly constrained and appropriately normed (SCAN) functional has been extensively demonstrated in recent years. Here, we further advance the modeling of water by building a more accurate model on the fourth rung of Jacob's ladder with the hybrid functional, SCAN0. In particular, we carry out both classical and Feynman path-integral molecular dynamics calculations of water with the SCAN0 functional and the isobaric-isothermal ensemble. To generate the equilibrated structure of water, a deep neural network potential is trained from the atomic potential energy surface based on ab initio data obtained from SCAN0 DFT calculations. For the electronic properties of water, a separate deep neural network potential is trained by using the Deep Wannier method based on the maximally localized Wannier functions of the equilibrated trajectory at the SCAN0 level. The structural, dynamic, and electric properties of water were analyzed. The hydrogen-bond structures, density, infrared spectra, diffusion coefficients, and dielectric constants of water, in the electronic ground state, are computed by using a large simulation box and long simulation time. For the properties involving electronic excitations, we apply the GW approximation within many-body perturbation theory to calculate the quasiparticle density of states and bandgap of water. Compared to the SCAN functional, mixing exact exchange mitigates the self-interaction error in the meta-generalized-gradient approximation and further softens liquid water toward the experimental direction. For most of the water properties, the SCAN0 functional shows a systematic improvement over the SCAN functional. However, some important discrepancies remain. The H-bond network predicted by the SCAN0 functional is still slightly overstructured compared to the experimental results.
Collapse
Affiliation(s)
- Chunyi Zhang
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Fujie Tang
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Mohan Chen
- HEDPS, Center for Applied Physics and Technology, College of Engineering, Peking University, Beijing 100871, China
| | - Jianhang Xu
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Linfeng Zhang
- Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, United States
| | - Diana Y Qiu
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06520, United States
| | - John P Perdew
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States.,Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Michael L Klein
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States.,Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Xifan Wu
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| |
Collapse
|
33
|
Li J, Hou C, Ma X, Guo S, Zhang H, Shi L, Liao C, Zheng B, Ye L, Yang L, He X. Entropy-Enthalpy Compensations Fold Proteins in Precise Ways. Int J Mol Sci 2021; 22:9653. [PMID: 34502559 PMCID: PMC8431812 DOI: 10.3390/ijms22179653] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 12/16/2022] Open
Abstract
Exploring the protein-folding problem has been a longstanding challenge in molecular biology and biophysics. Intramolecular hydrogen (H)-bonds play an extremely important role in stabilizing protein structures. To form these intramolecular H-bonds, nascent unfolded polypeptide chains need to escape from hydrogen bonding with surrounding polar water molecules under the solution conditions that require entropy-enthalpy compensations, according to the Gibbs free energy equation and the change in enthalpy. Here, by analyzing the spatial layout of the side-chains of amino acid residues in experimentally determined protein structures, we reveal a protein-folding mechanism based on the entropy-enthalpy compensations that initially driven by laterally hydrophobic collapse among the side-chains of adjacent residues in the sequences of unfolded protein chains. This hydrophobic collapse promotes the formation of the H-bonds within the polypeptide backbone structures through the entropy-enthalpy compensation mechanism, enabling secondary structures and tertiary structures to fold reproducibly following explicit physical folding codes and forces. The temperature dependence of protein folding is thus attributed to the environment dependence of the conformational Gibbs free energy equation. The folding codes and forces in the amino acid sequence that dictate the formation of β-strands and α-helices can be deciphered with great accuracy through evaluation of the hydrophobic interactions among neighboring side-chains of an unfolded polypeptide from a β-strand-like thermodynamic metastable state. The folding of protein quaternary structures is found to be guided by the entropy-enthalpy compensations in between the docking sites of protein subunits according to the Gibbs free energy equation that is verified by bioinformatics analyses of a dozen structures of dimers. Protein folding is therefore guided by multistage entropy-enthalpy compensations of the system of polypeptide chains and water molecules under the solution conditions.
Collapse
Affiliation(s)
- Jiacheng Li
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Chengyu Hou
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150080, China; (C.H.); (C.L.)
| | - Xiaoliang Ma
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Shuai Guo
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Hongchi Zhang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Liping Shi
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Chenchen Liao
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150080, China; (C.H.); (C.L.)
| | - Bing Zheng
- Key Laboratory of Functional Inorganic Material Chemistry (Ministry of Education), School of Chemistry and Materials Science, Heilongjiang University, Harbin 150001, China;
| | - Lin Ye
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Lin Yang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Xiaodong He
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
- Shenzhen STRONG Advanced Materials Research Institute Co., Ltd., Shenzhen 518035, China
| |
Collapse
|
34
|
Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions. Int J Mol Sci 2021; 22:ijms22179350. [PMID: 34502252 PMCID: PMC8431001 DOI: 10.3390/ijms22179350] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/13/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022] Open
Abstract
The biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide) and diglycine, by means of FTIR spectroscopy and molecular dynamics simulations. We isolated the spectroscopic share of water molecules that are simultaneously under the influence of peptide and osmolyte and determined the structural and energetic properties of these water molecules. Our experimental and computational results revealed that the changes in the structure of water around peptides, caused by the presence of stabilizing or destabilizing osmolyte, are significantly different for both NAGMA and diglycine. The main factor determining the influence of osmolytes on peptides is the structural-energetic similarity of their hydration spheres. We showed that the chosen peptides can serve as models for various fragments of the protein surface: NAGMA for the protein backbone and diglycine for the protein surface with polar side chains.
Collapse
|
35
|
Panja S, Dietrich B, Trabold A, Zydel A, Qadir A, Adams DJ. Varying the hydrophobic spacer to influence multicomponent gelation. Chem Commun (Camb) 2021; 57:7898-7901. [PMID: 34286734 DOI: 10.1039/d1cc02786g] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mixing low molecular weight gelators (LMWGs) shows promise as a means of preparing innovative materials with exciting properties. Here, we investigate the effect of increasing hydrophobic chain length on the properties of the resulting multicomponent systems which are capable of showing ambidextrous phase behaviour on pH perturbation.
Collapse
Affiliation(s)
- Santanu Panja
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Bart Dietrich
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Adriana Trabold
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Agata Zydel
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Aleena Qadir
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Dave J Adams
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK.
| |
Collapse
|
36
|
Gouda M, Huang Z, Liu Y, He Y, Li X. Physicochemical impact of bioactive terpenes on the microalgae biomass structural characteristics. BIORESOURCE TECHNOLOGY 2021; 334:125232. [PMID: 33965853 DOI: 10.1016/j.biortech.2021.125232] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
This study aimed to evaluate the functionality of bioactive terpenes on Spirulina (Arthrospira platensis; AP) and Chlorella (Chlorella vulgaris; CV) biomasses. The two microalgae species were treated with 0.01%, 0.05%, and 0.1% of thymol (THY), trans-cinnamaldehyde (TC), menthol (MEN), and vanillin (VAN). Raman micro-spectroscopy (RMS) was correlated with other physicochemical methods to confirm their functional mechanisms. In results, THY (0.1%) decreased (P < 0.05) RMS intensity at 1196 cm-1 that represents the protein's secondary amines wavenumber. Also, VAN (0.1%) decreased significantly A. platensis α-helix to 16.60 ± 0.52% compared to the control with 19.83 ± 0.32%. While, 0.1% TC increased (P < 0.05) the viscosity to 2.52 ± 0.61 Pa.s. This work demonstrated that terpenes could differently affect the physicochemical structure of microalgae biomass. The RMS's uniqueness comes from its ability to evaluate the functionality of terpenes during microalgae cultivation. Besides, chemometrics led to focus on the most important variances.
Collapse
Affiliation(s)
- Mostafa Gouda
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China; Department of Nutrition & Food Science, National Research Centre, Dokki, Giza, Egypt.
| | - Zhenxiong Huang
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Yufei Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Yong He
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China.
| | - Xiaoli Li
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China.
| |
Collapse
|
37
|
Kharbikar BN, Chendke GS, Desai TA. Modulating the foreign body response of implants for diabetes treatment. Adv Drug Deliv Rev 2021; 174:87-113. [PMID: 33484736 PMCID: PMC8217111 DOI: 10.1016/j.addr.2021.01.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/30/2020] [Accepted: 01/10/2021] [Indexed: 02/06/2023]
Abstract
Diabetes Mellitus is a group of diseases characterized by high blood glucose levels due to patients' inability to produce sufficient insulin. Current interventions often require implants that can detect and correct high blood glucose levels with minimal patient intervention. However, these implantable technologies have not reached their full potential in vivo due to the foreign body response and subsequent development of fibrosis. Therefore, for long-term function of implants, modulating the initial immune response is crucial in preventing the activation and progression of the immune cascade. This review discusses the different molecular mechanisms and cellular interactions involved in the activation and progression of foreign body response (FBR) and fibrosis, specifically for implants used in diabetes. We also highlight the various strategies and techniques that have been used for immunomodulation and prevention of fibrosis. We investigate how these general strategies have been applied to implants used for the treatment of diabetes, offering insights on how these devices can be further modified to circumvent FBR and fibrosis.
Collapse
Affiliation(s)
- Bhushan N Kharbikar
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gauree S Chendke
- University of California Berkeley - University of California San Francisco Graduate Program in Bioengineering, San Francisco, CA 94143, USA
| | - Tejal A Desai
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; University of California Berkeley - University of California San Francisco Graduate Program in Bioengineering, San Francisco, CA 94143, USA; Department of Bioengineering, University of California, Berkeley, CA 94720, USA.
| |
Collapse
|
38
|
Larocca M, Floresta G, Cilibrizzi A. Principles that rule the calculation of dihedral angles in secondary structures: the cases of an α-helix and a β-sheet. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
39
|
Karlsson E, Paissoni C, Erkelens AM, Tehranizadeh ZA, Sorgenfrei FA, Andersson E, Ye W, Camilloni C, Jemth P. Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. J Biol Chem 2021; 295:17698-17712. [PMID: 33454008 PMCID: PMC7762952 DOI: 10.1074/jbc.ra120.015645] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/15/2020] [Indexed: 12/24/2022] Open
Abstract
Intrinsically disordered protein domains often have multiple binding partners. It is plausible that the strength of pairing with specific partners evolves from an initial low affinity to a higher affinity. However, little is known about the molecular changes in the binding mechanism that would facilitate such a transition. We previously showed that the interaction between two intrinsically disordered domains, NCBD and CID, likely emerged in an ancestral deuterostome organism as a low-affinity interaction that subsequently evolved into a higher-affinity interaction before the radiation of modern vertebrate groups. Here we map native contacts in the transition states of the low-affinity ancestral and high-affinity human NCBD/CID interactions. We show that the coupled binding and folding mechanism is overall similar but with a higher degree of native hydrophobic contact formation in the transition state of the ancestral complex and more heterogeneous transient interactions, including electrostatic pairings, and an increased disorder for the human complex. Adaptation to new binding partners may be facilitated by this ability to exploit multiple alternative transient interactions while retaining the overall binding and folding pathway.
Collapse
Affiliation(s)
- Elin Karlsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Cristina Paissoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Amanda M Erkelens
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Zeinab A Tehranizadeh
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Frieda A Sorgenfrei
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Weihua Ye
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| |
Collapse
|
40
|
Quesada-Moreno MM, Pinacho P, Pérez C, Šekutor M, Schreiner PR, Schnell M. Do Docking Sites Persist Upon Fluorination? The Diadamantyl Ether-Aromatics Challenge for Rotational Spectroscopy and Theory. Chemistry 2021; 27:6198-6203. [PMID: 33512017 PMCID: PMC8048501 DOI: 10.1002/chem.202100078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Indexed: 12/28/2022]
Abstract
Fluorinated derivatives of biological molecules have proven to be highly efficient at modifying the biological activity of a given protein through changes in the stability and the kind of docking interactions. These interactions can be hindered or facilitated based on the hydrophilic/hydrophobic character of a particular protein region. Diadamantyl ether (C20H30O) possesses both kinds of docking sites, serving as a good template to model these important contacts with aromatic fluorinated counterparts. In this work, an experimental study on the structures of several complexes between diadamantyl ether and benzene as well as a series of fluorinated benzenes is reported to analyze the effect of H→F substitution on the interaction and structure of the resulting molecular clusters using rotational spectroscopy. All experimentally observed complexes are largely dominated by London dispersion interactions with the hydrogen‐terminated surface areas of diadamantyl ether. Already single substitution of one hydrogen atom with fluorine changes the preferred docking site of the complexes. However, the overall contributions of the different intermolecular interactions are similar for the different complexes, contrary to previous studies focusing on the difference in interactions using fluorinated and non‐fluorinated molecules.
Collapse
Affiliation(s)
| | - Pablo Pinacho
- Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany
| | - Cristóbal Pérez
- Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany
| | - Marina Šekutor
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany.,Institute of Physical Chemistry, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, 24118, Kiel, Germany
| |
Collapse
|
41
|
Ashoorirad M, Fallah A, Saviz M. Measuring and assessment of impedance spectrum of collagen thin films in the presence of deionized water. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
42
|
Structure-based drug repurposing to inhibit the DNA gyrase of Mycobacterium tuberculosis. Biochem J 2020; 477:4167-4190. [PMID: 33030198 DOI: 10.1042/bcj20200462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/02/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022]
Abstract
Drug repurposing is an alternative avenue for identifying new drugs to treat tuberculosis (TB). Despite the broad-range of anti-tubercular drugs, the emergence of multi-drug-resistant and extensively drug-resistant strains of Mycobacterium tuberculosis (Mtb) H37Rv, as well as the significant death toll globally, necessitates the development of new and effective drugs to treat TB. In this study, we have employed a drug repurposing approach to address this drug resistance problem by screening the drugbank database to identify novel inhibitors of the Mtb target enzyme, DNA gyrase. The compounds were screened against the ATPase domain of the gyrase B subunit (MtbGyrB47), and the docking results showed that echinacoside, doxorubicin, epirubicin, and idarubicin possess high binding affinities against MtbGyrB47. Comprehensive assessment using fluorescence spectroscopy, surface plasmon resonance spectroscopy (SPR), and circular dichroism (CD) titration studies revealed echinacoside as a potent binder of MtbGyrB47. Furthermore, ATPase, and DNA supercoiling assays exhibited an IC50 values of 2.1-4.7 µM for echinacoside, doxorubicin, epirubicin, and idarubicin. Among these compounds, the least MIC90 of 6.3 and 12 μM were observed for epirubicin and echinacoside, respectively, against Mtb. Our findings indicate that echinacoside and epirubicin targets mycobacterial DNA gyrase, inhibit its catalytic cycle, and retard mycobacterium growth. Further, these compounds exhibit potential scaffolds for optimizing novel anti-mycobacterial agents that can act on drug-resistant strains.
Collapse
|
43
|
Aghaei H, Ghavi M, Hashemkhani G, Keshavarz M. Utilization of two modified layered doubled hydroxides as supports for immobilization of Candida rugosa lipase. Int J Biol Macromol 2020; 162:74-83. [DOI: 10.1016/j.ijbiomac.2020.06.145] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/08/2020] [Accepted: 06/15/2020] [Indexed: 01/11/2023]
|
44
|
Heller GT, Aprile FA, Michaels TCT, Limbocker R, Perni M, Ruggeri FS, Mannini B, Löhr T, Bonomi M, Camilloni C, De Simone A, Felli IC, Pierattelli R, Knowles TPJ, Dobson CM, Vendruscolo M. Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer's disease. SCIENCE ADVANCES 2020; 6:6/45/eabb5924. [PMID: 33148639 PMCID: PMC7673680 DOI: 10.1126/sciadv.abb5924] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/22/2020] [Indexed: 05/15/2023]
Abstract
Disordered proteins are challenging therapeutic targets, and no drug is currently in clinical use that modifies the properties of their monomeric states. Here, we identify a small molecule (10074-G5) capable of binding and sequestering the intrinsically disordered amyloid-β (Aβ) peptide in its monomeric, soluble state. Our analysis reveals that this compound interacts with Aβ and inhibits both the primary and secondary nucleation pathways in its aggregation process. We characterize this interaction using biophysical experiments and integrative structural ensemble determination methods. We observe that this molecule increases the conformational entropy of monomeric Aβ while decreasing its hydrophobic surface area. We also show that it rescues a Caenorhabditis elegans model of Aβ-associated toxicity, consistent with the mechanism of action identified from the in silico and in vitro studies. These results illustrate the strategy of stabilizing the monomeric states of disordered proteins with small molecules to alter their behavior for therapeutic purposes.
Collapse
Affiliation(s)
- Gabriella T Heller
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Francesco A Aprile
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Thomas C T Michaels
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Ryan Limbocker
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Michele Perni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Francesco Simone Ruggeri
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Benedetta Mannini
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Thomas Löhr
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Massimiliano Bonomi
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry. CNRS UMR 3528, C3BI, CNRS USR 3756, Institut Pasteur, Paris, France
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Alfonso De Simone
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK
- Department of Pharmacy, University of Naples "Federico II," 80131 Naples, Italy
| | - Isabella C Felli
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff," University of Florence, 50019 Sesto Fiorentino, Italy
| | - Roberta Pierattelli
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff," University of Florence, 50019 Sesto Fiorentino, Italy
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
| |
Collapse
|
45
|
Gontero D, Veglia AV, Bracamonte AG. In flow metal-enhanced fluorescence for biolabelling and biodetection. Photochem Photobiol Sci 2020; 19:1168-1188. [PMID: 32677642 DOI: 10.1039/d0pp00145g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Escherichia coli bacteria were determined by in flow cytometry with laser excitation and fluorescence detection applying ultraluminescent core-shell nanoparticles based on Metal Enhanced Fluorescence (MEF). Core-shell nanoparticles consisted of a 40 nm core modified with a silica spacer grafted with Rhodamine B (RhB). The electromagnetic field in the near field of the core surface enhanced the fluorescence of RhB by plasmonic and fluorophore coupling. The hydrophilic silica spacer allowed the non-covalent interaction with the polar E. coli surface and thus ultraluminescent bacteria biolabelling was developed. Clearly, well defined and bright bacteria imaging was recorded by Laser Fluorescence Microscopy based on the non-covalent deposition of the ultraluminescent nano-emitters. Using these nano-labellers, it was possible to detect labelled E. coli by in flow cytometry. Higher values of Side-scattered light (SSC) and Forward-scattered light (FSC), and number of fluorescent event detections, were observed for labelled bacteria compared to those non-labelled. The sensitivity of the methodology was evaluated by varying bacteria concentration and acceptable analytical figures of merit were determined. Applying this methodology we could quantify E. coli from a synthetic real sample of fortified water. Similar results were obtained by bacteria counting with Laser Fluorescence Microscopy and with a cell-bacteria counter.
Collapse
Affiliation(s)
- Daniela Gontero
- Laboratorio de Análisis Clínicos y Bacteriológicos, Clínica de la Familia II, 5850, Río Tercero, Córdoba, Argentina
| | - Alicia V Veglia
- Instituto de Investigaciones en Físico Química de Córdoba (INFIQC), Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, 5000, Córdoba, Argentina
| | - A Guillermo Bracamonte
- Instituto de Investigaciones en Físico Química de Córdoba (INFIQC), Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, 5000, Córdoba, Argentina. .,Departement de chimie and Centre d'optique, photonique et laser (COPL), Université Laval, Québec, QC, Canada.
| |
Collapse
|
46
|
Roy S, Xie O, Dorval Courchesne N. Challenges in engineering conductive protein fibres: Disentangling the knowledge. CAN J CHEM ENG 2020. [DOI: 10.1002/cjce.23836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sophia Roy
- Department of Chemical Engineering McGill University Montréal Québec Canada
| | - Oliver Xie
- Department of Chemical Engineering McGill University Montréal Québec Canada
| | | |
Collapse
|
47
|
Bapolisi AM, Nkanga CI, Walker RB, Krause RWM. Simultaneous liposomal encapsulation of antibiotics and proteins: Co-loading and characterization of rifampicin and Human Serum Albumin in soy-liposomes. J Drug Deliv Sci Technol 2020. [DOI: 10.1016/j.jddst.2020.101751] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
48
|
Pang WC, Ramli ANM, Hamid AAA. Comparative modelling studies of fruit bromelain using molecular dynamics simulation. J Mol Model 2020; 26:142. [PMID: 32417971 DOI: 10.1007/s00894-020-04398-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 04/28/2020] [Indexed: 12/25/2022]
Abstract
Fruit bromelain is a cysteine protease accumulated in pineapple fruits. This proteolytic enzyme has received high demand for industrial and therapeutic applications. In this study, fruit bromelain sequences QIM61759, QIM61760 and QIM61761 were retrieved from the National Center for Biotechnology Information (NCBI) Genbank Database. The tertiary structure of fruit bromelain QIM61759, QIM61760 and QIM61761 was generated by using MODELLER. The result revealed that the local stereochemical quality of the generated models was improved by using multiple templates during modelling process. Moreover, by comparing with the available papain model, structural analysis provides an insight on how pro-peptide functions as a scaffold in fruit bromelain folding and contributing to inactivation of mature protein. The structural analysis also disclosed the similarities and differences between these models. Lastly, thermal stability of fruit bromelain was studied. Molecular dynamics simulation of fruit bromelain structures at several selected temperatures demonstrated how fruit bromelain responds to elevation of temperature.
Collapse
Affiliation(s)
- Wei Cheng Pang
- Faculty of Industrial Science & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Aizi Nor Mazila Ramli
- Faculty of Industrial Science & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia. .,Bio Aromatic Research Centre of Excellence, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia.
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia.,Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia
| |
Collapse
|
49
|
Singha DL, Maharana J, Panda D, Dehury B, Modi MK, Singh S. Understanding the thermal response of rice eukaryotic transcription factor eIF4A1 towards dynamic temperature stress: insights from expression profiling and molecular dynamics simulation. J Biomol Struct Dyn 2020; 39:2575-2584. [PMID: 32367760 DOI: 10.1080/07391102.2020.1751295] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Eukaryotic translation initiation factors (eIFs) are the group of regulatory proteins that are involved in the initiation of translation events. Among them, eIF4A1, a member of the DEAD-box RNA helicase family, participates in a wide spectrum of activities which include, RNA splicing, ribosome biogenesis, and RNA degradation. It is well known that ATP-binding and subsequent hydrolysis activities are crucial for the functionality of such helicases. Although the stress-responsive upregulation of eIF4A1 has been reported in plants during stress, it is difficult to anticipate the functionality of the corresponding protein product. Therefore, to understand the activity of eIF4A1 in rice in response to temperature stress, we first conducted an expression analysis of the gene and further investigated the structural stability of the eIF4A1-ATP/Mg2+ complex through molecular dynamics (MD) simulations at different temperature conditions (277 K, 300 K, and 315 K). Our results demonstrated a three to fourfold increased expression of rice eIF4A1 both in root and shoot at 42 °C compared to control. Furthermore, the MD simulation portrayed strong ATP/Mg2+ binding at a higher temperature in comparison to control and cold temperature. Overall, the increased expression pattern of eIF4A1 and strong ATP/Mg2+ binding at higher temperature indicated the heat stress-tolerant capacity of the gene in rice. The results from our study will help in understanding the activity of gene and guide the researchers for screening of novel stress inducible candidate genes for the engineering of temperature stress tolerant plants.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Dhanawantari L Singha
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Jitendra Maharana
- Distributed Information Centre (DIC), Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Debashis Panda
- Distributed Information Centre (DIC), Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Budheswar Dehury
- Department of Biochemistry, University of Cambridge, Cambridge, UK.,Department of Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mahendra Kumar Modi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India.,Distributed Information Centre (DIC), Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Salvinder Singh
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| |
Collapse
|
50
|
Lee J, Der BS, Karamitros CS, Li W, Marshall NM, Lungu OI, Miklos AE, Xu J, Kang TH, Lee CH, Tan B, Hughes RA, Jung ST, Ippolito GC, Gray JJ, Zhang Y, Kuhlman B, Georgiou G, Ellington AD. Computer-based Engineering of Thermostabilized Antibody Fragments. AIChE J 2020; 66:e16864. [PMID: 32336757 PMCID: PMC7181397 DOI: 10.1002/aic.16864] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We used the molecular modeling program Rosetta to identify clusters of amino acid substitutions in antibody fragments (scFvs and scAbs) that improve global protein stability and resistance to thermal deactivation. Using this methodology, we increased the melting temperature (Tm) and resistance to heat treatment of an antibody fragment that binds to the Clostridium botulinum hemagglutinin protein (anti-HA33). Two designed antibody fragment variants with two amino acid replacement clusters, designed to stabilize local regions, were shown to have both higher Tm compared to the parental scFv and importantly, to retain full antigen binding activity after 2 hours of incubation at 70 °C. The crystal structure of one thermostabilized scFv variants was solved at 1.6 Å and shown to be in close agreement with the RosettaAntibody model prediction.
Collapse
Affiliation(s)
- Jiwon Lee
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755
| | - Bryan S. Der
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | | | - Wenzong Li
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Nicholas M. Marshall
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Oana I. Lungu
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Aleksandr E. Miklos
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, APGEA, MD 21010
| | - Jianqing Xu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MA 21218
| | - Tae Hyun Kang
- Biopharmaceutical Chemistry Major, School of Applied Chemistry, Kookmin University, Seongbuk-gu, Seoul 02707, Republic of Korea
| | - Chang-Han Lee
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Bing Tan
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Randall A. Hughes
- US Army Research Laboratory, Austin, TX 78712,Applied Research Laboratories, The University of Texas at Austin, Austin, TX 78712
| | - Sang Taek Jung
- Department of Biomedical Science, Graduate School of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Gregory C. Ippolito
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MA 21218
| | - Yan Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | - George Georgiou
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712,Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712,Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712,To whom correspondence should be addressed: George Georgiou () and Andrew D. Ellington ()
| | - Andrew D. Ellington
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712,Department of Chemistry, The University of Texas at Austin, Austin, TX 78712,To whom correspondence should be addressed: George Georgiou () and Andrew D. Ellington ()
| |
Collapse
|