51
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Thermostabilization of VPR, a kinetically stable cold adapted subtilase, via multiple proline substitutions into surface loops. Sci Rep 2020; 10:1045. [PMID: 31974391 PMCID: PMC6978356 DOI: 10.1038/s41598-020-57873-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/27/2019] [Indexed: 11/24/2022] Open
Abstract
Protein stability is a widely studied topic, there are still aspects however that need addressing. In this paper we examined the effects of multiple proline substitutions into loop regions of the kinetically stable proteinase K-like serine protease VPR, using the thermostable structural homologue AQUI as a template. Four locations for proline substitutions were chosen to imitate the structure of AQUI. Variants were produced and characterized using differential scanning calorimetry (DSC), circular dichroism (CD), steady state fluorescence, acrylamide fluorescence quenching and thermal inactivation experiments. The final product VPRΔC_N3P/I5P/N238P/T265P was greatly stabilized which was achieved without any noticeable detrimental effects to the catalytic efficiency of the enzyme. This stabilization seems to be derived from the conformation restrictive properties of the proline residue in its ability to act as an anchor point and strengthen pre-existing interactions within the protein and allowing for these interactions to prevail when thermal energy is applied to the system. In addition, the results underline the importance of the synergy between distant local protein motions needed to result in stabilizing effects and thus giving an insight into the nature of the stability of VPR, its unfolding landscape and how proline residues can infer kinetic stability onto protein structures.
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52
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STUDY ON THE EFFECT OF THE VITAMIN AND MINERAL COMPLEX CONTAINING ZINC L-ASPARTATE ON THE PERIODONTAL CONDITION OF RATS IN THE PRESENCE OF PERIODONTITIS MODELING. WORLD OF MEDICINE AND BIOLOGY 2020. [DOI: 10.26724/2079-8334-2020-3-73-242-247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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53
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Nandi T, Desai A, Ainavarapu SRK. The unfolding transition state of ubiquitin with charged residues has higher energy than that with hydrophobic residues. Phys Chem Chem Phys 2020; 22:23158-23168. [DOI: 10.1039/d0cp03876h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The native-state structure and folding pathways of a protein are encoded in its amino acid sequence.
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Affiliation(s)
- Tathagata Nandi
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai 400005
- India
| | - Amogh Desai
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai 400005
- India
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54
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Alaei L, Moosavi-Movahedi AA. Stability of multi-subunit proteins and conformational lock. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 150:145-152. [DOI: 10.1016/j.pbiomolbio.2019.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/17/2019] [Accepted: 08/21/2019] [Indexed: 12/24/2022]
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55
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Abstract
Abstract
While according to the thermodynamic hypothesis, protein folding reproducibility is ensured by the assumption that the native state corresponds to the minimum of the free energy in normal cellular conditions, here, the VES kinetic mechanism for folding in vivo is described according to which the nascent chain of all proteins is helical and the first and structure defining step in the folding pathway is the bending of that initial helix around a particular amino acid site. Molecular dynamics simulations are presented which indicate both the viability of this mechanism for folding and its limitations in the presence of a Markovian thermal bath. An analysis of a set of protein structures formed only of helices and loops suggests that bending sites are correlated with regions bounded, on the N-side, by positively charged amino acids like Lysine and Histidine and on the C-side by negatively charged amino acids like Aspartic acid.
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56
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Nandi T, Yadav A, Ainavarapu SRK. Experimental comparison of energy landscape features of ubiquitin family proteins. Proteins 2019; 88:449-461. [DOI: 10.1002/prot.25822] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/05/2019] [Accepted: 09/18/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Tathagata Nandi
- Department of Chemical SciencesTata Institute of Fundamental Research Mumbai India
| | - Anju Yadav
- Department of Chemical SciencesTata Institute of Fundamental Research Mumbai India
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57
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Giannini E, González LJ, Vila AJ. A simple protocol to characterize bacterial cell-envelope lipoproteins in a native-like environment. Protein Sci 2019; 28:2004-2010. [PMID: 31518027 DOI: 10.1002/pro.3728] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 01/04/2023]
Abstract
Physiological conditions in living cells are strictly regulated to allow, optimize, and coordinate biological processes. The bacterial cell envelope is the compartment where the communication with the external environment takes place. This involves membrane proteins, key players in many biological processes that ensure bacterial survival. The biochemical characterization of membrane proteins, either integral, lipidated or peripheral is challenging due to their mixed protein-lipid nature, making it difficult to purify and obtain considerable amounts of samples. In contrast to integral membrane proteins, lipidated proteins are usually purified as truncated soluble versions, neglecting the impact of the membrane environment. Here we report a simple and robust protocol to characterize bacterial lipidated proteins in spheroplasts from Escherichia coli using a β-lactamase as a model. The Metallo-β-lactamase NDM-1 is an enzyme anchored to the inner leaflet of the outer membrane of Gram-negative bacteria. Kinetic parameters and stability of the lipidated NDM-1 and the soluble unbound version (NDM-1 C26A) were measured in spheroplasts and periplasm, respectively. These studies revealed that membrane anchoring increases the KM of the enzyme, consequently decreasing the catalytic efficiency, while not affecting its kinetic stability. This approach can be used to characterize lipidated proteins avoiding the purification step while mimicking its native environment. This approach also helps in filling the gap between in vitro and in vivo studies.
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Affiliation(s)
- Estefanía Giannini
- Laboratorio de Metaloproteínas, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina
| | - Lisandro J González
- Laboratorio de Metaloproteínas, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina.,Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Alejandro J Vila
- Laboratorio de Metaloproteínas, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina.,Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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58
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Sedlák E, Sedláková D, Marek J, Hančár J, Garajová K, Žoldák G. Ion-Specific Protein/Water Interface Determines the Hofmeister Effect on the Kinetic Stability of Glucose Oxidase. J Phys Chem B 2019; 123:7965-7973. [DOI: 10.1021/acs.jpcb.9b05195] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Erik Sedlák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park P.J. Šafárik University, Jesenna 5, 041 54 Košice, Slovakia
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Moyzesova 11, 04001 Košice, Slovakia
| | - Dagmar Sedláková
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 04001 Košice, Slovakia
| | - Jozef Marek
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 04001 Košice, Slovakia
| | - Jozef Hančár
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Moyzesova 11, 04001 Košice, Slovakia
| | - Katarína Garajová
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Moyzesova 11, 04001 Košice, Slovakia
| | - Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park P.J. Šafárik University, Jesenna 5, 041 54 Košice, Slovakia
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59
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Xiong W, Tang TX, Littleton E, Karcini A, Lazar IM, Capelluto DGS. Preferential phosphatidylinositol 5-phosphate binding contributes to a destabilization of the VHS domain structure of Tom1. Sci Rep 2019; 9:10868. [PMID: 31350523 PMCID: PMC6659632 DOI: 10.1038/s41598-019-47386-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/16/2019] [Indexed: 12/21/2022] Open
Abstract
Tom1 transports endosomal ubiquitinated proteins that are targeted for degradation in the lysosomal pathway. Infection of eukaryotic cells by Shigella flexneri boosts oxygen consumption and promotes the synthesis of phosphatidylinositol-5-phosphate (PtdIns5P), which triggers Tom1 translocation to signaling endosomes. Removing Tom1 from its cargo trafficking function hinders protein degradation in the host and, simultaneously, enables bacterial survival. Tom1 preferentially binds PtdIns5P via its VHS domain, but the effects of a reducing environment as well as PtdIns5P on the domain structure and function are unknown. Thermal denaturation studies demonstrate that, under reducing conditions, the monomeric Tom1 VHS domain switches from a three-state to a two-state transition behavior. PtdIns5P reduced thermostability, interhelical contacts, and conformational compaction of Tom1 VHS, suggesting that the phosphoinositide destabilizes the protein domain. Destabilization of Tom1 VHS structure was also observed with other phospholipids. Isothermal calorimetry data analysis indicates that, unlike ubiquitin, Tom1 VHS endothermically binds to PtdIns5P through two noncooperative binding sites, with its acyl chains playing a relevant role in the interaction. Altogether, these findings provide mechanistic insights about the recognition of PtdIns5P by the VHS domain that may explain how Tom1, when in a different VHS domain conformational state, interacts with downstream effectors under S. flexneri infection.
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Affiliation(s)
- Wen Xiong
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Fralin Life Sciences Institute, and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, 24061, United States
| | - Tuo-Xian Tang
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Fralin Life Sciences Institute, and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, 24061, United States
| | - Evan Littleton
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Fralin Life Sciences Institute, and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, 24061, United States
| | - Arba Karcini
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, United States
| | - Iulia M Lazar
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, United States
| | - Daniel G S Capelluto
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Fralin Life Sciences Institute, and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, 24061, United States.
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60
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Enzymatic activity and thermoresistance of improved microbial transglutaminase variants. Amino Acids 2019; 52:313-326. [DOI: 10.1007/s00726-019-02764-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 07/17/2019] [Indexed: 01/31/2023]
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61
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Wang W, Ohtake S. Science and art of protein formulation development. Int J Pharm 2019; 568:118505. [PMID: 31306712 DOI: 10.1016/j.ijpharm.2019.118505] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 02/07/2023]
Abstract
Protein pharmaceuticals have become a significant class of marketed drug products and are expected to grow steadily over the next decade. Development of a commercial protein product is, however, a rather complex process. A critical step in this process is formulation development, enabling the final product configuration. A number of challenges still exist in the formulation development process. This review is intended to discuss these challenges, to illustrate the basic formulation development processes, and to compare the options and strategies in practical formulation development.
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Affiliation(s)
- Wei Wang
- Biological Development, Bayer USA, LLC, 800 Dwight Way, Berkeley, CA 94710, United States.
| | - Satoshi Ohtake
- Pharmaceutical Research and Development, Pfizer Biotherapeutics Pharmaceutical Sciences, Chesterfield, MO 63017, United States
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62
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Abstract
In order to improve stability of a peptide marine drug lead, α-conotoxin TxID, we synthesized and modified TxID at the N-terminal with DSPE-PEG-NHS by a nucleophilic substitution reaction to prepare the DSPE-PEG-TxID for the first time. The reaction conditions, including solvent, ratio, pH, and reaction time, were optimized systematically and the optimal one was reacted in dimethyl formamide at pH 8.2 with triethylamine at room temperature for 120 h. The in vitro stabilities in serum, simulated gastric juice, and intestinal fluid were tested, and improved dramatically compared with TxID. The PEG-modified peptide was functionally tested on α3β4 nicotinic acetylcholine receptor (nAChR) heterologously expressed in Xenopus laevis oocytes. The DSPE-PEG-TxID showed an obvious inhibition effect on α3β4 nAChR. All in all, the PEG modification of TxID was improved in stability, resistance to enzymatic degradation, and may prolong the half-life in vivo, which may pave the way for the future application in smoking cessation and drug rehabilitation, as well as small cell lung cancer.
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63
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Chattopadhyay G, Varadarajan R. Facile measurement of protein stability and folding kinetics using a nano differential scanning fluorimeter. Protein Sci 2019; 28:1127-1134. [PMID: 30993730 DOI: 10.1002/pro.3622] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 01/17/2023]
Abstract
With advancements in high-throughput generation of phenotypic data on mutant proteins, it has become important to individually characterize different proteins or their variants rapidly and with minimal sample consumption. We have made use of a nano differential scanning fluorimetric device, from NanoTemper technologies, to rapidly carry out isothermal chemical denaturation and measure folding/unfolding kinetics of proteins and compared these to corresponding data obtained from conventional spectrofluorimetry. We show that using sample volumes 10-50-fold lower than with conventional fluorimetric techniques, one can rapidly and accurately measure thermodynamic and kinetic stability, as well as folding/unfolding kinetics. This method also facilitates characterization of proteins that are difficult to express and purify.
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Affiliation(s)
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.,Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore, India
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64
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Thibeault J, Patrick J, Martin A, Ortiz-Perez B, Hill S, Zhang S, Xia K, Colón W. Sarkosyl: A milder detergent than SDS for identifying proteins with moderately high hyperstability using gel electrophoresis. Anal Biochem 2019; 571:21-24. [PMID: 30779907 DOI: 10.1016/j.ab.2019.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 10/27/2022]
Abstract
Sodium dodecyl sulfate (SDS) is a detergent used as a strong denaturant of proteins in gel electrophoresis. It has previously been shown that certain hyperstable, also known as kinetically stable, proteins are resistant to SDS and thus require heating for their denaturation in the presence of SDS. Because of its high denaturing strength, relatively few proteins are resistant to SDS thereby limiting the current use of SDS-PAGE for identifying hyperstable degradation-resistant proteins. In this study, we show that sarkosyl, a milder detergent than SDS, is able to identify proteins with moderately high kinetic stability that lack SDS-resistance. Our assay involves running and subsequently comparing boiled and unheated protein samples containing sarkosyl, instead of SDS, on PAGE gels and identifying subsequent differences in protein migration. Our results also show that sarkosyl and SDS may be combined in PAGE experiments at varying relative percentages to obtain semi-quantitative information about a protein's kinetic stability in a range inaccessible by probing through native- or SDS-PAGE. Using protein extracts from various legumes as model systems, we detected proteins with a range of protein stability from nearly SDS-resistant to barely sarkosyl resistant.
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Affiliation(s)
- Jane Thibeault
- Biochemistry and Biophysics Graduate Program, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Jessica Patrick
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Alexi Martin
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Brian Ortiz-Perez
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Shakeema Hill
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Songjie Zhang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Ke Xia
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Wilfredo Colón
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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65
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Dumbrepatil AB, Ghosh S, Zegalia KA, Malec PA, Hoff JD, Kennedy RT, Marsh ENG. Viperin interacts with the kinase IRAK1 and the E3 ubiquitin ligase TRAF6, coupling innate immune signaling to antiviral ribonucleotide synthesis. J Biol Chem 2019; 294:6888-6898. [PMID: 30872404 DOI: 10.1074/jbc.ra119.007719] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/06/2019] [Indexed: 01/01/2023] Open
Abstract
Virus-inhibitory protein, endoplasmic reticulum-associated, interferon-inducible (viperin) is a radical SAM enzyme that plays a multifaceted role in the cellular antiviral response. Viperin has recently been shown to catalyze the SAM-dependent formation of 3'-deoxy-3',4'-didehydro-CTP (ddhCTP), which inhibits some viral RNA polymerases. Viperin is also implicated in regulating Lys-63-linked polyubiquitination of interleukin-1 receptor-associated kinase-1 (IRAK1) by the E3 ubiquitin ligase tumor necrosis factor receptor-associated factor 6 (TRAF6) as part of the Toll-like receptor-7 and -9 (TLR7/9) innate immune signaling pathways. In these pathways, the poly-ubiquitination of IRAK1 by TRAF6 is necessary to activate IRAK1, which then phosphorylates downstream targets and ultimately leads to the production of type I interferons. That viperin is a component of these pathways suggested that its enzymatic activity might be regulated by interactions with partner proteins. To test this idea, we have reconstituted the interactions between viperin, IRAK1, and TRAF6 by transiently expressing these enzymes in HEK 293T cells. We show that IRAK1 and TRAF6 increase viperin activity ∼10-fold to efficiently catalyze the radical-mediated dehydration of CTP to ddhCTP. Furthermore, we found that TRAF6-mediated ubiquitination of IRAK1 requires the association of viperin with both IRAK1 and TRAF6. Ubiquitination appears to depend on structural changes in viperin induced by SAM binding, but, significantly, does not require catalytically active viperin. We conclude that the synergistic activation of viperin and IRAK1 provides a mechanism that couples innate immune signaling with the production of the antiviral nucleotide ddhCTP.
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Affiliation(s)
| | | | | | | | | | | | - E Neil G Marsh
- From the Departments of Chemistry, .,Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
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66
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Mondal A, Das M, Mazumdar S. Substitution of iron with cobalt in the prosthetic group of bacterial cytochrome P450: Effects on the stability and structure of the protein. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2018.12.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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67
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Williams LJ, Schendt BJ, Fritz ZR, Attali Y, Lavroff RH, Yarmush ML. A protein interaction free energy model based on amino acid residue contributions: Assessment of point mutation stability of T4 lysozyme. TECHNOLOGY 2019; 7:12-39. [PMID: 32211456 PMCID: PMC7093156 DOI: 10.1142/s233954781950002x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Here we present a model to estimate the interaction free energy contribution of each amino acid residue of a given protein. Protein interaction energy is described in terms of per-residue interaction factors, μ. Multibody interactions are implicitly captured in μ through the combination of amino acid terms (γ) guided by local conformation indices (σ). The model enables construction of an interaction factor heat map for a protein in a given fold, allows prima facie assessment of the degree of residue-residue interaction, and facilitates a qualitative and quantitative evaluation of protein association properties. The model was used to compute thermal stability of T4 bacteriophage lysozyme mutants across seven sites. Qualitative assessment of mutational effects provides a straightforward rationale regarding whether a particular site primarily perturbs native or non-native states, or both. The presented model was found to be in good agreement with experimental mutational data (R 2 = 0.73) and suggests an approach by which to convert structure space into energy space.
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Affiliation(s)
- Lawrence J Williams
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Rd., Piscataway, NJ 08854, USA
| | - Brian J Schendt
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Rd., Piscataway, NJ 08854, USA
| | - Zachary R Fritz
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Yonatan Attali
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Rd., Piscataway, NJ 08854, USA
| | - Robert H Lavroff
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Rd., Piscataway, NJ 08854, USA
| | - Martin L Yarmush
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, 599 Taylor Road, Piscataway, NJ 08854, USA
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68
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Sun Z, Liu Q, Qu G, Feng Y, Reetz MT. Utility of B-Factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability. Chem Rev 2019; 119:1626-1665. [PMID: 30698416 DOI: 10.1021/acs.chemrev.8b00290] [Citation(s) in RCA: 275] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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69
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Schulte‐Sasse M, Pardo‐Ávila F, Pulido‐Mayoral NO, Vázquez‐Lobo A, Costas M, García‐Hernández E, Rodríguez‐Romero A, Fernández‐Velasco DA. Structural, thermodynamic and catalytic characterization of an ancestral triosephosphate isomerase reveal early evolutionary coupling between monomer association and function. FEBS J 2019; 286:882-900. [DOI: 10.1111/febs.14741] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 11/01/2018] [Accepted: 12/23/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Mariana Schulte‐Sasse
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Mexico
| | - Fátima Pardo‐Ávila
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Mexico
| | - Nancy O. Pulido‐Mayoral
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Mexico
| | - Alejandra Vázquez‐Lobo
- Centro de Investigación en Biodiversidad y Conservación Universidad Autónoma del Estado de Morelos Cuernavaca Mexico
| | - Miguel Costas
- Laboratorio de Biofisicoquímica Departamento de Fisicoquímica Facultad de Química Universidad Nacional Autónoma de México Mexico
| | | | | | - Daniel Alejandro Fernández‐Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Mexico
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70
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Balakrishna S, Nagarajappa C, Rangappa S. Misfolding linked mutations of SERPINA1 gene are uncommon in preeclampsia. ARCHIVES OF MEDICINE AND HEALTH SCIENCES 2019. [DOI: 10.4103/amhs.amhs_79_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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71
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Musil M, Konegger H, Hon J, Bednar D, Damborsky J. Computational Design of Stable and Soluble Biocatalysts. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03613] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Milos Musil
- Loschmidt Laboratories, Centre for Toxic Compounds in the Environment (RECETOX), and Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, 612 66 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Hannes Konegger
- Loschmidt Laboratories, Centre for Toxic Compounds in the Environment (RECETOX), and Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Hon
- Loschmidt Laboratories, Centre for Toxic Compounds in the Environment (RECETOX), and Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, 612 66 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Centre for Toxic Compounds in the Environment (RECETOX), and Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Centre for Toxic Compounds in the Environment (RECETOX), and Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
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72
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Whittington AC, Rokyta DR. Biophysical Spandrels form a Hot-Spot for Kosmotropic Mutations in Bacteriophage Thermal Adaptation. J Mol Evol 2018; 87:27-36. [PMID: 30564861 DOI: 10.1007/s00239-018-9882-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/15/2018] [Indexed: 12/18/2022]
Abstract
Temperature plays a dominating role in protein structure and function, and life has evolved myriad strategies to adapt proteins to environmental thermal stress. Cellular systems can utilize kosmotropic osmolytes, the products of complex biochemical pathways, to act as chemical chaperones. These extrinsic molecules, e.g., trehalose, alter local water structure to modulate the strength of the hydrophobic effect and increase protein stability. In contrast, simpler genetic systems must rely on intrinsic mutation to affect protein stability. In naturally occurring microvirid bacteriophages of the subfamily Bullavirinae, capsid stability is randomly distributed across the phylogeny, suggesting it is not phylogenetically linked and could be altered through adaptive mutation. We hypothesized that these phages could utilize an adaptive mechanism that mimics the stabilizing effects of the kosmotrope trehalose through mutation. Kinetic stability of wild-type ID8, a relative of ΦX174, displays a saturable response to trehalose. Thermal adaptation mutations in ID8 improve capsid stability and reduce responsiveness to trehalose suggesting the mutations move stability closer to the kosmotropic saturation point, mimicking the kosmotropic effect of trehalose. These mutations localize to and modulate the hydrophobicity of a cavern formation at the interface of phage coat and spike proteins-an evolutionary spandrel. Across a series of genetically distinct phages, responsiveness to trehalose correlates positively with cavern hydrophobicity suggesting that the level of hydrophobicity of the cavern may provide a biophysical gating mechanism constraining or permitting adaptation in a lineage-specific manner. Our results demonstrate that a single mutation can exploit pre-existing, non-adaptive structural features to mimic the adaptive effects of complex biochemical pathways.
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Affiliation(s)
- A Carl Whittington
- Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL, 32306, USA.
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL, 32306, USA
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73
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Dual-Family Peptidylprolyl Isomerases (Immunophilins) of Select Monocellular Organisms. Biomolecules 2018; 8:biom8040148. [PMID: 30445770 PMCID: PMC6316441 DOI: 10.3390/biom8040148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 12/19/2022] Open
Abstract
The dual-family peptidylprolyl cis-trans isomerases (immunophilins) represent a naturally occurring chimera of the classical FK506-binding protein (FKBP) and cyclophilin (CYN), connected by a flexible linker. They are found exclusively in monocellular organisms. The modular builds of these molecules represent two distinct types: CYN-(linker)-FKBP and FKBP-3TPR (tetratricopeptide repeat)-CYN. Abbreviated respectively as CFBP and FCBP, the two classes also exhibit distinct organism preference, the CFBP being found in prokaryotes, and the FCBP in eukaryotes. This review summarizes the mystery of these unique class of prolyl isomerases, focusing on their host organisms, potential physiological role, and likely routes of evolution.
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74
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Steric Repulsion Forces Contributed by PEGylation of Interleukin-1 Receptor Antagonist Reduce Gelation and Aggregation at the Silicone Oil-Water Interface. J Pharm Sci 2018; 108:162-172. [PMID: 30395835 DOI: 10.1016/j.xphs.2018.10.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/24/2018] [Accepted: 10/24/2018] [Indexed: 01/19/2023]
Abstract
Silicone oil, used as a lubricating coating in pharmaceutical containers, has been implicated as a cause of therapeutic protein aggregation. After adsorbing to silicone oil-water interfaces, proteins may form interfacial gels, which can be transported into solution as insoluble aggregates if the interfaces are perturbed. Mechanical interfacial perturbation of both monomeric recombinant human interleukin-1 receptor antagonist (rhIL-1ra) and PEGylated rhIL-1ra (PEG rhIL-1ra) in siliconized syringes resulted in losses of soluble monomeric protein. However, the loss of rhIL-1ra was twice that for PEG rhIL-1ra; even though in solution, PEG rhIL-1ra had a lower ΔGunf and exhibited a more perturbed tertiary structure at the interface. Net protein-protein interactions in solution for rhIL-1ra were attractive but increased steric repulsion because of PEGylation led to net repulsive interactions for PEG rhIL-1ra. Attractive interactions for rhIL-1ra were associated with increases in intermolecular β-sheet content at the interface, whereas no intermolecular β-sheet structures were observed for adsorbed PEG rhIL-1ra. rhIL-1ra formed interfacial gels that were 5 times stronger than those formed by PEG rhIL-1ra. Thus, the steric repulsion contributed by the PEGylation resulted in decreased interfacial gelation and in the reduction of aggregation, in spite of the destabilizing effects of PEGylation on the protein's conformational stability.
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75
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Li M, Martinez S, Hausinger RP, Emerson JP. Thermodynamics of Iron(II) and Substrate Binding to the Ethylene-Forming Enzyme. Biochemistry 2018; 57:5696-5705. [PMID: 30183265 PMCID: PMC7199160 DOI: 10.1021/acs.biochem.8b00730] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ethylene-forming enzyme (EFE), like many other 2-oxoglutarate (2OG)-dependent nonheme iron(II) oxygenases, catalyzes the oxidative decarboxylation of 2OG to succinate and CO2 to generate a highly reactive iron species that hydroxylates a specific alkane C-H bond, in this case targeting l-arginine (Arg) for hydroxylation. However, the prominently observed reactivity of EFE is the transformation of 2OG into ethylene and three molecules of CO2. Crystallographic and biochemical studies have led to several proposed mechanisms for this 2-fold reactivity, but the detailed reaction steps are still obscure. Here, the thermodynamics associated with iron(II), 2OG, and Arg binding to EFE are studied using calorimetry (isothermal titration calorimetry and differential scanning calorimetry) to gain insight into how these binding equilibria organize the active site of EFE, which may have an impact on the O2 activation pathways observed in this system. Calorimetric data show that the addition of iron(II), Arg, and 2OG increases the stability over that of the apoenzyme, and there is distinctive cooperativity between substrate and cofactor binding. The energetics of binding of 2OG to Fe·EFE are consistent with a unique monodentate binding mode, which is different than the prototypical 2OG coordination mode in other 2OG-dependent oxygenases. This difference in the pre-O2 activation equilibria may be important for supporting the alternative ethylene-forming chemistry of EFE.
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Affiliation(s)
- Mingjie Li
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Salette Martinez
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, United States
| | - Robert P. Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-4320, United States
| | - Joseph P. Emerson
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
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76
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Cis/trans isomerization of proline peptide bonds in the backbone of cyclic disulfide‐bridged peptides. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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77
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Wu T, Jiang Q, Wu D, Hu Y, Chen S, Ding T, Ye X, Liu D, Chen J. What is new in lysozyme research and its application in food industry? A review. Food Chem 2018; 274:698-709. [PMID: 30372997 DOI: 10.1016/j.foodchem.2018.09.017] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/04/2018] [Accepted: 09/03/2018] [Indexed: 02/06/2023]
Abstract
Lysozyme, an important bacteriostatic protein, is widely distributed in nature. It is generally believed that the high efficiency of lysozyme in inhibiting gram-positive bacteria is caused by its ability to cleave the β-(1,4)-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine. In recent years, there has been growing interest in modifying lysozyme via physical or chemical interactions in order to improve its sensitivity against gram-negative bacterial strains. This review addresses some significant techniques, including sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), infrared (IR) spectra, fluorescence spectroscopy, nuclear magnetic resonance (NMR), UV-vis spectroscopy, circular dichroism (CD) spectra and differential scanning calorimetry (DSC), which can be used to characterize lysozymes and methods that modify lysozymes with carbohydrates to enhance their various physicochemical characteristics. The applications of biomaterials based on lysozymes in different food matrices are also discussed.
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Affiliation(s)
- Tiantian Wu
- National Engineering Laboratory of Intelligent Food Technoklogy and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Qingqing Jiang
- National Engineering Laboratory of Intelligent Food Technoklogy and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China; Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Dan Wu
- Zhiwei Guan Foods Co., Ltd, Hangzhou 311199, China
| | - Yaqin Hu
- National Engineering Laboratory of Intelligent Food Technoklogy and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.
| | - Shiguo Chen
- National Engineering Laboratory of Intelligent Food Technoklogy and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Tian Ding
- National Engineering Laboratory of Intelligent Food Technoklogy and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Xingqian Ye
- National Engineering Laboratory of Intelligent Food Technoklogy and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Donghong Liu
- National Engineering Laboratory of Intelligent Food Technoklogy and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Jianchu Chen
- National Engineering Laboratory of Intelligent Food Technoklogy and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
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78
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Investigating the role of loop 131–140 in activity and thermal stability of chondroitinase ABC I. Int J Biol Macromol 2018; 116:811-816. [DOI: 10.1016/j.ijbiomac.2018.05.094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 11/22/2022]
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79
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Beerens K, Mazurenko S, Kunka A, Marques SM, Hansen N, Musil M, Chaloupkova R, Waterman J, Brezovsky J, Bednar D, Prokop Z, Damborsky J. Evolutionary Analysis As a Powerful Complement to Energy Calculations for Protein Stabilization. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01677] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Koen Beerens
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Antonin Kunka
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Sergio M. Marques
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Milos Musil
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- Department of Information Systems, Faculty of Information Technology, Brno University of Technology, 612 66 Brno, Czech Republic
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jitka Waterman
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
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80
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Quezada AG, Cabrera N, Piñeiro Á, Díaz-Salazar AJ, Díaz-Mazariegos S, Romero-Romero S, Pérez-Montfort R, Costas M. A strategy based on thermal flexibility to design triosephosphate isomerase proteins with increased or decreased kinetic stability. Biochem Biophys Res Commun 2018; 503:3017-3022. [PMID: 30143261 DOI: 10.1016/j.bbrc.2018.08.087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 08/11/2018] [Indexed: 11/19/2022]
Abstract
Kinetic stability of proteins determines their susceptibility to irreversibly unfold in a time-dependent process, and therefore its half-life. A residue displacement analysis of temperature-induced unfolding molecular dynamics simulations was recently employed to define the thermal flexibility of proteins. This property was found to be correlated with the activation energy barrier (Eact) separating the native from the transition state in the denaturation process. The Eact was determined from the application of a two-state irreversible model to temperature unfolding experiments using differential scanning calorimetry (DSC). The contribution of each residue to the thermal flexibility of proteins is used here to propose multiple mutations in triosephosphate isomerase (TIM) from Trypanosoma brucei (TbTIM) and Trypanosoma cruzi (TcTIM), two parasites closely related by evolution. These two enzymes, taken as model systems, have practically identical structure but large differences in their kinetic stability. We constructed two functional TIM variants with more than twice and less than half the activation energy of their respective wild-type reference structures. The results show that the proposed strategy is able to identify the crucial residues for the kinetic stability in these enzymes. As it occurs with other protein properties reflecting their complex behavior, kinetic stability appears to be the consequence of an extensive network of inter-residue interactions, acting in a concerted manner. The proposed strategy to design variants can be used with other proteins, to increase or decrease their functional half-life.
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Affiliation(s)
- Andrea G Quezada
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México City 04510, Mexico.
| | - Nallely Cabrera
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, 04510, Mexico
| | - Ángel Piñeiro
- Soft Matter and Molecular Biophysics Group, Departamento de Física Aplicada, Facultad de Física, Universidad de Santiago de Compostela, Campus Vida s/n, E-15782, Santiago de Compostela, Spain
| | - A Jessica Díaz-Salazar
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México City 04510, Mexico
| | - Selma Díaz-Mazariegos
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, 04510, Mexico
| | - Sergio Romero-Romero
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México City, 04510, Mexico
| | - Ruy Pérez-Montfort
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, 04510, Mexico
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México City 04510, Mexico.
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81
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Mesa-Torres N, Betancor-Fernández I, Oppici E, Cellini B, Salido E, Pey AL. Evolutionary Divergent Suppressor Mutations in Conformational Diseases. Genes (Basel) 2018; 9:E352. [PMID: 30011855 PMCID: PMC6071075 DOI: 10.3390/genes9070352] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/09/2018] [Accepted: 07/11/2018] [Indexed: 12/26/2022] Open
Abstract
Neutral and adaptive mutations are key players in the evolutionary dynamics of proteins at molecular, cellular and organismal levels. Conversely, largely destabilizing mutations are rarely tolerated by evolution, although their occurrence in diverse human populations has important roles in the pathogenesis of conformational diseases. We have recently proposed that divergence at certain sites from the consensus (amino acid) state during mammalian evolution may have rendered some human proteins more vulnerable towards disease-associated mutations, primarily by decreasing their conformational stability. We herein extend and refine this hypothesis discussing results from phylogenetic and structural analyses, structure-based energy calculations and structure-function studies at molecular and cellular levels. As proof-of-principle, we focus on different mammalian orthologues of the NQO1 (NAD(P)H:quinone oxidoreductase 1) and AGT (alanine:glyoxylate aminotransferase) proteins. We discuss the different loss-of-function pathogenic mechanisms associated with diseases involving the two enzymes, including enzyme inactivation, accelerated degradation, intracellular mistargeting, and aggregation. Last, we take into account the potentially higher robustness of mammalian orthologues containing certain consensus amino acids as suppressors of human disease, and their relation with different intracellular post-translational modifications and protein quality control capacities, to be discussed as sources of phenotypic variability between human and mammalian models of disease and as tools for improving current therapeutic approaches.
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Affiliation(s)
- Noel Mesa-Torres
- Department of Physical Chemistry, University of Granada, 18010 Granada, Spain.
| | - Isabel Betancor-Fernández
- Hospital Universitario de Canarias, Center for Rare Diseases (CIBERER), University of La Laguna, 38320 Tenerife, Spain.
| | - Elisa Oppici
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, 37134 Verona, Italy.
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy.
| | - Eduardo Salido
- Hospital Universitario de Canarias, Center for Rare Diseases (CIBERER), University of La Laguna, 38320 Tenerife, Spain.
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, 18010 Granada, Spain.
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82
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Gandhi AV, Arlotta KJ, Chen HN, Owen SC, Carpenter JF. Biophysical Properties and Heating-Induced Aggregation of Lysine-Conjugated Antibody-Drug Conjugates. J Pharm Sci 2018; 107:1858-1869. [DOI: 10.1016/j.xphs.2018.03.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/17/2018] [Accepted: 03/27/2018] [Indexed: 12/12/2022]
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83
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Unusual duplication mutation in a surface loop of human transthyretin leads to an aggressive drug-resistant amyloid disease. Proc Natl Acad Sci U S A 2018; 115:E6428-E6436. [PMID: 29941560 DOI: 10.1073/pnas.1802977115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transthyretin (TTR) is a globular tetrameric transport protein in plasma. Nearly 140 single amino acid substitutions in TTR cause life-threatening amyloid disease. We report a one-of-a-kind pathological variant featuring a Glu51, Ser52 duplication mutation (Glu51_Ser52dup). The proband, heterozygous for the mutation, exhibited an unusually aggressive amyloidosis that was refractory to treatment with the small-molecule drug diflunisal. To understand the poor treatment response and expand therapeutic options, we explored the structure and stability of recombinant Glu51_Ser52dup. The duplication did not alter the protein secondary or tertiary structure but decreased the stability of the TTR monomer and tetramer. Diflunisal, which bound with near-micromolar affinity, partially restored tetramer stability. The duplication had no significant effect on the free energy and enthalpy of diflunisal binding, and hence on the drug-protein interactions. However, the duplication induced tryptic digestion of TTR at near-physiological conditions, releasing a C-terminal fragment 49-129 that formed amyloid fibrils under conditions in which the full-length protein did not. Such C-terminal fragments, along with the full-length TTR, comprise amyloid deposits in vivo. Bioinformatics and structural analyses suggested that increased disorder in the surface loop, which contains the Glu51_Ser52dup duplication, not only helped generate amyloid-forming fragments but also decreased structural protection in the amyloidogenic residue segment 25-34, promoting misfolding of the full-length protein. Our studies of a unique duplication mutation explain its diflunisal-resistant nature, identify misfolding pathways for amyloidogenic TTR variants, and provide therapeutic targets to inhibit amyloid fibril formation by variant TTR.
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84
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Kawade R, Akiba H, Entzminger K, Maruyama T, Okumura CJ, Tsumoto K. Roles of the disulfide bond between the variable and the constant domains of rabbit immunoglobulin kappa chains in thermal stability and affinity. Protein Eng Des Sel 2018; 31:243-247. [DOI: 10.1093/protein/gzy008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 04/13/2018] [Indexed: 12/17/2022] Open
Affiliation(s)
- Raiji Kawade
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Hiroki Akiba
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
- Laboratory of Pharmacokinetic Optimization, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki City, Osaka, Japan
| | - Kevin Entzminger
- Abwiz Bio Inc., 9823 Pacific Heights Blvd Suite J, San Diego, CA, USA
| | - Toshiaki Maruyama
- Abwiz Bio Inc., 9823 Pacific Heights Blvd Suite J, San Diego, CA, USA
| | - C J Okumura
- Abwiz Bio Inc., 9823 Pacific Heights Blvd Suite J, San Diego, CA, USA
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
- Laboratory of Pharmacokinetic Optimization, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki City, Osaka, Japan
- Medical Proteomics Laboratory, Institute of Medical Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan
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85
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The structural basis of nanobody unfolding reversibility and thermoresistance. Sci Rep 2018; 8:7934. [PMID: 29784954 PMCID: PMC5962586 DOI: 10.1038/s41598-018-26338-z] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/10/2018] [Indexed: 12/17/2022] Open
Abstract
Nanobodies represent the variable binding domain of camelid heavy-chain antibodies and are employed in a rapidly growing range of applications in biotechnology and biomedicine. Their success is based on unique properties including their reported ability to reversibly refold after heat-induced denaturation. This view, however, is contrasted by studies which involve irreversibly aggregating nanobodies, asking for a quantitative analysis that clearly defines nanobody thermoresistance and reveals the determinants of unfolding reversibility and aggregation propensity. By characterizing nearly 70 nanobodies, we show that irreversible aggregation does occur upon heat denaturation for the large majority of binders, potentially affecting application-relevant parameters like stability and immunogenicity. However, by deriving aggregation propensities from apparent melting temperatures, we show that an optional disulfide bond suppresses nanobody aggregation. This effect is further enhanced by increasing the length of a complementarity determining loop which, although expected to destabilize, contributes to nanobody stability. The effect of such variations depends on environmental conditions, however. Nanobodies with two disulfide bonds, for example, are prone to lose their functionality in the cytosol. Our study suggests strategies to engineer nanobodies that exhibit optimal performance parameters and gives insights into general mechanisms which evolved to prevent protein aggregation.
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86
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Microcirculation-mediated preconditioning and intracellular hypothermia. Med Hypotheses 2018; 115:8-12. [PMID: 29685204 DOI: 10.1016/j.mehy.2018.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 03/19/2018] [Indexed: 01/08/2023]
Abstract
Microcirculation is a network of perfused capillaries that connects macrocirculation with the cells. Although research has provided insight into microcirculatory blood flow, our knowledge remains limited. In this article, we propose a new role of microcirculation in physiological and shock states. In healthy individuals, microcirculation maintains cellular homeostasis via preconditioning. When blood volume decreases, the ensuing microcirculatory changes result in heterogeneity of perfusion and tissue oxygenation. Initially, this is partly compensated by the preserved autoregulation and the increase in the metabolism rate of cells, but at later stages, the loss of autoregulation activates the cascade of intracellular hypothermia.
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87
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Buldun CM, Jean JX, Bedford MR, Howarth M. SnoopLigase Catalyzes Peptide–Peptide Locking and Enables Solid-Phase Conjugate Isolation. J Am Chem Soc 2018; 140:3008-3018. [DOI: 10.1021/jacs.7b13237] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Can M. Buldun
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
| | - Jisoo X. Jean
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
| | | | - Mark Howarth
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
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88
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Haaga J, Gunton JD, Buckles CN, Rickman JM. Early stage aggregation of a coarse-grained model of polyglutamine. J Chem Phys 2018; 148:045106. [DOI: 10.1063/1.5010888] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Jason Haaga
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - J. D. Gunton
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - C. Nadia Buckles
- Department of Physics and Astronomy, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - J. M. Rickman
- Department of Materials Science and Engineering and Department of Physics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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89
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90
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Betancor-Fernández I, Timson DJ, Salido E, Pey AL. Natural (and Unnatural) Small Molecules as Pharmacological Chaperones and Inhibitors in Cancer. Handb Exp Pharmacol 2018; 245:155-190. [PMID: 28993836 DOI: 10.1007/164_2017_55] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mutations causing single amino acid exchanges can dramatically affect protein stability and function, leading to disease. In this chapter, we will focus on several representative cases in which such mutations affect protein stability and function leading to cancer. Mutations in BRAF and p53 have been extensively characterized as paradigms of loss-of-function/gain-of-function mechanisms found in a remarkably large fraction of tumours. Loss of RB1 is strongly associated with cancer progression, although the molecular mechanisms by which missense mutations affect protein function and stability are not well known. Polymorphisms in NQO1 represent a remarkable example of the relationships between intracellular destabilization and inactivation due to dynamic alterations in protein ensembles leading to loss of function. We will review the function of these proteins and their dysfunction in cancer and then describe in some detail the effects of the most relevant cancer-associated single amino exchanges using a translational perspective, from the viewpoints of molecular genetics and pathology, protein biochemistry and biophysics, structural, and cell biology. This will allow us to introduce several representative examples of natural and synthetic small molecules applied and developed to overcome functional, stability, and regulatory alterations due to cancer-associated amino acid exchanges, which hold the promise for using them as potential pharmacological cancer therapies.
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Affiliation(s)
- Isabel Betancor-Fernández
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, Tenerife, 38320, Spain
| | - David J Timson
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton, BN2 4GJ, UK
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, Tenerife, 38320, Spain
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, Granada, 18071, Spain.
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91
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Bozelli JC, Hou YH, Epand RM. Thermodynamics of Methyl-β-cyclodextrin-Induced Lipid Vesicle Solubilization: Effect of Lipid Headgroup and Backbone. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:13882-13891. [PMID: 29120189 DOI: 10.1021/acs.langmuir.7b03447] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The low aqueous solubility of phospholipids makes necessary the use of lipid carriers in studies ranging from lipid traffic and metabolism to the engineering of model membranes bearing lipid transverse asymmetry. One particular lipid carrier that has proven to be particularly useful is methyl-β-cyclodextrin (MβCD). To assess the interaction of MβCD with structurally different phospholipids, the present work reports the results of isothermal titration calorimetry in conjunction with dynamic light scattering measurements. The results showed that the interaction of MβCD with large unilamellar vesicles composed of a single type of lipid led to the solubilization of the lipid vesicle and, consequently, the complexation of MβCD with the lipids. This interaction is dependent on the nature of the lipid headgroup, with a preferable interaction with phosphatidylglycerol in comparison to phosphatidylcholine. It was also possible to show a role played by the phospholipid backbone in this interaction. In many cases, the differences in the transfer energy between one lipid and another in going from a bilayer to a cyclodextrin-bound state can be qualitatively explained by the energy required to extract the lipid from a bilayer. In all cases, the data showed that the solubilization of the vesicles is entropically driven with a large negative ΔCp, suggesting a mechanism dependent on the hydrophobic effect.
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Affiliation(s)
- José Carlos Bozelli
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre , Hamilton, Ontario L8S 4K1 Canada
| | - Yu Heng Hou
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre , Hamilton, Ontario L8S 4K1 Canada
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre , Hamilton, Ontario L8S 4K1 Canada
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92
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Liyaghatdar Z, Emamzadeh R, Rasa SMM, Nazari M. Trehalose radial networks protect Renilla luciferase helical layers against thermal inactivation. Int J Biol Macromol 2017; 105:66-73. [DOI: 10.1016/j.ijbiomac.2017.06.113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 06/12/2017] [Accepted: 06/21/2017] [Indexed: 12/13/2022]
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93
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Mazurenko S, Kunka A, Beerens K, Johnson CM, Damborsky J, Prokop Z. Exploration of Protein Unfolding by Modelling Calorimetry Data from Reheating. Sci Rep 2017; 7:16321. [PMID: 29176711 PMCID: PMC5701188 DOI: 10.1038/s41598-017-16360-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/10/2017] [Indexed: 01/14/2023] Open
Abstract
Studies of protein unfolding mechanisms are critical for understanding protein functions inside cells, de novo protein design as well as defining the role of protein misfolding in neurodegenerative disorders. Calorimetry has proven indispensable in this regard for recording full energetic profiles of protein unfolding and permitting data fitting based on unfolding pathway models. While both kinetic and thermodynamic protein stability are analysed by varying scan rates and reheating, the latter is rarely used in curve-fitting, leading to a significant loss of information from experiments. To extract this information, we propose fitting both first and second scans simultaneously. Four most common single-peak transition models are considered: (i) fully reversible, (ii) fully irreversible, (iii) partially reversible transitions, and (iv) general three-state models. The method is validated using calorimetry data for chicken egg lysozyme, mutated Protein A, three wild-types of haloalkane dehalogenases, and a mutant stabilized by protein engineering. We show that modelling of reheating increases the precision of determination of unfolding mechanisms, free energies, temperatures, and heat capacity differences. Moreover, this modelling indicates whether alternative refolding pathways might occur upon cooling. The Matlab-based data fitting software tool and its user guide are provided as a supplement.
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Affiliation(s)
- Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic
| | - Antonin Kunka
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Koen Beerens
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic
| | - Christopher M Johnson
- Biophysics Facilities, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic.
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic.
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94
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Pasquevich MY, Dreon MS, Qiu JW, Mu H, Heras H. Convergent evolution of plant and animal embryo defences by hyperstable non-digestible storage proteins. Sci Rep 2017; 7:15848. [PMID: 29158565 PMCID: PMC5696525 DOI: 10.1038/s41598-017-16185-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/08/2017] [Indexed: 11/09/2022] Open
Abstract
Plants have evolved sophisticated embryo defences by kinetically-stable non-digestible storage proteins that lower the nutritional value of seeds, a strategy that have not been reported in animals. To further understand antinutritive defences in animals, we analysed PmPV1, massively accumulated in the eggs of the gastropod Pomacea maculata, focusing on how its structure and structural stability features affected its capacity to withstand passage through predator guts. The native protein withstands >50 min boiling and resists the denaturing detergent sodium dodecyl sulphate (SDS), indicating an unusually high structural stability (i.e., kinetic stability). PmPV1 is highly resistant to in vitro proteinase digestion and displays structural stability between pH 2.0-12.0 and 25-85 °C. Furthermore, PmPV1 withstands in vitro and mice digestion and is recovered unchanged in faeces, supporting an antinutritive defensive function. Subunit sequence similarities suggest a common origin and tolerance to mutations. This is the first known animal genus that, like plant seeds, lowers the nutritional value of eggs by kinetically-stable non-digestible storage proteins that survive the gut of predators unaffected. The selective pressure of the harsh gastrointestinal environment would have favoured their appearance, extending by convergent evolution the presence of plant-like hyperstable antinutritive proteins to unattended reproductive stages in animals.
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Affiliation(s)
- María Yanina Pasquevich
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), Universidad Nacional de La Plata (UNLP) - CONICET CCT-La Plata, La Plata, Argentina.,Cátedra de Bioquímica y Biología Molecular, Facultad de Ciencias Médicas, UNLP, Argentina
| | - Marcos Sebastián Dreon
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), Universidad Nacional de La Plata (UNLP) - CONICET CCT-La Plata, La Plata, Argentina.,Cátedra de Bioquímica y Biología Molecular, Facultad de Ciencias Médicas, UNLP, Argentina
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, P.R. China
| | - Huawei Mu
- Department of Biology, Hong Kong Baptist University, Hong Kong, P.R. China
| | - Horacio Heras
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), Universidad Nacional de La Plata (UNLP) - CONICET CCT-La Plata, La Plata, Argentina. .,Cátedra de Química Biológica, Facultad de Ciencias Naturales y Museo, UNLP, Argentina.
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95
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Colón W, Church J, Sen J, Thibeault J, Trasatti H, Xia K. Biological Roles of Protein Kinetic Stability. Biochemistry 2017; 56:6179-6186. [PMID: 29087706 DOI: 10.1021/acs.biochem.7b00942] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A protein's stability may range from nonexistent, as in the case of intrinsically disordered proteins, to very high, as indicated by a protein's resistance to degradation, even under relatively harsh conditions. The stability of this latter group is usually under kinetic control because of a high activation energy for unfolding that virtually traps the protein in a specific conformation, thereby conferring resistance to proteolytic degradation and misfolding aggregation. The usual outcome of kinetic stability is a longer protein half-life. Thus, the protective role of protein kinetic stability is often appreciated, but relatively little is known about the extent of biological roles related to this property. In this Perspective, we will discuss several known or putative biological roles of protein kinetic stability, including protection from stressors to avoid aggregation or premature degradation, achieving long-term phenotypic change, and regulating cellular processes by controlling the trigger and timing of molecular motion. The picture that emerges from this analysis is that protein kinetic stability is involved in a myriad of known and yet to be discovered biological functions via its ability to confer degradation resistance and control the timing, extent, and permanency of molecular motion.
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Affiliation(s)
- Wilfredo Colón
- Department of Chemistry and Chemical Biology, ‡Center for Biotechnology and Interdisciplinary Studies, and §Biochemistry and Biophysics Graduate Program, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Jennifer Church
- Department of Chemistry and Chemical Biology, ‡Center for Biotechnology and Interdisciplinary Studies, and §Biochemistry and Biophysics Graduate Program, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Jayeeta Sen
- Department of Chemistry and Chemical Biology, ‡Center for Biotechnology and Interdisciplinary Studies, and §Biochemistry and Biophysics Graduate Program, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Jane Thibeault
- Department of Chemistry and Chemical Biology, ‡Center for Biotechnology and Interdisciplinary Studies, and §Biochemistry and Biophysics Graduate Program, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Hannah Trasatti
- Department of Chemistry and Chemical Biology, ‡Center for Biotechnology and Interdisciplinary Studies, and §Biochemistry and Biophysics Graduate Program, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Ke Xia
- Department of Chemistry and Chemical Biology, ‡Center for Biotechnology and Interdisciplinary Studies, and §Biochemistry and Biophysics Graduate Program, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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96
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Pazhang M, Mardi N, Mehrnejad F, Chaparzadeh N. The combinatorial effects of osmolytes and alcohols on the stability of pyrazinamidase: Methanol affects the enzyme stability through hydrophobic interactions and hydrogen bonds. Int J Biol Macromol 2017; 108:1339-1347. [PMID: 29129628 DOI: 10.1016/j.ijbiomac.2017.11.039] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/01/2017] [Accepted: 11/08/2017] [Indexed: 11/24/2022]
Abstract
Inside the cells, proteins are surrounded by mixtures of different osmolytes. However, our current understanding of the combinatorial effects of such mixtures on the stability of proteins remains elusive. In the present study, the stability and structure of recombinant pyrazinamidase (PZase) from Mycobacterium tuberculosis were analyzed in the presence of stabilizing osmolytes (sorbitol, sucrose and glycerol) and alcohols (methanol, ethanol, isopropanol and n-propanol). The far-UV and near-UV circular dichroism (CD), intrinsic fluorescence and thermostability results indicated that methanol, unexpectedly, has stronger effect on destabilization of the enzyme compared to ethanol which has larger log P. Interestingly, the relative half-life of PZase was longer in mixtures methanol with the osmolytes, sorbitol or sucrose (expectedly), or glycerol (unexpectedly), compared to other alcohols. Molecular dynamics simulation results showed that methanol increases the flexibility of region 5-40 and loop 51-71 in the PZase, which are potentially crucial for the stability and activity of the enzyme, respectively. Our results indicated that methanol can interact with PZase via hydrophobic interactions and hydrogen bonds, and therefore resulting in destabilization of the structure of the enzyme. In addition, glycerol probably increases the stability of the enzyme in methanol by disrupting the unfavorable hydrophobic interactions and hydrogen bonds.
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Affiliation(s)
- Mohammad Pazhang
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran.
| | - Narges Mardi
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Faramarz Mehrnejad
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Nader Chaparzadeh
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
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97
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Quezada AG, Díaz-Salazar AJ, Cabrera N, Pérez-Montfort R, Piñeiro Á, Costas M. Interplay between Protein Thermal Flexibility and Kinetic Stability. Structure 2017; 25:167-179. [PMID: 28052236 DOI: 10.1016/j.str.2016.11.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/18/2016] [Accepted: 11/22/2016] [Indexed: 02/07/2023]
Abstract
Kinetic stability is a key parameter to comprehend protein behavior and it plays a central role to understand how evolution has reached the balance between function and stability in cell-relevant timescales. Using an approach that includes simulations, protein engineering, and calorimetry, we show that there is a clear correlation between kinetic stability determined by differential scanning calorimetry and protein thermal flexibility obtained from a novel method based on temperature-induced unfolding molecular dynamics simulations. Thermal flexibility quantitatively measures the increment of the conformational space available to the protein when energy in provided. The (β/α)8 barrel fold of two closely related by evolution triosephosphate isomerases from two trypanosomes are used as model systems. The kinetic stability-thermal flexibility correlation has predictive power for the studied proteins, suggesting that the strategy and methodology discussed here might be applied to other proteins in biotechnological developments, evolutionary studies, and the design of protein based therapeutics.
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Affiliation(s)
- Andrea G Quezada
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México City 04510, México
| | - A Jessica Díaz-Salazar
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México City 04510, México
| | - Nallely Cabrera
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, México
| | - Ruy Pérez-Montfort
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, México
| | - Ángel Piñeiro
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela, Santiago de Compostela 15782, Spain.
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México City 04510, México.
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98
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Chaturvedi D, Mahalakshmi R. Transmembrane β-barrels: Evolution, folding and energetics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2467-2482. [PMID: 28943271 DOI: 10.1016/j.bbamem.2017.09.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/16/2017] [Accepted: 09/19/2017] [Indexed: 12/23/2022]
Abstract
The biogenesis of transmembrane β-barrels (outer membrane proteins, or OMPs) is an elaborate multistep orchestration of the nascent polypeptide with translocases, barrel assembly machinery, and helper chaperone proteins. Several theories exist that describe the mechanism of chaperone-assisted OMP assembly in vivo and unassisted (spontaneous) folding in vitro. Structurally, OMPs of bacterial origin possess even-numbered strands, while mitochondrial β-barrels are even- and odd-stranded. Several underlying similarities between prokaryotic and eukaryotic β-barrels and their folding machinery are known; yet, the link in their evolutionary origin is unclear. While OMPs exhibit diversity in sequence and function, they share similar biophysical attributes and structure. Similarly, it is important to understand the intricate OMP assembly mechanism, particularly in eukaryotic β-barrels that have evolved to perform more complex functions. Here, we deliberate known facets of β-barrel evolution, folding, and stability, and attempt to highlight outstanding questions in β-barrel biogenesis and proteostasis.
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Affiliation(s)
- Deepti Chaturvedi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India.
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India.
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99
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Knies JL, Cai F, Weinreich DM. Enzyme Efficiency but Not Thermostability Drives Cefotaxime Resistance Evolution in TEM-1 β-Lactamase. Mol Biol Evol 2017; 34:1040-1054. [PMID: 28087769 PMCID: PMC5400381 DOI: 10.1093/molbev/msx053] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A leading intellectual challenge in evolutionary genetics is to identify the specific phenotypes that drive adaptation. Enzymes offer a particularly promising opportunity to pursue this question, because many enzymes' contributions to organismal fitness depend on a comparatively small number of experimentally accessible properties. Moreover, on first principles the demands of enzyme thermostability stand in opposition to the demands of catalytic activity. This observation, coupled with the fact that enzymes are only marginally thermostable, motivates the widely held hypothesis that mutations conferring functional improvement require compensatory mutations to restore thermostability. Here, we explicitly test this hypothesis for the first time, using four missense mutations in TEM-1 β-lactamase that jointly increase cefotaxime Minimum Inhibitory Concentration (MIC) ∼1500-fold. First, we report enzymatic efficiency (kcat/KM) and thermostability (Tm, and thence ΔG of folding) for all combinations of these mutations. Next, we fit a quantitative model that predicts MIC as a function of kcat/KM and ΔG. While kcat/KM explains ∼54% of the variance in cefotaxime MIC (∼92% after log transformation), ΔG does not improve explanatory power of the model. We also find that cefotaxime MIC rises more slowly in kcat/KM than predicted. Several explanations for these discrepancies are suggested. Finally, we demonstrate substantial sign epistasis in MIC and kcat/KM, and antagonistic pleiotropy between phenotypes, in spite of near numerical additivity in the system. Thus constraints on selectively accessible trajectories, as well as limitations in our ability to explain such constraints in terms of underlying mechanisms are observed in a comparatively "well-behaved" system.
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Affiliation(s)
- Jennifer L Knies
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI
| | - Fei Cai
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI
| | - Daniel M Weinreich
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI
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100
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González Flecha FL. Kinetic stability of membrane proteins. Biophys Rev 2017; 9:563-572. [PMID: 28921106 DOI: 10.1007/s12551-017-0324-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/29/2017] [Indexed: 12/25/2022] Open
Abstract
Although membrane proteins constitute an important class of biomolecules involved in key cellular processes, study of the thermodynamic and kinetic stability of their structures is far behind that of soluble proteins. It is known that many membrane proteins become unstable when removed by detergent extraction from the lipid environment. In addition, most of them undergo irreversible denaturation, even under mild experimental conditions. This process was found to be associated with partial unfolding of the polypeptide chain exposing hydrophobic regions to water, and it was proposed that the formation of kinetically trapped conformations could be involved. In this review, we will describe some of the efforts toward understanding the irreversible inactivation of membrane proteins. Furthermore, its modulation by phospholipids, ligands, and temperature will be herein discussed.
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Affiliation(s)
- F Luis González Flecha
- Universidad de Buenos Aires, CONICET, Laboratorio de Biofísica Molecular, Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina.
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