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Zhou P, Wang H, Chen Z, Liu Q. Context contribution to the intermolecular recognition of human ACE2-derived peptides by SARS-CoV-2 spike protein: implications for improving the peptide affinity but not altering the peptide specificity by optimizing indirect readout. Mol Omics 2020; 17:86-94. [PMID: 33174576 DOI: 10.1039/d0mo00103a] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an etiological agent of the current rapidly growing outbreak of coronavirus disease (COVID-19), which is straining health systems around the world. Disrupting the intermolecular association of SARS-CoV-2 spike glycoprotein (S protein) with its cell surface receptor human angiotensin-converting enzyme 2 (hACE2) has been recognized as a promising therapeutic strategy against COVID-19. The association is a typical peptide-mediated interaction, where the hACE adopts an α1-helix, which can form a two-helix bundle with the α2-helix, to pack against a flat pocket on the S protein surface. Here, we demonstrate that the protein context of full-length hACE plays an essential role in supporting the hACE2 α1-helix recognition by viral S protein. Energetic analysis reveals that the α1-helical peptide (αHP) and also the two-helix bundle peptide (tBP) cannot bind effectively to S protein when they are split from the hACE protein. The context contributes moderately and considerably to the direct readout (DR) and indirect readout (IR) of peptide recognition, respectively. Dynamics simulation suggests that the two free peptides exhibit a large intrinsic disorder without the support of protein context, which would incur a considerable entropy penalty upon binding to S protein. To restore the IR effect lost by splitting peptides from hACE, we herein propose employing hydrocarbon stapling and cyclization strategies to constrain the free αHP and tBP peptides into their native ordered conformations, respectively. The stapling and cyclization are carefully designed in order to avoid influencing the peptide DR effect, which has been demonstrated to improve the peptide binding affinity (but not specificity) to S protein. The stapling/cyclization-imposed conformational constraint can effectively minimize the unfavorable IR effect (i) by reducing the peptide flexibility and entropy cost upon their binding to S protein, and (ii) by helping peptide pre-folding into their native state to facilitate the conformational selection by S protein.
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Affiliation(s)
- Peng Zhou
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, No. 2006 Xiyuan Ave West Hi-Tech Zone, Chengdu 611731, China.
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2
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Wälchli R, Ressurreição M, Vogg S, Feidl F, Angelo J, Xu X, Ghose S, Jian Li Z, Le Saoût X, Souquet J, Broly H, Morbidelli M. Understanding mAb aggregation during low pH viral inactivation and subsequent neutralization. Biotechnol Bioeng 2019; 117:687-700. [PMID: 31784982 DOI: 10.1002/bit.27237] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/22/2019] [Accepted: 11/22/2019] [Indexed: 12/31/2022]
Abstract
Monoclonal antibodies (mAbs) and related recombinant proteins continue to gain importance in the treatment of a great variety of diseases. Despite significant advances, their manufacturing can still present challenges owing to their molecular complexity and stringent regulations with respect to product purity, stability, safety, and so forth. In this context, protein aggregates are of particular concern due to their immunogenic potential. During manufacturing, mAbs routinely undergo acidic treatment to inactivate viral contamination, which can lead to their aggregation and thereby to product loss. To better understand the underlying mechanism so as to propose strategies to mitigate the issue, we systematically investigated the denaturation and aggregation of two mAbs at low pH as well as after neutralization. We observed that at low pH and low ionic strength, mAb surface hydrophobicity increased whereas molecular size remained constant. After neutralization of acidic mAb solutions, the fraction of monomeric mAb started to decrease accompanied by an increase on average mAb size. This indicates that electrostatic repulsion prevents denatured mAb molecules from aggregation under acidic pH and low ionic strength, whereas neutralization reduces this repulsion and coagulation initiates. Limiting denaturation at low pH by d-sorbitol addition or temperature reduction effectively improved monomer recovery after neutralization. Our findings might be used to develop innovative viral inactivation procedures during mAb manufacturing that result in higher product yields.
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Affiliation(s)
- Ruben Wälchli
- Department of Chemistry and Applied Biosciences, ETH Zurich, Institute for Chemical and Bioengineering, Zurich, Switzerland
| | - Mariana Ressurreição
- Department of Chemistry and Applied Biosciences, ETH Zurich, Institute for Chemical and Bioengineering, Zurich, Switzerland
| | - Sebastian Vogg
- Department of Chemistry and Applied Biosciences, ETH Zurich, Institute for Chemical and Bioengineering, Zurich, Switzerland
| | - Fabian Feidl
- Department of Chemistry and Applied Biosciences, ETH Zurich, Institute for Chemical and Bioengineering, Zurich, Switzerland
| | - James Angelo
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb Co., Devens, Massachusetts
| | - Xuankuo Xu
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb Co., Devens, Massachusetts
| | - Sanchayita Ghose
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb Co., Devens, Massachusetts
| | - Zheng Jian Li
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb Co., Devens, Massachusetts
| | - Xavier Le Saoût
- Biotech Process Sciences, Merck KGaA, Corsier-sur-Vevey, Vaud, Switzerland
| | - Jonathan Souquet
- Biotech Process Sciences, Merck KGaA, Corsier-sur-Vevey, Vaud, Switzerland
| | - Hervé Broly
- Biotech Process Sciences, Merck KGaA, Corsier-sur-Vevey, Vaud, Switzerland
| | - Massimo Morbidelli
- Department of Chemistry and Applied Biosciences, ETH Zurich, Institute for Chemical and Bioengineering, Zurich, Switzerland
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Laurin N, Célestin F, Clark M, Wilkinson D, Yamashita B, Frégeau C. New incompatibilities uncovered using the Promega DNA IQ™ chemistry. Forensic Sci Int 2015; 257:134-141. [DOI: 10.1016/j.forsciint.2015.07.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 07/06/2015] [Accepted: 07/16/2015] [Indexed: 10/23/2022]
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4
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Ultrasound, thermal and alkali treatments affect extracellular polymeric substances (EPSs) and improve waste activated sludge dewatering. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.01.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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Ahmad E, Rabbani G, Zaidi N, Khan MA, Qadeer A, Ishtikhar M, Singh S, Khan RH. Revisiting ligand-induced conformational changes in proteins: essence, advancements, implications and future challenges. J Biomol Struct Dyn 2013; 31:630-48. [DOI: 10.1080/07391102.2012.706081] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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6
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Torigoe H, Sato N, Nagasawa N. 2'-O,4'-C-ethylene bridged nucleic acid modification enhances pyrimidine motif triplex-forming ability under physiological condition. J Biochem 2012; 152:17-26. [PMID: 22563101 DOI: 10.1093/jb/mvs049] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Since pyrimidine motif triplex DNA is unstable at physiological neutral pH, triplex stabilization at physiological neutral pH is important for improvement of its potential to be applied to various methods in vivo, such as repression of gene expression, mapping of genomic DNA and gene-targeted mutagenesis. For this purpose, we studied the thermodynamic and kinetic effects of a chemical modification, 2'-O,4'-C-ethylene bridged nucleic acid (ENA) modification of triplex-forming oligonucleotide (TFO), on pyrimidine motif triplex formation at physiological neutral pH. Thermodynamic investigations indicated that the modification achieved more than 10-fold increase in the binding constant of the triplex formation. The increased number of the modification in TFO enhanced the increased magnitude of the binding constant. On the basis of the obtained thermodynamic parameters, we suggested that the remarkably increased binding constant by the modification may result from the increased stiffness of TFO in the unbound state. Kinetic studies showed that the considerably decreased dissociation rate constant resulted in the observed increased binding constant by the modification. We conclude that ENA modification of TFO could be a useful chemical modification to promote the triplex formation under physiological neutral condition, and may advance various triplex formation-based methods in vivo.
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Affiliation(s)
- Hidetaka Torigoe
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Tokyo 162-8601, Japan.
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7
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Yang M, Szyc Ł, Elsaesser T. Vibrational dynamics of the water shell of DNA studied by femtosecond two-dimensional infrared spectroscopy. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2011.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Chemical modification of triplex-forming oligonucleotide to promote pyrimidine motif triplex formation at physiological pH. Biochimie 2012; 94:1032-40. [PMID: 22245184 DOI: 10.1016/j.biochi.2012.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 01/04/2012] [Indexed: 11/21/2022]
Abstract
Extreme instability of pyrimidine motif triplex DNA at physiological pH severely limits its use in wide variety of potential applications, such as artificial regulation of gene expression, mapping of genomic DNA, and gene-targeted mutagenesis in vivo. Stabilization of pyrimidine motif triplex at physiological pH is, therefore, crucial for improving its potential in various triplex-formation-based strategies in vivo. To this end, we investigated the effect of 3'-amino-2'-O,4'-C-methylene bridged nucleic acid modification of triplex-forming oligonucleotide (TFO), in which 2'-O and 4'-C of the sugar moiety were bridged with the methylene chain and 3'-O was replaced by 3'-NH, on pyrimidine motif triplex formation at physiological pH. The modification not only significantly increased the thermal stability of the triplex but also increased the binding constant of triplex formation about 15-fold. The increased magnitude of the binding constant was not significantly changed when the number and position of the modification in TFO changed. The consideration of the observed thermodynamic parameters suggested that the increased rigidity of the modified TFO in the free state resulting from the bridging of different positions of the sugar moiety with an alkyl chain and the increased hydration of the modified TFO in the free state caused by the introduction of polar nitrogen atoms may significantly increase the binding constant at physiological pH. The study on the TFO viability in human serum showed that the modification significantly increased the resistance of TFO against nuclease degradation. This study presents an effective approach for designing novel chemically modified TFOs with higher binding affinity of triplex formation at physiological pH and higher nuclease resistance under physiological condition, which may eventually lead to progress in various triplex-formation-based strategies in vivo.
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Yang M, Szyc Ł, Elsaesser T. Decelerated water dynamics and vibrational couplings of hydrated DNA mapped by two-dimensional infrared spectroscopy. J Phys Chem B 2011; 115:13093-100. [PMID: 21972952 DOI: 10.1021/jp208166w] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Double-stranded DNA oligomers containing 23 alternating adenine-thymine base pairs are studied at different hydration levels by femtosecond two-dimensional (2D) infrared spectrosopy. Coupled NH stretching modes of the A-T pairs and OH stretching excitations of the water shell are discerned in the 2D spectra. Limited changes of NH stretching frequencies and line shapes with increasing hydration suggest spectral dynamics governed by DNA rather than water fluctuations. In contrast, OH stretching excitations of the water shell around fully hydrated DNA undergo spectral diffusion on a ~500 fs time scale. The center line slopes of the 2D spectra of hydrated DNA demonstrate a slower decay of the frequency-time correlation function (TCF) than that in neat water, as is evident from a comparison with 2D spectra of neat H(2)O and theoretical TCFs. We attribute this behavior to reduced structural fluctuations of the water shell and a reduced rate of resonant OH stretching energy transfer.
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Affiliation(s)
- Ming Yang
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin, Germany
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10
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Torigoe H, Rahman SMA, Takuma H, Sato N, Imanishi T, Obika S, Sasaki K. Interrupted 2'-o,4'-C-aminomethylene bridged nucleic acid modification enhances pyrimidine motif triplex-forming ability and nuclease resistance under physiological condition. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:63-81. [PMID: 21259164 DOI: 10.1080/15257770.2010.543118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Due to instability of pyrimidine motif triplex DNA at physiological pH, triplex stabilization at physiological pH is crucial in improving its potential in various triplex formation-based strategies in vivo, such as regulation of gene expression, mapping of genomic DNA, and gene-targeted mutagenesis. To this end, we investigated the effect of our previously reported chemical modification, 2'-O,4'-C-aminomethylene bridged nucleic acid (2',4'- BNA(NC)) modification, introduced into interrupted and continuous positions of triplex-forming oligonucleotide (TFO) on pyrimidine motif triplex formation at physiological pH. The interrupted 2',4'-BNA(NC) modifications of TFO increased the binding constant of the triplex formation at physiological pH by more than 10-fold, and significantly increased the nuclease resistance of TFO. On the other hand, the continuous 2',4'-BNA(NC) modification of TFO showed lower ability to promote the triplex formation at physiological pH than the interrupted 2',4'-BNA(NC) modifications of TFO, and did not significantly change the nuclease resistance of TFO. Selection of the interruptedly 2',4'-BNA(NC)-modified positions in TFO was more favorable for achieving the higher binding affinity of the pyrimidine motif triplex formation at physiological pH and the higher nuclease resistance of TFO than that of the continuously 2',4'-BNA(NC)-modified positions in TFO. We conclude that the interrupted 2',4'-BNA(NC) modification of TFO could be a key chemical modification to enhance pyrimidine motif triplex-forming ability and nuclease resistance under physiological condition, and may eventually lead to progress in various triplex formation-based strategies in vivo.
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Affiliation(s)
- Hidetaka Torigoe
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Tokyo, Japan.
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11
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Torigoe H, Rahman SMA, Takuma H, Sato N, Imanishi T, Obika S, Sasaki K. 2'-O,4'-C-aminomethylene-bridged nucleic acid modification with enhancement of nuclease resistance promotes pyrimidine motif triplex nucleic acid formation at physiological pH. Chemistry 2011; 17:2742-51. [PMID: 21264967 DOI: 10.1002/chem.201002745] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Revised: 11/28/2010] [Indexed: 11/08/2022]
Abstract
Due to the instability of pyrimidine motif triplex DNA at physiological pH, triplex stabilization at physiological pH is crucial in improving its potential in various triplex-formation-based strategies in vivo, such as gene expression regulation, genomic DNA mapping, and gene-targeted mutagenesis. To this end, we investigated the thermodynamic and kinetic effects of our previously reported chemical modification, 2'-O,4'-C-aminomethylene-bridged nucleic acid (2',4'-BNA(NC)) modification of triplex-forming oligonucleotide (TFO), on triplex formation at physiological pH. The thermodynamic analyses indicated that the 2',4'-BNA(NC) modification of TFO increased the binding constant of the triplex formation at physiological pH by more than 10-fold. The number and position of the 2',4'-BNA(NC) modification in TFO did not significantly affect the magnitude of the increase in the binding constant. The consideration of the observed thermodynamic parameters suggested that the increased rigidity and the increased degree of hydration of the 2',4'-BNA(NC)-modified TFO in the free state relative to the unmodified TFO may enable the significant increase in the binding constant. Kinetic data demonstrated that the observed increase in the binding constant by the 2',4'-BNA(NC) modification resulted mainly from the considerable decrease in the dissociation rate constant. The TFO stability in human serum showed that the 2',4'-BNA(NC) modification significantly increased the nuclease resistance of TFO. Our results support the idea that the 2',4'-BNA(NC) modification of TFO could be a key chemical modification to achieve higher binding affinity and higher nuclease resistance in the triplex formation under physiological conditions, and may lead to progress in various triplex-formation-based strategies in vivo.
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Affiliation(s)
- Hidetaka Torigoe
- Departmentof Applied Chemistry, Faculty of Science, Tokyo University of Science, Tokyo, Japan.
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12
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Szyc Ł, Yang M, Elsaesser T. Ultrafast energy exchange via water-phosphate interactions in hydrated DNA. J Phys Chem B 2010; 114:7951-7. [PMID: 20481569 DOI: 10.1021/jp101174q] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ionic phosphate groups in the DNA backbone play a key role for DNA hydration. We study ultrafast vibrational dynamics and local interactions of phosphate groups and water by femtosecond two-color pump-probe spectroscopy. The asymmetric (PO(2))(-) stretching vibration nu(AS)(PO(2))(-) of artificial DNA oligomers containing 23 alternating adenine-thymine base pairs displays a lifetime of 340 fs, independent of the hydration level. For DNA at zero relative humidity, excess energy from the decay of the phosphate excitation is transferred within DNA on a 20 ps time scale. For fully hydrated DNA, the water shells around the phosphates serve as a primary heat sink accepting vibrational excess energy from DNA on a femtosecond time scale. OH stretching excitation of water molecules around fully hydrated DNA induces an ultrafast nu(AS)(PO(2))(-) response which includes rearrangements of the hydration shell and a reduction of the average number of phosphate-water hydrogen bonds.
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Affiliation(s)
- Łukasz Szyc
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
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13
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Pliska V. Thermodynamic descriptors, profiles and driving forces in membrane receptor-ligand interactions. J Recept Signal Transduct Res 2010; 30:454-68. [DOI: 10.3109/10799893.2010.515594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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14
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Szyc Ł, Yang M, Nibbering E, Elsaesser T. Ultraschnelle Schwingungsdynamik und lokale Wechselwirkungen in hydratisierter DNA. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Szyc Ł, Yang M, Nibbering E, Elsaesser T. Ultrafast Vibrational Dynamics and Local Interactions of Hydrated DNA. Angew Chem Int Ed Engl 2010; 49:3598-610. [DOI: 10.1002/anie.200905693] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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16
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17
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Fast JL, Cordes AA, Carpenter JF, Randolph TW. Physical instability of a therapeutic Fc fusion protein: domain contributions to conformational and colloidal stability. Biochemistry 2010; 48:11724-36. [PMID: 19899812 DOI: 10.1021/bi900853v] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein therapeutics made up of artificially combined proteins or protein domains, so-called fusion proteins, are a novel and growing class of biopharmaceuticals. We have studied abatacept (Orencia), a fusion protein that is constructed of a modified IgG Fc domain and the soluble part of the T-cell receptor CTLA-4. In accelerated degradation studies conducted at 40 degrees C, a pH shift from 7.5 to 6.0 yields significantly faster aggregation kinetics, as measured by size-exclusion chromatography. To understand how the fusion domains and their interactions contribute to this result, we considered aggregation in light of the modified Lumry-Eyring reaction pathway. Protein conformational stabilities against chaotropes and temperature were measured. The structural consequences of these perturbations were observed by a variety of experimental techniques, including differential scanning calorimetry, circular dichroism, and intrinsic fluorescence. Abatacept's colloidal stability was studied by measuring zeta potentials and osmotic second virial coefficients, as well as by modeling electrostatic potentials on the protein's surface. The domains of abatacept exhibit different conformational stabilities that are highly pH dependent, whereas abatacept was weakly colloidally unstable at pH 6 or 7.5. These results are ascribed to conformational instability of the CTLA-4 and C(H)2 domains, which unfold to form a molten globule-like structure that is aggregation-prone. We suggest the instability against aggregation is determined by the least stable domains.
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Affiliation(s)
- Jonas L Fast
- Department of Chemical and Biological Engineering, Center for Pharmaceutical Biotechnology, University of Colorado, Boulder, Colorado 80309, USA.
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18
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Torigoe H, Sasaki K, Katayama T. Thermodynamic and Kinetic Effects of Morpholino Modification on Pyrimidine Motif Triplex Nucleic Acid Formation under Physiological Condition. J Biochem 2009; 146:173-83. [DOI: 10.1093/jb/mvp059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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Spuergin P, Abele U, Schulz GE. Stability, Activity and Structure of Adenylate Kinase Mutants. ACTA ACUST UNITED AC 2008. [DOI: 10.1111/j.1432-1033.1995.0405e.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Ferreira ST, Chapeaurouge A, De Felice FG. Stabilization of partially folded states in protein folding/misfolding transitions by hydrostatic pressure. Braz J Med Biol Res 2005; 38:1215-22. [PMID: 16082462 DOI: 10.1590/s0100-879x2005000800009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In the last few years, hydrostatic pressure has been extensively used in the study of both protein folding and misfolding/aggregation. Compared to other chemical or physical denaturing agents, a unique feature of pressure is its ability to induce subtle changes in protein conformation, which allow the stabilization of partially folded intermediate states that are usually not significantly populated under more drastic conditions (e.g., in the presence of chemical denaturants or at high temperatures). Much of the recent research in the field of protein folding has focused on the characterization of folding intermediates since these species appear to be involved in a variety of disease-causing protein misfolding and aggregation events. The exact mechanisms of these biological phenomena, however, are still poorly understood. Here, we review recent examples of the use of hydrostatic pressure as a tool to obtain insight into the forces and energetics governing the productive folding or the misfolding and aggregation of proteins.
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Affiliation(s)
- S T Ferreira
- Programa de Bioquímica e Biofísica Celular, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil.
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22
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Seefeldt MB, Ouyang J, Froland WA, Carpenter JF, Randolph TW. High-pressure refolding of bikunin: efficacy and thermodynamics. Protein Sci 2004; 13:2639-50. [PMID: 15388859 PMCID: PMC2286545 DOI: 10.1110/ps.04891204] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2004] [Revised: 07/06/2004] [Accepted: 07/06/2004] [Indexed: 10/26/2022]
Abstract
Bikunin is a glycosylated protein that aggregates extensively during mammalian cell culture, resulting in loss of activity, loss of native secondary structure, and the formation of nonnative disulfide bonds. We investigated the use of high hydrostatic pressure (1000-3000 bar) for the refolding of bikunin aggregates. The refolding yield obtained with pressure-modulated refolding at 2000 bar was 70 (+/-5%) by reverse-phase chromatography (RP-HPLC), significantly higher than the value of 55 (+/-6%) (RP-HPLC) obtained with traditional guanidine HCl "dilution-refolding." In addition, we determined the thermodynamics of pressure-modulated refolding. The change in volume for the transition of aggregate to monomer DeltaV(refolding) was calculated to be -28 (+/-5) mL/mole. Refolding was accompanied by a loss of hydrophobic exposure, resulting in a positive contribution to the DeltaV(refolding). These findings suggest that the disruption of electro-static interactions or the differences in size of solvent-free cavities between the aggregate and the monomer are the prevailing contributions to the negative DeltaV(refolding).
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Affiliation(s)
- Matthew B Seefeldt
- Department of Chemical and Biological Engineering, Center for Pharmaceutical Biotechnology, ECCH 111, University of Colorado, Boulder, CO 80309-0424, USA
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23
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Ueda H, Kristensen P, Winter G. Stabilization of antibody VH-domains by proteolytic selection. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.molcatb.2003.12.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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24
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The effect of dodecyl trimethylammonium bromide on the formation of methemoglobins and hemichrome. Colloids Surf B Biointerfaces 2002. [DOI: 10.1016/s0927-7765(02)00003-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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25
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Crowhurst KA, Tollinger M, Forman-Kay JD. Cooperative interactions and a non-native buried Trp in the unfolded state of an SH3 domain. J Mol Biol 2002; 322:163-78. [PMID: 12215422 DOI: 10.1016/s0022-2836(02)00741-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The presence of residual structure in the unfolded state of the N-terminal SH3 domain of Drosophila drk (drkN SH3 domain) has been investigated using far- and near-UV circular dichroism (CD), fluorescence, and NMR spectroscopy. The unfolded (U(exch)) state of the drkN SH3 domain is significantly populated and exists in equilibrium with the folded (F(exch)) state under non-denaturing conditions near physiological pH. Denaturation experiments have been performed on the drkN SH3 domain in order to monitor the change in ellipticity, fluorescence intensity, and chemical shift between the U(exch) state and chemically or thermally denatured states. Differences between the unfolded and chemically or thermally denatured states highlight specific areas of residual structure in the unfolded state that are cooperatively disrupted upon denaturation. Results provide evidence for cooperative interactions in the unfolded state involving residues of the central beta-sheet, particularly the beta4 strand. Denaturation as well as hydrogen-exchange experiments demonstrate a non-native burial of the Trp ring within this "cooperative" core of the unfolded state. These findings support the presence of non-native hydrophobic clusters, organised by Trp rings, within disordered states.
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Affiliation(s)
- Karin A Crowhurst
- Department of Structural Biology and Biochemistry, The Hospital for Sick Children, Toronto, Ont., Canada
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26
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Maksay G, Bíró T, Laube B. Hyperekplexia mutation of glycine receptors: decreased gating efficacy with altered binding thermodynamics. Biochem Pharmacol 2002; 64:285-8. [PMID: 12123749 DOI: 10.1016/s0006-2952(02)01111-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
[(3)H]Strychnine binding was studied to recombinant human alpha(1) and the hyperekplexia mutant alpha(1)R271L glycine receptors (GlyRs) transiently expressed in human embryonic kidney (HEK)-293 cell cultures at 0, 18 and 37 degrees. The alpha(1)R271L mutation did not affect the linear van't Hoff plots of the exothermic binding of the antagonist [3H]strychnine while it turned taurine into an antagonist with exothermic binding. The inhibition constants of the agonist glycine showed opposite temperature dependence on alpha(1) GlyRs, corresponding to endothermic binding driven by large entropic increases. The temperature dependence of displacement by the partial agonists taurine on alpha(1) GlyRs and glycine on alpha(1)R271L GlyRs was biphasic reflecting negative heat capacity changes, dehydration changes and/or a complex binding mechanism. The thermodynamic discrimination of efficacy is valid for native rat spinal and recombinant human GlyRs. The alpha(1)R271L mutation impairs the transduction mechanism and distorts gating of GlyRs. Thereby it reduces the potency and efficacy of agonists and affects their thermodynamic parameters of binding. The hyperekplexia mutation offers a model system to demonstrate the correlation among pathophysiology, gating efficacy and binding thermodynamics of GlyRs.
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Affiliation(s)
- Gábor Maksay
- Department of Molecular Pharmacology, Chemical Research Centre, Hungarian Academy of Sciences, P.O. Box 17, H-1525 Budapest, Hungary.
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Krishnan S, Chi EY, Webb JN, Chang BS, Shan D, Goldenberg M, Manning MC, Randolph TW, Carpenter JF. Aggregation of granulocyte colony stimulating factor under physiological conditions: characterization and thermodynamic inhibition. Biochemistry 2002; 41:6422-31. [PMID: 12009905 DOI: 10.1021/bi012006m] [Citation(s) in RCA: 149] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have investigated the aggregation of recombinant human granulocyte colony stimulating factor (rhGCSF), a protein that rapidly aggregates and precipitates at pH 6.9 and 37 degrees C. We observed that native monomeric rhGCSF reversibly forms a dimer under physiological conditions and that this dimeric species does not participate in the irreversible aggregation process. Sucrose, a thermodynamic stabilizer, inhibits the aggregation of rhGCSF. We postulate that sucrose acts by reducing the concentration of structurally expanded species, consistent with the hypothesis that preferential exclusion favors most compact species in the native state ensemble. Thermodynamic stability data from unfolding curves and hydrogen-deuterium exchange experimental results support the above hypothesis. Thus, the strategy of stabilizing the native state of the protein under physiological conditions using thermodynamic stabilizers, especially ligands binding with high affinity to the native state, is expected to protect against protein aggregation occurring under such nonperturbing solution conditions.
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Affiliation(s)
- Sampathkumar Krishnan
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA
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Mok YK, Elisseeva EL, Davidson AR, Forman-Kay JD. Dramatic stabilization of an SH3 domain by a single substitution: roles of the folded and unfolded states. J Mol Biol 2001; 307:913-28. [PMID: 11273710 DOI: 10.1006/jmbi.2001.4521] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The N-terminal SH3 domain of the Drosophila drk protein (drkN SH3) exists in equilibrium between folded and unfolded states under non-denaturing buffer conditions. In order to examine the origins of this instability, we have made mutations in the domain and characterized the thermodynamics and kinetics of folding. Results of substitutions of negatively charged residues to neutral amino acid residues suggest that the large electrostatic potential of the domain does not play a dominant role in the instability of the domain. Sequence alignment of a large number of SH3 domains reveals that the drkN SH3 domain has a threonine (T22) at a position corresponding to an otherwise highly conserved glycine residue in the diverging beta-turn connecting the beta3 and beta4 strands. Mutation of T22 to glycine results in significant stabilization of the drkN SH3 domain by 2.5 kcal/mole. To further characterize the basis for the stabilization of the T22 mutant relative to wild-type, we made additional mutant proteins with substitutions of residue T22. A strong correlation is seen between protein stability or folding rate and propensity for native beta-turn structure at this position. Correlation of folding rates with AGADIR predictions of non-native helical structure in the diverging turn region, along with our previous NMR evidence for non-native structure in this region of the unfolded state of the drkN SH3 domain, suggests that the free energy of the unfolded state also plays a role in stability. This result highlights the importance of both folded and unfolded states for understanding protein stability.
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Affiliation(s)
- Y K Mok
- Department of Biochemistry, Structural Biology and Biochemistry, Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
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30
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Torigoe H, Hari Y, Sekiguchi M, Obika S, Imanishi T. 2'-O,4'-C-methylene bridged nucleic acid modification promotes pyrimidine motif triplex DNA formation at physiological pH: thermodynamic and kinetic studies. J Biol Chem 2001; 276:2354-60. [PMID: 11035027 DOI: 10.1074/jbc.m007783200] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Extreme instability of pyrimidine motif triplex DNA at physiological pH severely limits its use in an artificial control of gene expression in vivo. Stabilization of the pyrimidine motif triplex at physiological pH is, therefore, crucial in improving its therapeutic potential. To this end, we have investigated the thermodynamic and kinetic effects of our previously reported chemical modification, 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA) modification of triplex-forming oligonucleotide (TFO), on pyrimidine motif triplex formation at physiological pH. The thermodynamic analyses indicated that the 2',4'-BNA modification of TFO increased the binding constant of the pyrimidine motif triplex formation at neutral pH by approximately 20 times. The number and position of the 2',4'-BNA modification introduced into the TFO did not significantly affect the magnitude of the increase in the binding constant. The consideration of the observed thermodynamic parameters suggested that the increased rigidity itself of the 2',4'-BNA-modified TFO in the free state relative to the unmodified TFO may enable the significant increase in the binding constant at neutral pH. Kinetic data demonstrated that the observed increase in the binding constant at neutral pH by the 2',4'-BNA modification of TFO resulted from the considerable decrease in the dissociation rate constant. Our results certainly support the idea that the 2',4'-BNA modification of TFO could be a key chemical modification and may eventually lead to progress in therapeutic applications of the antigene strategy in vivo.
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Affiliation(s)
- H Torigoe
- Tsukuba Life Science Center, Institute of Physical and Chemical Research (RIKEN), Ibaraki 305-0074, Japan.
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31
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Pandey JD, Haroon S, Dubey KK, Upadhyaya M, Dey R, Misra K. Interactions of 6-aminopurine (adenine) in water and aqueous urea solutions. CAN J CHEM 2000. [DOI: 10.1139/v00-141] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Density (ρ), ultrasonic velocity (U), viscosity (η), and absorbance (A) of adenine in water, 1 M, 3 M, and 6 M aqueous urea solutions have been measured in the presence (and absence) of different concentrations of salts, i.e., NaCl, KCl, and CaCl2. From these measured values, the apparent molar volume (ϕv), experimental slope (Sv), apparent molar compressibility (ϕK), viscosity coefficients A and B of JonesDole equation, specific acoustic impedance (Z), hydration number (Sn), internal pressure (Pi), molar absorptivity (ε), hypochromicity (h), and oscillator strength (f) have been calculated at 298.15 K. The increasing and (or) decreasing trends of all these parameters indicate a strong interaction of urea in moderate concentration (1 M and 3 M) with adenine especially at the hydrophilic/polar and ionic sites, particularly by hydrogen bonding. However, the interaction at hydrophobic sites are relatively weaker. Higher concentrations of urea (6 M) have more denaturation effect. The ππ interactions (stacking) in adenine are more prominent in concentrated solutions and are also strengthened by the presence of cations up to an optimum concentration of salts (cut-off point). The self-association of urea and adenine is more significant in concentrated aqueous solutions and becomes negligible on dilution.Key words: interaction, adenine, urea, density, viscosity, and ultrasonic velocity.
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32
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Riechmann L, Winter G. Novel folded protein domains generated by combinatorial shuffling of polypeptide segments. Proc Natl Acad Sci U S A 2000; 97:10068-73. [PMID: 10954734 PMCID: PMC27691 DOI: 10.1073/pnas.170145497] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It has been proposed that the architecture of protein domains has evolved by the combinatorial assembly and/or exchange of smaller polypeptide segments. To investigate this proposal, we fused DNA encoding the N-terminal half of a beta-barrel domain (from cold shock protein CspA) with fragmented genomic Escherichia coli DNA and cloned the repertoire of chimeric polypeptides for display on filamentous bacteriophage. Phage displaying folded polypeptides were selected by proteolysis; in most cases the protease-resistant chimeric polypeptides comprised genomic segments in their natural reading frames. Although the genomic segments appeared to have no sequence homologies with CspA, one of the originating proteins had the same fold as CspA, but another had a different fold. Four of the chimeric proteins were expressed as soluble polypeptides; they formed monomers and exhibited cooperative unfolding. Indeed, one of the chimeric proteins contained a set of very slowly exchanging amides and proved more stable than CspA itself. These results indicate that native-like proteins can be generated directly by combinatorial segment assembly from nonhomologous proteins, with implications for theories of the evolution of new protein folds, as well as providing a means of creating novel domains and architectures in vitro.
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Affiliation(s)
- L Riechmann
- Division for Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
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Abstract
An evolutionary trend towards increasing hydrophobicity of vertebrate arterial elastins suggests that there is an adaptive advantage to higher hydrophobicity. The swelling and dynamic mechanical properties of elastins from several species were measured to test whether hydrophobicity is associated with mechanical performance. Hydrophobicity was quantified according to amino acid composition (HI), and two behaviour-based indices: the Flory-Huggins solvent interaction parameter (chi1), and a swelling index relating tissue volumes at 60 and 1 degrees C. Swelling index values correlated with chi1 and, for most species studied, with HI, suggesting that the different approaches used to quantify hydrophobicity are equally valid. Dynamic mechanical properties were measured both in a closed system, to control the effects of water content, and in an open system, to determine whether the increased swelling of hydrophobic materials at low temperatures offsets the direct stiffening effect of cold. There were no biologically significant differences in mechanical behaviour in either open or closed systems that could be attributed to hydrophobicity. Therefore, although the original function of hydrophobicity in an ancestral elastin may have been to produce molecular mobility, mechanical performance did not drive a subsequent increase in hydrophobicity. Higher hydrophobicities may have arisen to facilitate the manufacture of the elastic fibre.
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Affiliation(s)
- G W Chalmers
- Department of Zoology, University of British Columbia, Vancouver, Canada V6T 1Z4
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Thermodynamics of denaturation of horseradish peroxidase with sodium n-dodecyl sulphate and n-dodecyl trimethylammonium bromide. Colloids Surf B Biointerfaces 1997. [DOI: 10.1016/s0927-7765(97)00016-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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35
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Fábián G, Benyhe S, Farkas J, Szücs M. Thermodynamic parameters of opioid binding in the presence and absence of G-protein coupling. J Recept Signal Transduct Res 1996; 16:151-68. [PMID: 8897309 DOI: 10.3109/10799899609039946] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have investigated the thermodynamic parameters of various opioid ligands interacting with their receptors in rat brain membranes. Affinity constants (Ka), enthalpy and entropy values were obtained from homologous displacement experiments performed at 0, 24 and 33 degrees C. It was found that all the opioid agonists tested ([3H]dihydromorphine (DHM) mu alkaloid; [3H]DAMGO mu peptide; [3H]deltorphin-B delta peptide) display endothermic binding accompanied with a large entropy increase, regardless of their chemical structure (alkaloid or peptide), or of their mu or delta receptor selectivity. In contrast, binding of the antagonist naloxone is exothermic, mainly enthalpy driven. Na+ or Mg2+ results only in quantitative changes of the thermodynamic parameters. In the presence of the GTP-analog Gpp(NH)p; or Gpp(NH)p + Na+; or Gpp(NH)p + Na- + Mg2+ the affinity of DHM binding dramatically decreases which might reflect functional uncoupling of the receptor-ligand complex and G-proteins. This altered molecular interactions are also indicated by curvilinear van't Hoff plot and entropy increase. It is concluded that the thermodynamic analysis provides means of determining the underlying driving forces of ligand binding and helps to delineate its mechanism.
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Affiliation(s)
- G Fábián
- Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
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36
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Kirschner KN, Sherer EC, Shields GC. Use of the Supermolecule Approach To Model the Syn and Anti Conformations of Solvated Cyclic 3‘,5‘-Adenosine Monophosphate. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp952658i] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karl N. Kirschner
- Department of Chemistry, Lake Forest College, Lake Forest, Illinois 60045
| | - Edward C. Sherer
- Department of Chemistry, Lake Forest College, Lake Forest, Illinois 60045
| | - George C. Shields
- Department of Chemistry, Lake Forest College, Lake Forest, Illinois 60045
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Spuergin P, Abele U, Schulz GE. Stability, activity and structure of adenylate kinase mutants. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 231:405-13. [PMID: 7635152 DOI: 10.1111/j.1432-1033.1995.tb20713.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Sequence/structure relationships have been explored by site-directed mutagenesis using a structurally known adenylate kinase. In particular the effects of helix capping and nonpolar core expansion on thermodynamic stability have been analyzed. Six point mutations were produced and characterized by SDS/PAGE, native PAGE, isoelectric focussing, electrophoretic titration, enzyme kinetics, and X-ray structure analysis. Heat-denaturation experiments yielded melting temperatures Tm and melting enthalpy changes delta Hm. The heat capacity change delta Cp of the wild-type enzyme was determined by guanidine hydrochloride denaturation in conjunction with Tm and delta Hm. Using the wild-type delta Cp value, Gibbs free energy changes delta G at room temperature were calculated for all mutants. Four mutants were designed for helix capping stabilization, but only one of them showed such an effect. Because of electrostatic interference with the induced-fit motion, one mutant decreased the catalytic activity strongly. Two mutants expanded nonpolar cores causing destabilization. The mutant with the lower stability could be crystallized and subjected to an X-ray analysis at 223-pm resolution which showed the structural changes. The enzyme was stabilized by adding a -Pro-His-His tail to the C-terminal alpha-helix for nickel-chelate chromatography. This addition constitutes a helix cap. Taken together, the results demonstrate that stabilization by helix capping is difficult to achieve because the small positive effect is drowned by adverse mutational disruption. Further addition of atoms to nonpolar cores destabilized the protein, although the involved geometry changes were very small, demonstrating the importance of efficient packing.
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Affiliation(s)
- P Spuergin
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Freiburg im Breisgau, Germany
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38
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Moosavi-Movahedi AA, Nazari K. Denaturation of horseradish peroxidase with urea and guanidine hydrochloride. Int J Biol Macromol 1995; 17:43-7. [PMID: 7772563 DOI: 10.1016/0141-8130(95)93517-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Favourable effects of urea and guanidine hydrochloride (Gdn HCl) on solubilization of the polar, non-polar and peptide groups of horseradish peroxidase (HRP), an example of a globular protein, provide the driving force for unfolding of HRP, in a reversible two-state process. The intrinsic or conformational stability of HRP at various pH values and temperatures has been estimated by the linear extrapolation method (LEM), a denaturant binding model (DBM) and Tanford's model. There is good agreement between these methods. Tanford's model shows that urea interacts with non-polar groups to a greater extent than Gdn HCl does, whereas Gdn HCl interacts more effectively with the peptide groups of HRP.
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Doublié S, Bricogne G, Gilmore C, Carter CW. Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase. Structure 1995; 3:17-31. [PMID: 7743129 DOI: 10.1016/s0969-2126(01)00132-0] [Citation(s) in RCA: 154] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND Tryptophanyl-tRNA synthetase (TrpRS) catalyzes activation of tryptophan by ATP and transfer to tRNA(Trp), ensuring translation of the genetic code for tryptophan. Interest focuses on mechanisms for specific recognition of both amino acid and tRNA substrates. RESULTS Maximum-entropy methods enabled us to solve the TrpRS structure. Its three parts, a canonical dinucleotide-binding fold, a dimer interface, and a helical domain, have enough structural homology to tyrosyl-tRNA synthetase (TyrRS) that the two enzymes can be described as conformational isomers. Structure-based sequence alignment shows statistically significant genetic homology. Structural elements interacting with the activated amino acid, tryptophanyl-5'AMP, are almost exactly as seen in the TyrRS:tyrosyl-5'AMP complex. Unexpectedly, side chains that recognize indole are also highly conserved, and require reorientation of a 'specificity-determining' helix containing a conserved aspartate to assure selection of tryptophan versus tyrosine. The carboxy terminus, which is disordered and therefore not seen in TyrRS, forms part of the dimer interface in TrpRS. CONCLUSIONS For the first time, the Bayesian statistical paradigm of entropy maximization and likelihood scoring has played a critical role in an X-ray structure solution. Sequence relatedness of structurally superimposable residues throughout TrpRS and TyrRS implies that they diverged more recently than most aminoacyl-tRNA synthetases. Subtle, tertiary structure changes are crucial for specific recognition of the two different amino acids. The conformational isomerism suggests that movement of the KMSKS loop, known to occur in the TyrRS transition state for amino acid activation, may provide a basis for conformational coupling during catalysis.
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Affiliation(s)
- S Doublié
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill 27599-7260, USA
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40
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Sheppard LJ. Causal mechanisms by which sulphate, nitrate and acidity influence frost hardiness in red spruce: review and hypothesis. THE NEW PHYTOLOGIST 1994; 127:69-82. [PMID: 33874399 DOI: 10.1111/j.1469-8137.1994.tb04260.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This paper summarizes results from four experiments in which red spruce seedlings (Picea rubens Sarg.) were exposed to simulated acid mist containing SO4 2- , NH4- , NO3 - and H+ ions. Seedlings were grown in compost, with or without fertilizer, in charcoal filtered air in open-top chambers near Edinburgh, Scotland. Plants were sprayed from bud burst between May and November with mist containing different concentrations and combinations of the four major ions to provide a range of doses, which were applied at different frequencies. Reductions in frost hardiness expressed in terms of the temperature which killed 50% of shoots (LT50 ) were significantly correlated with the dose of S received by the seedlings. Differences in foliar S concentrations between the controls and treated plants were correlated with S dose. Absolute S concentrations were, however, of limited use for predictive purposes. Seedlings appear to be more sensitive than older trees to S toxicity because the former have the greatest proportion of newly expanding needles which optimize conditions for foliar uptake. Seedlings are also least well equipped to export SO4 2- ions since they have a smaller resource of older foliage to supplement their assimilate pool. In conditions which promote uncontrolled SO4 2- ion uptake by foliage, i.e. high external SO4 2- concentrations and incompletely formed cuticles, the potential exists for the internal build up of SO4 2- ions. It is proposed that in the absence of sufficient assimilate and K the presence of these high concentrations of SO4 2- ions in the apoplast or cytosol can lead to protein denaturation and loss of membrane integrity. Reductions in frost hardiness appear to result through direct attack by SO4 2 ions on membrane proteins which impairs their function. Indirect effects on hardiness occur through both an increased consumption of sugars reducing the'pool'available for cryoprotection and a reduction in photosynthetic function, the ability to produce sugars. The presence of NO3- N mitigates the toxic effects of SO4 2 because SO4 2 ions are consumed in assimilation processes which both utilize and are facilitated by the presence of large amounts of fertilizer N. High concentrations of SO4 2 and H+ are found to be particularly toxic because of the synergistic effects these ions exert on their mutual uptake with devastating consequences for the control of cellular pH. Trees growing at high altitude sites are likely to be particularly sensitive to SO4 2- toxicity because (1) their carbon balance is low, (2) cuticle development is poor and (3) levels of soil available Ca2 tend to be low relative to Al3+ so that membranes may already be weakened as a result of insufficient Ca2+ ions for protein bridging.
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Affiliation(s)
- Lucy J Sheppard
- Institute of Terrestrial Ecology, Bush Estate, Penicuik, Midlothian EH26 OQB
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41
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Chong NW, Sugden D. Thermodynamic analysis of agonist and antagonist binding to the chicken brain melatonin receptor. Br J Pharmacol 1994; 111:295-301. [PMID: 8012710 PMCID: PMC1910046 DOI: 10.1111/j.1476-5381.1994.tb14059.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
1. The binding of 2-[125I]-iodomelatonin to chicken brain membranes, and the inhibition of binding by melatonin, N-acetyltryptamine and luzindole, were examined at temperatures between 4 degrees C and 37 degrees C. 2. At all temperatures studied, the binding affinity (Kd or Ki) for 2-[125I]-iodomelatonin, melatonin (both agonists) and, to a lesser extent, N-acetyltryptamine (a partial agonist) was reduced by inclusion of guanosine triphosphate (GTP, 1 mM) in the assay. GTP did not affect the Ki for luzindole, a melatonin receptor antagonist. 3. The maximal density of binding sites (Bmax) was not affected by temperature but the Kd showed a peak at 21 degrees C with lower values at both higher and lower temperatures giving curvilinear van't Hoff plots (lnKA vs l/temperature). 4. Derived changes in entropy (delta S degree) and enthalpy (delta H degree) of binding for all of the melatonin ligands decreased as temperature increased. 5. The affinity, and thus the free energy of binding, delta G degree, of these ligands at the melatonin receptor have identical values at several temperatures yet at these temperatures delta S degree and delta H degree were very different, implying that more than one intermolecular force must be involved in the binding of ligand and receptor. 6. Conceivably, the large positive delta S degree observed at low temperatures, perhaps as a result of hydrophobic interactions, is compensated by a corresponding, but opposite, change in enthalpy at higher temperatures. However, it is not clear what type of binding force(s) would show such a temperature-dependence. 7. These studies suggest that caution must be exercised in the molecular interpretation of derived measures of delta S degree and delta H degree obtained from direct measurements of delta G degree.
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Affiliation(s)
- N W Chong
- Biomedical Sciences Division, King's College, London
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42
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Bourhim N, Cantau P, Giraud P, Castanas E. Comparative thermodynamics of opioid receptor ligand interaction in the bovine adrenal medulla membranes--evidence of opioid site heterogeneity. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. C, COMPARATIVE PHARMACOLOGY AND TOXICOLOGY 1993; 105:435-42. [PMID: 7900966 DOI: 10.1016/0742-8413(93)90083-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
1. A marked dependence on temperature of agonist binding delta, mu and kappa 1-3 opioid sites in the bovine adrenal medulla was observed, at the range of 0 to 37 degrees C. These changes concern kinetic (k1) and equilibrium constants (Kd), but not binding capacities (Bmax). 2. These dependences are different for each ligand and each opioid receptor, suggesting their molecular heterogeneity. 3. The comparative thermodynamics indicates that the interaction of opioid agonists with their receptor is exergonic (delta G degree < 0) and entropy driven (delta S degree > 0). 4. The comparison of Van't Hoff and Arrhenius plots indicates a discrete mechanism in the binding of each opioid receptor.
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MESH Headings
- Adrenal Medulla/metabolism
- Animals
- Cattle
- In Vitro Techniques
- Kinetics
- Membranes/drug effects
- Membranes/metabolism
- Receptors, Opioid/drug effects
- Receptors, Opioid/metabolism
- Receptors, Opioid, kappa/drug effects
- Receptors, Opioid, kappa/metabolism
- Receptors, Opioid, mu/drug effects
- Receptors, Opioid, mu/metabolism
- Receptors, sigma/drug effects
- Receptors, sigma/metabolism
- Temperature
- Thermodynamics
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Affiliation(s)
- N Bourhim
- Laboratorie de Neuroendocrinologie Expérimentale Faculté de Medecine Nord, Marseille, France
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Waelbroeck M, Camus J, Tastenoy M, Lambrecht G, Mutschler E, Kropfgans M, Sperlich J, Wiesenberger F, Tacke R, Christophe J. Thermodynamics of antagonist binding to rat muscarinic M2 receptors: antimuscarinics of the pridinol, sila-pridinol, diphenidol and sila-diphenidol type. Br J Pharmacol 1993; 109:360-70. [PMID: 8102927 PMCID: PMC2175680 DOI: 10.1111/j.1476-5381.1993.tb13578.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
1. We studied the effect of temperature on the binding to rat heart M2 muscarinic receptors of antagonists related to the carbon/silicon pairs pridinol/sila-pridinol and diphenidol/sila-diphenidol (including three germanium compounds) and six structurally related pairs of enantiomers [(R)- and (S)-procyclidine, (R)- and (S)-trihexyphenidyl, (R)- and (S)-tricyclamol, (R)- and (S)-trihexyphenidyl methiodide, (R)- and (S)-hexahydro-diphenidol and (R)- and (S)-hexbutinol]. Binding affinities were determined in competition experiments using [3H]-N-methyl-scopolamine chloride as radioligand. The reference drugs were scopolamine and N-methyl-scopolamine bromide. 2. The affinity of the antagonists either increased or decreased with temperature. van't Hoff plots were linear in the 278-310 degrees K temperature range. Binding of all antagonists was entropy driven. Enthalpy changes varied from large negative values (down to -29 kJ mol-1) to large positive values (up to +30 kJ mol-1). 3. (R)-configurated drugs had a 10 to 100 fold greater affinity for M2 receptors than the corresponding (S)-enantiomers. Enthalpy and entropy changes of the respective enantiomers were different but no consistent pattern was observed. 4. When silanols (R3SiOH) were compared to carbinols (R3COH), the affinity increase caused by C/Si exchange varied between 3 and 10 fold for achiral drugs but was negligible in the case of chiral drugs. Silanols induced more favourable enthalpy and less favourable entropy changes than the corresponding carbinols when binding. Organogermanium compounds (R4Ge) when compared to their silicon counterparts (R4Si) showed no significant difference in affinity as well as in enthalpy and entropy changes. 5. Exchange of a cyclohexyl by a phenyl moiety was associated with an increase or a decrease in drug affinity (depending on the absolute configuration in the case of chiral drugs) and generally also with a more favourable enthalpy change and a less favourable entropy change of drug binding. 6. Replacement of a pyrrolidino by a piperidino group and increasing the length of the alkylene chain bridging the amino group and the central carbon or silicon atom were associated with either an increase or a decrease of entropy and enthalpy changes of drug binding. However, there was no clear correlation between these structural variations and the thermodynamic effects. 7. Taken together, these results suggest that hydrogen bond-forming OH groups and, to a lesser extent, polarizable phenyl groups contribute significantly to the thermodynamics of interactions between these classes of muscarinic antagonists and M2 muscarinic receptors.
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Affiliation(s)
- M Waelbroeck
- Department of Biochemistry and Nutrition, Medical School, Université Libre de Bruxelles, Belgium
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Abstract
Several harmonic models of protein fluctuations are used to calculate the heat capacity. They get the spectral density of conformational modes from inelastic neutron scattering, normal mode calculations, or macroscopic elasticity (Debye model). It is assumed that the low-frequency spectral density depends only weakly on temperature and protein species. The Debye model predicts temperatures below which modes are primarily in their ground states: 10 and 80 K for the lattice and conformational modes, respectively. The models differ most below 100 K. The mode calculations yield the most accurate predictions, though all three models are within twofold of the data. The heat capacity has the power law form aTb for T less than 30 K. The experimental b's of proteins are 1.6-1.8, and the theoretical, 1.1-1.3. One possible explanation for the discrepancy is the occurrence of transitions between discrete conformations. All of the models approach the measured data in the range 100-200 K. They are very similar above 200 K, where the heat capacity includes significant contributions from bond stretching and bending. This masks the possible anharmonic behavior of the conformational modes. Hydration substantially increases the heat capacity above 200 K. This effect seems to be a consequence of conformational transitions that have higher energy than the ones seen with low hydration. The analysis also predicts that denaturation with constant hydration produces a negligible increase of heat capacity. The larger increment in solution arises from the different hydration of the folded and unfolded states, and is responsible for the existence of cold denaturation. This phenomenon is thus predicted not to occur when the hydration is constant.
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Affiliation(s)
- J Edelman
- Department of Physiology and Biophysics, University of California, Irvine 92717
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Khechinashvili NN. Thermodynamic properties of globular proteins and the principle of stabilization of their native structure. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1040:346-54. [PMID: 2223840 DOI: 10.1016/0167-4838(90)90132-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A semi-empirical method has been used to estimate the thermodynamic parameters of hydration of buried surface areas of ribonuclease S, lysozyme and myoglobin from the model of complete unfolding according to Ooi et al. ((1987) Proc. Natl. Acad. Sci. USA 84, 3086-3090). The buried surface area of proteins is considered as the difference between the accessible surface area of native protein and the completely extended polypeptide chain according to Lee and Richards ((1971) J. Mol. Biol. 55, 379-400). The contributions of nonpolar and polar protein groups to the general value of Gibbs energy, enthalpy, entropy and heat capacity of hydration have been determined. The obtained results on the thermodynamic behavior of proteins in the process of complete unfolding are in good agreement with the results of microcalorimetric studies of thermal denaturation.
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Affiliation(s)
- N N Khechinashvili
- Institute of Biological Physics, Academy of Sciences, U.S.S.R., Moscow Region
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46
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Hanzlik RP, Zygmunt J, Moon JB. Reversible covalent binding of peptide nitriles to papain. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1035:62-70. [PMID: 2383580 DOI: 10.1016/0304-4165(90)90174-u] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The dissociation constants for reversible covalent binding of twelve peptide nitrile inhibitors to the active site of papain have been measured by means of fluorescence titration. The binding constants generally parallel the kinetic specificity constants (kcat/Km) for related papain substrates, supporting earlier suggestions that peptide nitriles behave as transition state analog inhibitors of papain. In ten cases the temperature dependence of binding was analyzed to determine the enthalpic and entropic contributions to the binding energy. A compensation plot of delta H vs. T delta S resulted in two parallel lines, one for 'specific' nitriles (i.e., N-Ac-L-aa-NHCH2CN; aa = Phe, Leu, Met) and the other for 'non-specific' nitriles (e.g., N-Ac-D-Phe-NHCH2CN, PhCH2CH2CONHCH2CN hippurylnitrile, etc.). For both specific and nonspecific nitriles representing an 1800-fold range of Kd values (0.27 microM-490 microM), the solvent deuterium isotope effect on binding (Kd(H2O)/Kd(D2O) = DKd) was very close to 2.0. This isotope effect could be accounted for entirely by the simple protonic change which occurs upon the reversible addition of the active site sulfhydryl of papain to the nitrile group of the peptide derivative to form a covalent thioimidate linkage. In contrast, six closely related non-nitrile ligands containing identical peptide side chains but having C-terminal groups incapable of binding covalently to papain had unmeasureably high dissociation constants. Collectively, these results indicate that strong binding of peptide nitrile substrate analogs to papain requires a combination of (1) hydrophobic interaction (especially at the P2 position), (2) specific intermolecular hydrogen bonding and (3) covalent interaction of the nitrile with the active site sulfhydryl group.
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Affiliation(s)
- R P Hanzlik
- Department of Medicinal Chemistry, University of Kansas, Lawrence 66045-2506
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Mozhaev VV, Martinek K. Structure-stability relationships in proteins: a guide to approaches to stabilizing enzymes. Adv Drug Deliv Rev 1990. [DOI: 10.1016/0169-409x(90)90028-q] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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48
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Marky LA, Kupke DW. Probing the hydration of the minor groove of A.T synthetic DNA polymers by volume and heat changes. Biochemistry 1989; 28:9982-8. [PMID: 2559775 DOI: 10.1021/bi00452a016] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The minor-groove ligand netropsin provides a sensitive probe of the hydration difference between poly(dA).poly(dT) and poly[d(AT)].poly[d(AT)]. We have measured the volume change delta V accompanying binding of netropsin to these polymers, using an improved magnetic suspension densimeter. For poly(dA).poly(dT) we find delta V = +97 mL/mol of bound netropsin at pH 7.0 and 10 mM sodium phosphate buffer. For poly[d(AT)].poly[d(AT)] we find delta V = -16 mL/mol of bound netropsin. This striking differential effect suggests that the poly(dA).poly(dT) duplex compresses more water (or is more extensively hydrated). From our enthalpy and entropy results we estimate the approximately 10 water molecules, immobilized in the minor groove of this system, are displaced by each netropsin bound. The volume increase, however, is substantially larger than can be explained by a simple melting of these immobilized water molecules in the minor groove. A decompression of at least 40 water molecules must attend the complexation to the poly(dA).poly(dT) duplex. This suggests that the conformation change attending the binding of the drug to this polymer duplex causes a further dehydration, whereas no such change in dehydration and configuration for the heteropolymer system is indicated.
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Affiliation(s)
- L A Marky
- Department of Chemistry, New York University, New York 10003
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49
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Stein M, Lazaro JJ, Wolosiuk RA. Concerted action of cosolvents, chaotropic anions and thioredoxin on chloroplast fructose-1,6-bisphosphatase. Reactivity to iodoacetamide. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 185:425-31. [PMID: 2555190 DOI: 10.1111/j.1432-1033.1989.tb15132.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The incubation of chloroplast fructose-1,6-bisphosphatase with both dithiothreitol and protein denaturants made sulfhydryl groups available for reaction with [1-14C]iodoacetamide (10-12 mol iodoacetamide incorporated/mol enzyme). Digestion of S-carboxyamidomethylated enzyme with trypsin and polyacrylamide gel electrophoresis, in the presence of sodium dodecylsulfate, yielded two 14C-labeled fragments whose apparent molecular mass were 10 kDa and 16 kDa. In the absence of either dithiothreitol or protein denaturants the incorporation of iodoacetamide to the enzyme was lower than 4 mol. When chloroplast fructose-1,6-bisphosphatase was initially incubated with dithiothreitol (2.5 mM) and (a) high concentrations of both fructose 1,6-bisphosphate (4 mM) and Ca2+ (0.3 mM) or (b) low concentrations of both fructose 1,6-bisphosphate (0.8 mM) and Ca2+ (0.05 mM) in the presence of either 2-propanol (15%, by vol.), trichloroacetate (0.15 M) or chloroplast thioredoxin-f (0.5 microM) and subsequently subjected to proteolysis and electrophoresis, S-carboxyamidomethylated tryptic fragments had similar molecular masses. Thus, conditions that stimulated the specific activity of chloroplast fructose-1,6-bisphosphatase caused conformational changes which favoured both the reduction of disulfide bridges and the exposure of sulfhydryl groups. In this aspect, thioredoxin exerted structural and kinetic effects similar to compounds not involved in redox reactions (organic solvents, chaotropic anions). These results indicated that the modification of hydrophobic (intramolecular) interactions in chloroplast fructose-1,6-bisphosphatase constituted the underlying mechanism in light-activation by the ferredoxin-thioredoxin system.
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Affiliation(s)
- M Stein
- Instituto de Investigaciones Bioquímicas, Fundación Campomar, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
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50
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Kuwajima K, Mitani M, Sugai S. Characterization of the critical state in protein folding. Effects of guanidine hydrochloride and specific Ca2+ binding on the folding kinetics of alpha-lactalbumin. J Mol Biol 1989; 206:547-61. [PMID: 2716061 DOI: 10.1016/0022-2836(89)90500-7] [Citation(s) in RCA: 154] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The reversible unfolding and refolding kinetics of alpha-lactalbumin induced by concentration jump of guanidine hydrochloride were measured at pH 7.0 and 25 degrees C using tryptophan absorption at 292 nm, with varying concentrations of the denaturant and free Ca2+. The refolding reaction of alpha-lactalbumin from the fully unfolded (D) state occurs through the two stages: (1) instantaneous formation of a compact intermediate (the A state) that has a native-like secondary structure; (2) tight packing of the preformed secondary structure segments to lead finally to the native structure, this stage being the rate-determining step of the reaction and associated with acquisition of the specific structure necessary for strong Ca2+ binding. Under strongly native conditions, the observed kinetics of refolding is also complicated by the presence of a slow-folding species (10%) in the unfolded state. Considering these facts, the microscopic rate constants in folding and unfolding directions have been evaluated from the observed kinetics and from the equilibrium constants of the transitions among the native (N), A and D states. Close linear relationships have been found in the plots of the activation free energies, obtained from the microscopic rate constants, against the denaturant concentration. They are similar to the linear relationship between the free energy of unfolding and the denaturant concentration. It was demonstrated that the slope of the plots should be approximately proportional to a change in accessible surface area of the protein during the respective activation process, and that only a third of the difference in accessible surface area between A and N is buried in the critical activated state of folding. However, the selective effect of Ca2+ binding on the folding rate constant has been observed also, demonstrating that the specific Ca2+-binding substructure in the N state is already organized in the activated state. Thus, only a part of the protein molecule involving the Ca2+-binding region is organized in the activated state, with the other part of the molecule being left less organized, suggesting that the second stage of folding may be a sequential growing process of organized assemblage of the performed secondary structure segments.
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Affiliation(s)
- K Kuwajima
- Department of Polymer Science, Faculty of Science, Hokkaido University, Japan
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