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Szoszkiewicz R, Milescu L, Fernandez JM. Dwell Time And Maximum Likelihood Analysis Of Single Molecule Disulfide Bond Reduction Events While Under A Stretching Force. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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52
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Kuo T, Badilla CL, Fernandez JM. Investigating The Mechanical Stability Of Sap-1 Transcription Factor By Single Molecule Force Spectroscopy. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.3075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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53
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Rodriguez-Larrea D, Perez-Jimenez R, Sanchez-Romero I, Arco-Gonzalez R, Delgado A, Fernandez JM, Sanchez-Ruiz JM. Super-proteins From Fitness-threshold Selection Statistics. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.3098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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54
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Dougan L, Badilla CL, Fernandez JM. Extreme Mechanical Stability In Polyglutamine Chains Identified Using Single Molecule Force-clamp Spectroscopy. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.1596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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55
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Liang J, Fernandez JM. The Temperature Dependency of Disulfide Bond Reduction Events Measured by Single-molecule Force Clamp Spectroscopy. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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56
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Perez-Jimenez R, Li J, Kosuri P, Berne BJ, Fernandez JM. Chemical Diversity and Origin of Thioredoxin Catalysis Revealed by Force-clamp Spectroscopy. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.3402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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57
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Dougan L, Koti ASR, Genchev G, Lu H, Fernandez JM. A single-molecule perspective on the role of solvent hydrogen bonds in protein folding and chemical reactions. Chemphyschem 2009; 9:2836-47. [PMID: 19058277 DOI: 10.1002/cphc.200800572] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We present an array of force spectroscopy experiments that aim to identify the role of solvent hydrogen bonds in protein folding and chemical reactions at the single-molecule level. In our experiments we control the strength of hydrogen bonds in the solvent environment by substituting water (H(2)O) with deuterium oxide (D(2)O). Using a combination of force protocols, we demonstrate that protein unfolding, protein collapse, protein folding and a chemical reaction are affected in different ways by substituting H(2)O with D(2)O. We find that D(2)O molecules form an integral part of the unfolding transition structure of the immunoglobulin module of human cardiac titin, I27. Strikingly, we find that D(2)O is a worse solvent than H(2)O for the protein I27, in direct contrast with the behaviour of simple hydrocarbons. We measure the effect of substituting H(2)O with D(2)O on the force dependent rate of reduction of a disulphide bond engineered within a single protein. Altogether, these experiments provide new information on the nature of the underlying interactions in protein folding and chemical reactions and demonstrate the power of single-molecule techniques to identify the changes induced by a small change in hydrogen bond strength.
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Perez-Jimenez R, Wiita AP, Rodriguez-Larrea D, Kosuri P, Gavira JA, Sanchez-Ruiz JM, Fernandez JM. Force-clamp spectroscopy detects residue co-evolution in enzyme catalysis. J Biol Chem 2008; 283:27121-9. [PMID: 18687682 DOI: 10.1074/jbc.m803746200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Understanding how the catalytic mechanisms of enzymes are optimized through evolution remains a major challenge in molecular biology. The concept of co-evolution implicates that compensatory mutations occur to preserve the structure and function of proteins. We have combined statistical analysis of protein sequences with the sensitivity of single molecule force-clamp spectroscopy to probe how catalysis is affected by structurally distant correlated mutations in Escherichia coli thioredoxin. Our findings show that evolutionary anti-correlated mutations have an inhibitory effect on enzyme catalysis, whereas positively correlated mutations rescue the catalytic activity. We interpret these results in terms of an evolutionary tuning of both the enzyme-substrate binding process and the chemistry of the active site. Our results constitute a direct observation of distant residue co-evolution in enzyme catalysis.
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Vano E, Martinez D, Fernandez JM, Ordiales JM, Prieto C, Floriano A, Ten JI. Paediatric entrance doses from exposure index in computed radiography. Phys Med Biol 2008; 53:3365-80. [DOI: 10.1088/0031-9155/53/12/020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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60
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Koti Ainavarapu SR, Wiita AP, Dougan L, Uggerud E, Fernandez JM. Single-molecule force spectroscopy measurements of bond elongation during a bimolecular reaction. J Am Chem Soc 2008; 130:6479-87. [PMID: 18433129 DOI: 10.1021/ja800180u] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
It is experimentally challenging to directly obtain structural information of the transition state (TS), the high-energy bottleneck en route from reactants to products, for solution-phase reactions. Here, we use single-molecule experiments as well as high-level quantum chemical calculations to probe the TS of disulfide bond reduction, a bimolecular nucleophilic substitution (S N2) reaction. We use an atomic force microscope in force-clamp mode to apply mechanical forces to a protein disulfide bond and obtain force-dependent rate constants of the disulfide bond reduction initiated by a variety of nucleophiles. We measure distances to the TS or bond elongation (Delta x), along a 1-D reaction coordinate imposed by mechanical force, of 0.31 +/- 0.05 and 0.44 +/- 0.03 A for thiol-initiated and phosphine-initiated disulfide bond reductions, respectively. These results are in agreement with quantum chemical calculations, which show that the disulfide bond at the TS is longer in phosphine-initiated reduction than in thiol-initiated reduction. We also investigate the effect of solvent environment on the TS geometry by incorporating glycerol into the aqueous solution. In this case, the Delta x value for the phosphine-initiated reduction is decreased to 0.28 +/- 0.04 A whereas it remains unchanged for thiol-initiated reduction, providing a direct test of theoretical calculations of the role of solvent molecules in the reduction TS of an S N2 reaction. These results demonstrate that single-molecule force spectroscopy represents a novel experimental tool to study mechanochemistry and directly probe the sub-ångström changes in TS structure of solution-phase reactions. Furthermore, this single-molecule method opens new doors to gain molecular level understanding of chemical reactivity when combined with quantum chemical calculations.
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Dougan L, Feng G, Lu H, Fernandez JM. Solvent molecules bridge the mechanical unfolding transition state of a protein. Proc Natl Acad Sci U S A 2008; 105:3185-90. [PMID: 18305176 PMCID: PMC2265161 DOI: 10.1073/pnas.0706075105] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Indexed: 11/18/2022] Open
Abstract
We demonstrate a combination of single molecule force spectroscopy and solvent substitution that captures the presence of solvent molecules in the transition state structure. We measure the effect of solvent substitution on the rate of unfolding of the I27 titin module, placed under a constant stretching force. From the force dependency of the unfolding rate, we determine Deltax(u), the distance to the transition state. Unfolding the I27 protein in water gives a Deltax(u) = 2.5 A, a distance that compares well to the size of a water molecule. Although the height of the activation energy barrier to unfolding is greatly increased in both glycerol and deuterium oxide solutions, Deltax(u) depends on the size of the solvent molecules. Upon replacement of water by increasing amounts of the larger glycerol molecules, Deltax(u) increases rapidly and plateaus at its maximum value of 4.4 A. In contrast, replacement of water by the similarly sized deuterium oxide does not change the value of Deltax(u). From these results we estimate that six to eight water molecules form part of the unfolding transition state structure of the I27 protein, and that the presence of just one glycerol molecule in the transition state is enough to lengthen Deltax(u). Our results show that solvent composition is important for the mechanical function of proteins. Furthermore, given that solvent composition is actively regulated in vivo, it may represent an important modulatory pathway for the regulation of tissue elasticity and other important functions in cellular mechanics.
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Vano E, Segarra A, Fernandez JM, Ordiales JM, Simon R, Gallego JJ, del Cerro J, Casasola E, Verdu JF, Ballester T, Sotil J, Aspiazu A, Garcia MA, Moreno F, Carreras F, Canis M, Soler MM, Palmero J, Ciudad J, Diaz F, Hernandez J, Gonzalez M, Rosales P. A pilot experience launching a national dose protocol for vascular and interventional radiology. RADIATION PROTECTION DOSIMETRY 2008; 129:46-49. [PMID: 18310098 DOI: 10.1093/rpd/ncn025] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The design of a national dose protocol for interventional radiology has been one of the tasks during the European SENTINEL Coordination Action. The present paper describes the pilot experience carried out in cooperation with the Spanish Society on Vascular and Interventional Radiology (SERVEI). A prospective sample of procedures was initially agreed. A common quality control of the X-ray systems was carried out, including calibration of the air kerma area product (KAP) meters. Occupational doses of the radiologists involved in the survey were also included in the survey. A total of 10 Spanish hospitals with interventional X-ray units were involved. Six hundred and sixty-four patient dose data were collected from 397 diagnostic and 267 therapeutic procedures. Occupational doses were evaluated in a sample of 635 values. The obtained KAP median/mean values (Gy.cm2) for the gathered procedures were: biliary drainage (30.6/68.9), fistulography (4.5/9.8), lower limb arteriography (52.2/60.7), hepatic chemoembolisation (175.8/218.3), iliac stent (45.9/73.2) and renal arteriography (39.1/59.8). Occupational doses (mean monthly values, in mSv) were 1.9 (over apron); 0.3 (under apron) and 4.5 (on hands). With this National experience, a protocol was agreed among the SENTINEL partners to conduct future similar surveys in other European countries.
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63
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Simon R, Vano E, Prieto C, Fernandez JM, Ordiales JM, Martinez D. Criteria to optimise a dynamic flat detector system used for interventional radiology. RADIATION PROTECTION DOSIMETRY 2008; 129:261-264. [PMID: 18304958 DOI: 10.1093/rpd/ncn027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
An analysis of the relationship between image quality and incident air kerma has been carried out for a dynamic flat detector X-ray system used for interventional radiology. A phantom of polymethyl methacrylate (PMMA) to simulate patients and two different image test objects, Leeds TOR 18FG and NEMA XR 21, were used to evaluate the quality of the obtained images. Measurements were made simulating clinical configuration with different PMMA thicknesses (16, 20, 24 and 28 cm), available fields of view of 22, 31, 42 and 48 cm (diagonal dimension), in the three default fluoroscopy modes and in one of the most used digital subtraction angiography image acquisition modes. The obtained results are being used to help in the optimisation of clinical procedures.
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Szoszkiewicz R, Ainavarapu SRK, Wiita AP, Perez-Jimenez R, Sanchez-Ruiz JM, Fernandez JM. Dwell time analysis of a single-molecule mechanochemical reaction. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:1356-1364. [PMID: 17999545 DOI: 10.1021/la702368b] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Force-clamp spectroscopy is a novel technique for studying mechanochemistry at the single-bond level. Single disulfide bond reduction events are accurately detected as stepwise increases in the length of polyproteins that contain disulfide bonds and that are stretched at a constant force with the cantilever of an atomic force microscope (AFM). The kinetics of this reaction has been measured from single-exponential fits to ensemble averages of the reduction events. However, exponential fits are notoriously ambiguous to use in cases of kinetic data showing multiple reaction pathways. Here we introduce a dwell time analysis technique, of widespread use in the single ion channel field, that we apply to the examination of the kinetics of reduction of disulfide bonds measured from single-molecule force-clamp spectroscopy traces. In this technique, exponentially distributed dwell time data is plotted as a histogram with a logarithmic time scale and a square root ordinate. The advantage of logarithmic histograms is that exponentially distributed dwell times appear as well-defined peaks in the distribution, greatly enhancing our ability to detect multiple kinetic pathways. We apply this technique to examine the distribution of dwell times of 4488 single disulfide bond reduction events measured in the presence of two very different kinds of reducing agents: tris-(2-carboxyethyl)phosphine hydrochloride (TCEP) and the enzyme thioredoxin (TRX). A different clamping force is used for each reducing agent to obtain distributions of dwell times on a similar time scale. In the case of TCEP, the logarithmic histogram of dwell times showed a single peak, corresponding to a single reaction mechanism. By contrast, similar experiments done with TRX showed two well-separated peaks, marking two distinct modes of chemical reduction operating simultaneously. These experiments demonstrate that dwell time analysis techniques are a powerful approach to studying chemical reactions at the single-molecule level.
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65
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Fernandez JM, Ordiales JM, Guibelalde E, Prieto C, Vano E. Physical image quality comparison of four types of digital detector for chest radiology. RADIATION PROTECTION DOSIMETRY 2008; 129:140-143. [PMID: 18283060 DOI: 10.1093/rpd/ncn026] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Image quality for similar exposure conditions has been compared for two computed radiography (CR) systems (needle-based and conventional storage phosphor) and two flat-panel (DR) systems from different manufacturers mainly devoted to chest radiology. Image quality was assessed with a contrast-detail object and acrylic material to simulate clinical conditions. Specific image evaluation software was used to measure the contrast and obtain an image quality figure. Phantom and detector incident air kerma were measured for all images. Image quality differences were significant, and in the range of 100-300 microGy (phantom incident air kerma) the needle-based CR system and one of the DR systems show similar image quality and they are quite superior when compared with the conventional CR system.
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66
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Vano E, Ten JI, Fernandez JM, Prieto C, Ordiales JM, Martinez D. Quality control and patient dosimetry in digital radiology. On line system: new features and transportability. RADIATION PROTECTION DOSIMETRY 2008; 129:144-146. [PMID: 18283057 DOI: 10.1093/rpd/ncn030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
New features have been added to a system (QCONLINE) for auditing patient dosimetric and technical parameters 'on line', working on a digital radiology department and using the information contained in the DICOM header of some modalities. The audit of other parameters than patient doses have been included, setting alarm conditions to alert on malfunction of the X-ray system or bad operation modes, in addition to the evaluation of patient doses. A new module to analyse, collect and process the relevant information transferred by the modality performed procedure step (MPPS) service has been launched. Several examples with the exploitation of the new features are presented. The transportability of the system has been tested in two remote hospitals during several months. The new MPPS module has demonstrated to be a good tool to complement the information existing in the DICOM header. The system allows to help in the optimisation of digital radiology departments managing patient dosimetry and procedure data in real time.
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Ainavarapu SRK, Wiita AP, Huang HH, Fernandez JM. A Single-Molecule Assay to Directly Identify Solvent-Accessible Disulfide Bonds and Probe Their Effect on Protein Folding. J Am Chem Soc 2007; 130:436-7. [DOI: 10.1021/ja077851s] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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68
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Wiita AP, Perez-Jimenez R, Walther KA, Gräter F, Berne BJ, Holmgren A, Sanchez-Ruiz JM, Fernandez JM. Probing the chemistry of thioredoxin catalysis with force. Nature 2007; 450:124-7. [PMID: 17972886 DOI: 10.1038/nature06231] [Citation(s) in RCA: 225] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2007] [Accepted: 09/07/2007] [Indexed: 02/07/2023]
Abstract
Thioredoxins are enzymes that catalyse disulphide bond reduction in all living organisms. Although catalysis is thought to proceed through a substitution nucleophilic bimolecular (S(N)2) reaction, the role of the enzyme in modulating this chemical reaction is unknown. Here, using single-molecule force-clamp spectroscopy, we investigate the catalytic mechanism of Escherichia coli thioredoxin (Trx). We applied mechanical force in the range of 25-600 pN to a disulphide bond substrate and monitored the reduction of these bonds by individual enzymes. We detected two alternative forms of the catalytic reaction, the first requiring a reorientation of the substrate disulphide bond, causing a shortening of the substrate polypeptide by 0.79 +/- 0.09 A (+/- s.e.m.), and the second elongating the substrate disulphide bond by 0.17 +/- 0.02 A (+/- s.e.m.). These results support the view that the Trx active site regulates the geometry of the participating sulphur atoms with sub-ångström precision to achieve efficient catalysis. Our results indicate that substrate conformational changes may be important in the regulation of Trx activity under conditions of oxidative stress and mechanical injury, such as those experienced in cardiovascular disease. Furthermore, single-molecule atomic force microscopy techniques, as shown here, can probe dynamic rearrangements within an enzyme's active site during catalysis that cannot be resolved with any other current structural biological technique.
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69
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Dougan L, Fernandez JM. Tandem repeating modular proteins avoid aggregation in single molecule force spectroscopy experiments. J Phys Chem A 2007; 111:12402-8. [PMID: 18020430 DOI: 10.1021/jp076095+] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have used single molecule force spectroscopy to explore the unfolding and refolding behavior of the immunoglobulin-like I27 protein in aqueous 2,2,2-trifluoroethanol (TFE). In bulk solution experiments, a 28% v/v TFE solution has previously been observed to enhance intermolecular attractions and lead to misfolding and aggregation of tandem modular proteins of high sequence identity. In our single molecule experiments, however, we measure successful refolding of the polyprotein I27(8) in all TFE solutions up to 35% v/v. Using a single molecule micromanipulation technique, we have shown that refolding of a polyprotein with identical repeats is not hindered by the presence of this cosolvent. These experimental results provide new insight into the properties of tandem repeating proteins and raise interesting questions as to the evolutionary success of such proteins in avoiding misfolding and aggregation.
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Walther KA, Gräter F, Dougan L, Badilla CL, Berne BJ, Fernandez JM. Signatures of hydrophobic collapse in extended proteins captured with force spectroscopy. Proc Natl Acad Sci U S A 2007; 104:7916-21. [PMID: 17470816 PMCID: PMC1876547 DOI: 10.1073/pnas.0702179104] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Indexed: 11/18/2022] Open
Abstract
We unfold and extend single proteins at a high force and then linearly relax the force to probe their collapse mechanisms. We observe a large variability in the extent of their recoil. Although chain entropy makes a small contribution, we show that the observed variability results from hydrophobic interactions with randomly varying magnitude from protein to protein. This collapse mechanism is common to highly extended proteins, including nonfolding elastomeric proteins like PEVK from titin. Our observations explain the puzzling differences between the folding behavior of highly extended proteins, from those folding after chemical or thermal denaturation. Probing the collapse of highly extended proteins with force spectroscopy allows separation of the different driving forces in protein folding.
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71
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Brujic J, Hermans RIZ, Garcia-Manyes S, Walther KA, Fernandez JM. Dwell-time distribution analysis of polyprotein unfolding using force-clamp spectroscopy. Biophys J 2007; 92:2896-903. [PMID: 17259284 PMCID: PMC1831696 DOI: 10.1529/biophysj.106.099481] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Using the recently developed single molecule force-clamp technique we quantitatively measure the kinetics of conformational changes of polyprotein molecules at a constant force. In response to an applied force of 110 pN, we measure the dwell times of 1647 unfolding events of individual ubiquitin modules within each protein chain. We then establish a rigorous method for analyzing force-clamp data using order statistics. This allows us to test the success of a history-independent, two-state model in describing the kinetics of the unfolding process. We find that the average unfolding trajectory is independent of the number of protein modules N in each trajectory, which varies between 3 and 12 (the engineered protein length), suggesting that the unfolding events in each chain are uncorrelated. We then derive a binomial distribution of dwell times to describe the stochastic dynamics of protein unfolding. This distribution successfully describes 81% of the data with a single rate constant of alpha = 0.6 s(-1) for all N. The remainder of the data that cannot be accounted for suggests alternative unfolding barriers in the energy landscape of the protein. This method investigates the statistical features of unfolding beyond the average measurement of a single rate constant, thus providing an attractive alternative for measuring kinetics by force-clamp spectroscopy.
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72
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Cerón MC, García-Malea MC, Rivas J, Acien FG, Fernandez JM, Del Río E, Guerrero MG, Molina E. Antioxidant activity of Haematococcus pluvialis cells grown in continuous culture as a function of their carotenoid and fatty acid content. Appl Microbiol Biotechnol 2006; 74:1112-9. [PMID: 17171393 DOI: 10.1007/s00253-006-0743-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2006] [Revised: 10/31/2006] [Accepted: 11/02/2006] [Indexed: 10/23/2022]
Abstract
The influence of culture conditions on the quality of Haematococcus pluvialis biomass is assessed. Continuously grown cells have been characterised with respect to their astaxanthin, fatty acid content, and antioxidant activity and compared with those of non-growing haematocysts. Moderate limitation of nitrate availability (1.7 mM) under continuous growth conditions favoured the production of reddish palmelloid cells whose extracts possessed antioxidant activity equivalent to that of haematocyst extracts, despite the lower astaxanthin content (0.6%d.wt.), which is compensated by a higher fatty acid level (7.6%d.wt.). Green cells produced under nitrate saturation conditions (>4.7 mM) exhibit only 40% antioxidant activity than palmelloid. In addition, the major fatty acid present in palmelloid cells was oleic acid (40%f.a.), whereas, in both green cells and haematocysts, the main fatty acids were myristic, palmitic, and oleic acid (20-30%f.a. each). Biomass extracts were fractionated and analysed. The antioxidant capacity was a function of both the carotenoid and the fatty acid profiles, the antioxidant capacity of astaxanthin diesters fraction being 60% higher than astaxanthin monoesters fraction and twice than free astaxanthin. In such a way, the evaluation of the quality of H. pluvialis biomass must take into account both variables. When considering the production of H. pluvialis biomass for human consumption, special attention should be paid to the one-step continuous system approach for the generation of cells rich in both astaxanthin and fatty acids, as they have high antioxidant activity but without thick hard cell wall.
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Abstract
We use the GCN4 oligomerization domain to engineer a covalently linked parallel polyprotein dimer based on the well-studied I27 domain of titin. We use single molecule atomic force microscopy techniques to stretch single polyprotein fibers and verify their mechanical properties. We find that the engineered polyprotein dimers extend in perfect register, doubling the unfolding force and halving the persistence length while keeping the contour length increase unchanged. These experiments directly confirm the mechanical scaling laws proposed for parallel bundles of modular proteins.
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74
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Perez-Jimenez R, Garcia-Manyes S, Ainavarapu SRK, Fernandez JM. Mechanical unfolding pathways of the enhanced yellow fluorescent protein revealed by single molecule force spectroscopy. J Biol Chem 2006; 281:40010-4. [PMID: 17082195 DOI: 10.1074/jbc.m609890200] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We used single molecule force spectroscopy to characterize the mechanical stability of the enhanced yellow fluorescent protein (EYFP) (a mutant form of the green fluorescent protein (GFP)) and two of its circularly permutated variants. In all three constructs, we found two main unfolding peaks; the first corresponds to a transition state placed close to the termini and the second to a transition state placed halfway through the molecule. We attribute the second transition state to the shear rupture of the beta1- and beta6-strands, which we verified by introducing a point mutation in this region. Although both unfolding peaks were observed in all three EYFP variants, their relative frequency of occurrence varied. Our results demonstrated that the mechanical unfolding pathways in EYFP could be deciphered through the use of circular permutation.
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75
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Ainavarapu SRK, Brujic J, Huang HH, Wiita AP, Lu H, Li L, Walther KA, Carrion-Vazquez M, Li H, Fernandez JM. Contour length and refolding rate of a small protein controlled by engineered disulfide bonds. Biophys J 2006; 92:225-33. [PMID: 17028145 PMCID: PMC1697845 DOI: 10.1529/biophysj.106.091561] [Citation(s) in RCA: 227] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The introduction of disulfide bonds into proteins creates additional mechanical barriers and limits the unfolded contour length (i.e., the maximal extension) measured by single-molecule force spectroscopy. Here, we engineer single disulfide bonds into four different locations of the human cardiac titin module (I27) to control the contour length while keeping the distance to the transition state unchanged. This enables the study of several biologically important parameters. First, we are able to precisely determine the end-to-end length of the transition state before unfolding (53 Angstrom), which is longer than the end-to-end length of the protein obtained from NMR spectroscopy (43 Angstrom). Second, the measured contour length per amino acid from five different methods (4.0 +/- 0.2 Angstrom) is longer than the end-to-end length obtained from the crystal structure (3.6 Angstrom). Our measurement of the contour length takes into account all the internal degrees of freedom of the polypeptide chain, whereas crystallography measures the end-to-end length within the "frozen" protein structure. Furthermore, the control of contour length and therefore the number of amino acids unraveled before reaching the disulfide bond (n) facilitates the test of the chain length dependence on the folding time (tau(F)). We find that both a power law scaling tau(F) lambda n(lambda) with lambda = 4.4, and an exponential scaling with n(0.6) fit the data range, in support of different protein-folding scenarios.
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