Electrophoresis: Focusing Strategy and Influence of Conductivity On Isoelectric Focusing in Immobilized PH Gradients
Electrophoresis: Focusing Strategy and Influence of Conductivity On Isoelectric Focusing in Immobilized PH Gradients
          The equilibrium current is the current generated by all the                    IEF was carried out in the PROTEAN IEF cell. The 7 cm
          species as they diffuse around their equilibrium position,                     pH 3–10 strips were subjected to the following IEF program:
          including ions close to the electrode and proteins in the IPG                  50 V for 15 min, 250 V for 15 min, linear gradient to 4,000 V
          as they are converted between their neutral and ionic forms.                   over 2 hr, and 4,000 V for 2 hr. The longer 17 cm pH 3–10
          The equilibrium current is proportional to the concentration of                strips were subjected to three different IEF program strategies:
          all ionized species in the sample. In contrast to the moving                   1) a “direct progressive voltage” (50 V for 15 min, 250 V for
          current that decreases with time at constant voltage, the                      15 min, linear gradient to 10,000 V over 5 hr, and 10,000 V
          equilibrium current is linearly proportional to the voltage.                   for 5 hr, or, for the protein-containing mixture, for a total of
                                                                                         40 kV-hr ); 2) a “desalting step and progressive voltage” (50 V
          The convection current may be driven by electroendosmotic
                                                                                         for 9 hr, 200 V for 1 hr, linear gradient to 1,000 V over 1 hr,
          movement, a component of hydrodynamic transport.
                                                                                         linear gradient to 10,000 V over 6 hr, and 10,000 V for a total
          For safety from overheating, a limit of 50 µA per 3 mm wide                    of 40 kV-hr for the entire run) as described in Joubert-Caron et
          strip is advised for commercial apparatus. If the current                      al. (2000); and 3) a “desalting step and rapid voltage” (50 V for
          reaches 50 µA when the voltage is set to increase linearly,                    9 hr, 10,000 V to 40 kV-hr). The current was limited to 50 µA
          the voltage will then be regulated by the current limit, and the               per strip, and the running temperature was 20°C. The strips
          resulting voltage increase will no longer be linear. Once the                  were run in duplicate for samples that contained buffers in
          current decreases below 50 µA, the voltage will again drive                    the absence of proteins, and in triplicate for in-gel protein
          the linear progression of the gradient. One of the major                       incorporation. For protein-containing samples, the strips were
          problems encountered by novices to 2-D electrophoresis is                      stored at -20°C until used for the second dimension.
          the inability to reach the voltage they want.                                  Connection of a PROTEAN IEF Cell to a Computer
          We evaluated the contribution of various compounds to                          To monitor electrical properties during IEF, a modem cable
          the electrical field. We show how recording the electrical                     was connected from the RS-232 port of the PROTEAN IEF
          parameters helps to identify artifacts, allowing adjustment of                 cell to the serial port of a PC. The HyperTerminal software
          the profile and the duration of each IEF step, and adaptation                  was opened from the Start menu of the Windows 95
          of the protocol to the sample and the buffers used.                            operating system. The setup configuration was 9,600 bits/sec,
                                                                                         8 data bits, no parity, stop bit at 1, material control flow.
          Methods                                                                        The PROTEAN IEF cell exported run data every 5 min to
          First-Dimension Electrophoresis
                                                                                         HyperTerminal software. At the end of the run, the data were
          All reagents and materials were obtained from Bio-Rad unless
                                                                                         entered into an Excel spreadsheet for plotting.
          otherwise indicated. The loading volumes were 125 µl and
          300 µl for ReadyStrip™ 7 cm and 17 cm IPG strips, respectively.                Second-Dimension Electrophoresis
          Passive rehydration was carried out in the PROTEAN® IEF cell                   Prior to SDS-PAGE, IPG strips were equilibrated as previously
          at 20°C. The rehydration step was 2 hr long for test samples                   described in Joubert-Caron et al. (2000). They were loaded on
          that contained buffers in the absence of proteins, and 6 – 9 hr                PROTEAN II Ready Gel® 8 –16%T precast gels and run for 1 hr
          for in-gel protein incorporation.                                              at 40 V followed by 15 hr at 150 V in a PROTEAN II XL cell.
                                                                                         The gels were silver stained and one gel per condition was
          Three different premade reagents were tested: ReadyPrep™                       scanned with a GS-700 scanner and quantitated as described
          reagent 1, reagent 2, and reagent 3.* For protein in-gel                       by Joubert-Caron et al. (1999) and Poirier et al. (2001) with
          incorporation, the salt-free rehydration solution was 7 M urea,                Melanie 3 software (Genebio, Geneva, Switzerland).
          2 M thiourea, 4% (w/v) CHAPS, 0.24% (v/v) Triton X-100,
          0.2% (w/v) Bio-Lyte 3/10. Rehydration solution (280 µl) was
          mixed with 20 µl (100 µg) of soluble proteins extracted from
          the lymphoblastoid cell line PRI as previously described in
          Joubert-Caron et al. (2000). To evaluate the effect of DTT on
          the current, lyophilized reagent 2 was reconstituted with
          deionized water and with either 10 mM or 20 mM DTT.
                                                                                     2
02-102 2778 remy tnote.qxd                  5/1/02        5:00 PM         Page 5
                              40
                                                                                                           and without protein both showed the same equilibrium current
                                                                                        Voltage, kV
                                                                           32 µA
                                                                                                           profile and values. The difference in migration time can be
                              30                                                    2
                                                                                                           attributed to the proteins, which are amphoteric molecules,
                                                                 29 µA                                     and to the presence of ions in the protein extract. Assuming
                              20
                                                                           24 µA                           an average protein molecular weight of 40 kD, loading 100 µg
                                                                                    1
                                                                                                           in 300 µl corresponds to an 8.3 µM concentration. The
                              10
                                                                                                           associated conductivity is insignificant compared to the
                                                                                                           contribution of any salts or ionic contaminants. The high current
                               0                                                    0                      contributed by a salt (such as Tris at only 40 mM) versus 100 µg
                                   1           2           3               4                               of protein, emphasizes the importance of desalting samples as
                                              Run time, hr
                                                                                                           extensively as possible.
              Fig. 1. Current and voltage profiles of different solutions loaded on IPG strips             Electrical Strategies
              (current, thick lines; voltage, thin lines). Solutions (125 µl) were loaded onto
              7 cm pH 3 –10 strips. A, lyophilized reagent 2 reconstituted with either                     Three different voltage regimens were tested. In the experiment
              demineralized water (blue) or deionized water (red). B, reagent 2                            illustrated in Figure 2A, the molecules were first mobilized at
              supplemented with no DTT (blue), 10 mM DTT (red), or 20 mM DTT (black).                      low voltage for a short time. Then the voltage was increased
              The IEF program was 50 V for 15 min, 250 V for 15 min, linear gradient to
              4,000 V over 2 hr, and 4,000 V for 2 hr.
                                                                                                           linearly to 10,000 V over 5 hr. Complete focusing was
                                                                                                           achieved at 10,000 V for 5 hr or a total of 40 kV-hr for the
                                                                                                           protein-containing solution. For both the rehydration solution
                                                                                                           alone, and the protein-containing sample, it took only 3 hr for
                                                                                                           the moving current to reach zero. The remaining current, due
                                                                                                           to the equilibrium current, was then determined only by the
                                                                                                           voltage according to Ohm’s Law. The graphical representation
                                                                                                       3
02-102 2778 remy tnote.qxd                               5/1/02         5:00 PM                Page 6
10
                                                                                       Voltage, kV
                                  30                                                                                                                     This step has also been described as a preliminary desalting
                                                                                  8
                                                                          19 µA
                                                                                                                                                         step (Righetti and Bossi 1997). This second strategy was
                                                                                  6
                                  20                                                                                                                     used in the “desalting step and progressive voltage” program
                                                                                  4                                                                      described in the Methods section.
                                  10                                      5 µA
                                                                                  2
                                                                                                                                                         As shown in Figure 2B, the global current profile looked very
                                   0                                              0                                                                      different from the previous profile shown in Figure 2A. A
                                          2       4       6        8      10
                                                      Run time, hr                                                                                       desalting process was apparent in the first step at 50 V for
                        B              Desalting step and progressive voltage                                                                            almost 7 hr, after which the current stabilized. This step could
                                  50                                                                                              14                     hence be reduced from 9 hr to 7 hr. After this initial step, all
                                                                                                           47 µA
                                                                                                                                  12                     tested mixtures except reagent 3 followed the voltage ramp
                                  40
                                                                                                                                                         without current limitation. The rehydration solutions, with or
          Current, µA/strip
                                                                                                                                  10
                                                                                                                                                         without proteins, showed similar profiles, with a return to
                                                                                                                                       Voltage, kV
                                  30                                                                                              8
                                                                                                                                                         equilibrium after 2 hr at the last gradient step. These data
                                                                                                              18 µA               6
                                  20                                                                                                                     suggest that the duration of the gradient could be reduced
                                                                                                                                  4                      from 6 hr to 2 – 3 hr. Reagent 1 (40 mM Tris) reacted to the
                                  10                                                                                                                     gradient step with a high but short peak of current, due to
                                                                                                                                  2
                                                                                                                  8 µA
                                                                                                                                                         the previous extended desalting step at 50 V. Even reagent 3
                                   0                                                                                              0
                                          2       4       6       8       10      12                 14       16                                         (the mixture with Tris) showed a zero moving current before
                                                              Run time, hr
                                                                                                                                                         the end of the gradient step, which could therefore be
                        C              Desalting step and rapid voltage
                                                                                                          45 µA
                                                                                                                                                         reduced from 6 hr to 4 hr. It is noteworthy that in both
                                  50                                                                                14                                   electrical strategies, the values of the equilibrium current
                                                                                                                    12                                   were the same.
                                  40
          Current, µA per strip
                                                                                                                                                     4
02-102 2778 remy tnote.qxd                     5/1/02        5:00 PM    Page 1
          A, Direct progressive voltage, 7 hr run                      B, Desalting step and progressive voltage, 17.5 hr run         C, Desalting step and rapid voltage, 14 hr run
                              50                                10     50                                                 10          50                                                10
                              40                                8      40                                                 8           40                                                8
          Current, µA/strip
                                                                                                                                                                                             Voltage, kV
                              30                                6      30                                                 6           30                                                6
20 4 20 4 20 4
10 2 10 2 10 2
                              0                                 0       0                                                 0            0                                                0
                                   2            4        6                     2    4     6     8 10 12        14   16                         2     4      6     8    10   12     14
                                          Run time, hr                                        Run time, hr                                                 Run time, hr
             Analysis of 2-D gels allowed further comparison of the three                               The third strategy, however, with its sudden voltage increase,
             protocols. Each of the 2-D gels of samples subjected to the                                showed fewer large protein spots and many more small
             “direct progressive voltage”, the “desalting and progressive                               protein spots compared to the two other strategies. One can
             voltage”, and the “desalting and rapid voltage” IEF runs                                   hypothesize that the small, more mobile molecules in a
             (Figure 3A, B, and C, respectively) appeared similar and                                   complex mixture respond first to the suddenly applied field.
             showed almost the same number of spots (1,005, SEM <1%).                                   As the applied voltage increases, the molecules could be
             The IEF run durations were 7 hr, 17.5 hr, and 14 hr, respectively.                         progressively subjected to the field and mobilized, and the
             Image analysis of the gels showed that the distribution of                                 movement of the larger ones would be better regulated by
             protein spots, however, was not identical. The number of                                   the applied current.
             spots was determined in three molecular weight intervals:
             small proteins <25 kD; proteins between 25 kD and 100 kD;                                  Table. Number and distribution of protein spots focused using different
                                                                                                        electrical strategies by mass intervals. Data from gels in Figure 3.
             and large proteins >100 kD (see Table). The sum of the spots
                                                                                                                                               Focusing Strategy
             counted in the three intervals slightly differed from the total
                                                                                                        Mass              Direct               Desalting Step          Desalting Step
             number of spots per gel; some spots could have been                                        Range, kD         Progressive          and Progressive         and Rapid
             counted twice because they lie near the boundary between                                                     Voltage              Voltage                 Voltage
             intervals. The three electrical strategies gave similar numbers                            >100                    119                  132                      76
             of spots for the proteins between 25 kD and 100 kD (739,                                   25–100                  740                  745                    732
             SEM <1%). This corresponds to the mass range that is well                                  0–25                    143                  132                    191
             separated by 2-D electrophoresis. For these common proteins,
             intense evaluation of different electrical strategies is not                               Looking at the distribution of spots in various pH intervals
             necessary once the moving current reaches zero. The fastest                                (Figure 4), proteins with pIs in the ranges of 5 – 6 and 6 –7,
             strategy (7 hr in this case) can be chosen. For both large and                             which are the most abundant in the sample (Joubert-Caron
             small proteins, the first two strategies, which have a                                     et al. 2000), were present in the same proportion at all of the
             progressive voltage gradient in common, showed similar                                     voltage regimens applied (SEM around 1%). The extremely
             numbers of spots. The initial low-voltage step at 50 V did not                             acidic (pH 3.5 – 4) and alkaline (pH 9 – 9.5) regions also showed
             give a significant increase in the number of large protein spots.                          similar numbers of spots but the small number of spots
                                                                                                 5
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