J Biol Chem, Vol. 274, Issue 44, 31506-31514, October 29, 1999
Lethal Kinesin Mutations Reveal Amino Acids Important for
ATPase Activation and Structural Coupling*
Katherine M.
Brendza
§,
Debra J.
Rose
,
Susan P.
Gilbert¶
, and
William M.
Saxton
**
From the
Department of Biology, Jordan Hall, Indiana
University, Bloomington, Indiana 47405 and the ¶ Department of
Biological Sciences, Langley Hall, University of Pittsburgh,
Pittsburgh, Pennsylvania 15260
 |
ABSTRACT |
To study the relationship between conventional
kinesin's structure and function, we identified 13 lethal mutations in
the Drosophila kinesin heavy chain motor domain and tested
a subset for effects on mechanochemistry. S246F is a moderate mutation that occurs in loop 11 between the ATP- and microtubule-binding sites.
While ATP and microtubule binding appear normal, there is a 3-fold
decrease in the rate of ATP turnover. This is consistent with the
hypothesis that loop 11 provides a structural link that is important
for the activation of ATP turnover by microtubule binding. T291M is a
severe mutation that occurs in
-helix 5 near the center of the
microtubule-binding surface. It impairs the microtubule-kinesin
interaction and directly effects the ATP-binding pocket, allowing an
increase in ATP turnover in the absence of microtubules. The T291M
mutation may mimic the structure of a microtubule-bound, partially
activated state. E164K is a moderate mutation that occurs at the
-sheet 5a/loop 8b junction, remote from the ATP pocket.
Surprisingly, it causes both tighter ATP-binding and a 2-fold decrease
in ATP turnover. We propose that E164 forms an ionic bridge with
-helix 5 and speculate that it helps coordinate the alternating site
catalysis of dimerized kinesin heavy chain motor domains.
 |
INTRODUCTION |
Conventional kinesin is an abundant microtubule motor protein that
functions in a number of important intracellular transport processes
(reviewed in Ref. 1). It is a heterotetramer comprised of 2 kinesin
heavy chains (KHCs)1 and 2 light chains. The heavy chains dimerize to form an elongated stalk with
2 amino-terminal globular domains ("motor domains") at one end and
the light chains at the other end. The light chains and stalk are
expected to bind the cytoplasmic cargoes that conventional kinesin
transports. Each motor domain couples a cycle of ATP turnover to
conformational changes and a cycle of microtubule binding and release
that generates displacement toward the microtubule plus end. A single
motor domain is not processive (2, 3). In contrast, dimerized motor
domains are remarkably processive, making hundreds of steps before
releasing from the microtubule (4, 5). This feature is probably
critical for the resolute transport of small organelles that can
present only one or a few kinesin molecules to a microtubule.
The pathway of ATP hydrolysis has been studied in detail, and there is
general agreement on a number of features of kinesin's alternating
site mechanism (6-13). The model in Fig.
1 illustrates some of those features in
the context of its mechanochemical cycle. Free in solution, kinesin
exists with ADP bound in its active site. The ATPase cycle begins as
one motor domain binds to the microtubule, leading to rapid release of
ADP (step 1). ATP binding at this empty active site (step 2) stimulates
binding of the second motor domain to the microtubule and release of
its ADP (step 3). Thus, the two motor domains of the dimer are coupled
through this step. After ATP hydrolysis by the first head (step 4), a
rate-limiting step occurs (step 5) encompassing both detachment from
the microtubule and phosphate release. ATP binding to the second head
and rebinding of the first head to the next forward site on the
microtubule lattice 16 nm away advances the kinesin dimer center of
mass by 8 nm (step 2'; Ref. 14). For KHC, recent evidence has ruled out
step distances other than 8 nm and coupling ratios other than 1 ATP per
8 nm step (15-17).

View larger version (18K):
[in this window]
[in a new window]
|
Fig. 1.
A model for dimeric kinesin ATPase
mechanism. The ATPase cycle begins as one motor domain binds to
the microtubule, leading to rapid release of ADP (step 1). ATP binding
(step 2) stimulates binding of the second motor domain to the
microtubule and release of its ADP (step 3). Subsequently, ATP
hydrolysis (step 4) occurs forming an intermediate in which both motor
domains are bound to the microtubule but the nucleotide state of each
is different. Step 5 is the slowest in the pathway, encompassing both
detachment of the motor domain from the microtubule and phosphate
release. Step 6 positions the detached motor domain toward the
microtubule plus end. Rebinding of the detached head to the next
available microtubule-binding site is rapid (step 2 and 3) and advances
the center of mass of the dimer by 8 nm, thereby completing one step
cycle. The cycle repeats for the second head, resulting in 2 steps
driven by the hydrolysis of 2 ATPs. 0, no nucleotide at active site.
k1 = 300 s 1;
k2 = 2 µM 1
s 1; k-2 = 70 s 1;
k3 = 200 s 1;
k4 = 100 s 1;
k5 = 50 s 1;
kcat = 20 s 1 per kinesin active
site, 40 s 1 per dimer.
|
|
The structure of the KHC mechanochemical domain in both monomer and
dimer forms has been studied by x-ray crystallography and electron
microscopy (18-29). The crystallographic analysis of KHC monomers with
ADP bound revealed an extended
-sheet flanked on each side by 3
-helices (see Fig. 4B). The nucleotide-binding site is
near the top of the sheet on the side occupied by helices 1-3.
Evidence to date indicates that the binding of kinesin to microtubules
is mediated by multiple contacts on the side of the molecule occupied
by helices 4-6. These studies include structural evidence based on
electron micrographs of microtubule·KHC complexes (18-20, 22, 23,
25, 28, 30). Crystallographic studies of rat KHC dimers with ADP bound
showed the same motor domain structure seen with monomers and revealed
that the heads are joined by coiled-coil interactions at
7. The
dimer structure also revealed that a negatively charged portion of L8b
on one head can approach a positively charged portion of L10 on the
other head (Fig. 8). The opposing charges and proximity of these loops
has raised the possibility of a salt bridge forming between the motor
domains that may be important for the coordination of their
mechanochemical cycles and consequently for the processive movement of kinesin.
To gain insight into how kinesin moves, the effects of specific
structural changes on the mechanochemistry of KHC have been studied.
Woehlke et al. (31) have discovered a number of probable microtubule-KHC contact sites by changing solvent-exposed, polar amino
acids to alanine and testing for effects on both motility and
microtubule stimulated ATPase activity. Several of those sites are
concentrated in L11,
4, L12, and
5. Two additional in
vitro mutagenesis studies have focused on the contributions of the
KHC hinge I and neck regions to motor velocity and processivity.
Changes in hinge I, which connects the neck to the beginning of the
kinesin stalk, can alter the velocity of gliding movements
dramatically, indicating that hinge I is important for normal motor
domain mechanochemistry (32). Changes in
7 and other neck sequences
can alter processivity but do not abolish it, suggesting that
structural interactions between dimerized motor domains outside the
neck region also contribute to processivity (33).
We have addressed questions of KHC structure-function using an approach
that combines in vivo genetics and in vitro
mechanochemical tests. We reasoned that by screening for missense
mutations that disrupt axonal transport (34) and cause lethality in
Drosophila, amino acid substitutions would be identified
that affect kinesin mechanochemistry in ways that are physiologically
relevant. By testing purified mutant motor domain dimers for motility,
microtubule interaction, nucleotide-binding, and steady-state ATP
turnover, we have identified two amino acids that are important for
communication from the microtubule-binding site to the
nucleotide-binding site and one likely to form an ionic bridge between
5a/L8b and
5; a bridge that influences nucleotide binding and may
be involved in coordinating the ATPase and microtubule-binding cycles
of dimerized heads.
 |
EXPERIMENTAL PROCEDURES |
Materials--
[
-32P]ATP (>3000 Ci/mmol) was
from NEN Life Sciences (Boston, MA), polyethyleneimine (PEI)-cellulose
TLC plates (EM Science of Merck, 20 × 20 cm, plastic backed) were
from VWR Scientific (Bridgeport, NJ), Taxol (Taxus
brevifolia) was from CalBiochem-NoveBiochem International (San
Diego, CA), QIAmp Tissue Kit and Qiaquick gel extraction kit were from
Qiagen (Valencia, CA), Thermo Sequenase sequencing kit was from
Amersham Pharmacia Biotech, T4 DNA ligase and restriction enzymes were
from New England Biolabs (Beverley, MA), Chameleon Double-Stranded
Site-Directed Mutagenesis Kit was from Stratagene, Inc. (La Jolla, CA),
ATP, GTP, AMP-PNP, S-Sepharose and DEAE-Sephacel were from Amersham
Pharmacia Biotech, Bio-Rad Protein Assay, ovalbumin, and IgG were from
Bio-Rad.
Genetics--
Drosophila were cultured at 25 °C
with a 12-h light and 12-h dark cycle on standard soft medium (0.5%
agar, 7% molasses, 6% cornmeal, and 0.8% killed yeast) seeded with
live yeast. Descriptions of some of the mutations used in this study
can be found in Lindsley and Zimm (35). Description of
Khc1-Khc13 can be found
in Saxton et al. (36). All other Khc alleles were isolated in a standard F2 screen for new recessive-lethal alleles of
Khc.2 Chromosomes
mutagenized with ethylmethane sulfonate were tested over
Khc8, a null mutation. Those that failed to
complement Khc8 were retested over
Df(2R)Jp6, a deletion that removes Khc. They were
then tested over Df(2R)Jp6 with a wild-type Khc
transgene present in the background. Chromosomes that failed to
complement Df(2R)Jp6 and were rescued by the Khc
transgene were maintained in balanced stocks for subsequent tests.
To determine the lethal profiles caused by the Khc mutations
reported here, adult males and virgin females of the genotypes Khcm/T (2, 3) CyO TM6B, Tb Hu, and
Df(2R)Jp6/T(2,3)CyO TM6B, Tb Hu were mated. After hatching,
second instar larvae of the genotype
Khcm/Df(2R)Jp6 were isolated and then
observed for lethality throughout development as described previously
(36).
Stability of Mutant KHCs--
Adult male flies that carried each
Khc allele in the following genotype: w;
Khcm/Df (2R) Jp6; P{w+,wumk9}/+, were
collected and stored at
80 °C.
P{w+,wumk9} is a stable P-element insert
that contains a wild-type copy of Khc cDNA fused to a
c-myc epitope tag (37). High level expression is driven by a
ubiquitin promoter. The Myc-KHC fusion protein completely rescues the
lethality caused by Khcnull mutations.
Total protein was extracted from male flies by homogenization in cold
extraction buffer as described previously at a volume of 8 µl of
extraction buffer/animal (38). The homogenates were clarified by
centrifugation: 2 fly equivalents of each supernatant were run on a
5-10% SDS-polyacrylamide gradient gel and then transferred to
nitrocellulose (38). The Myc-KHC fusion protein migrated more slowly
than native KHCs in SDS-polyacrylamide gel electrophoresis, allowing
comparison of their relative levels. Both KHCs were detected by
incubation in a mouse monoclonal anti-Drosophila KHC
antibody, Flyk-2, diluted 1:50 followed by incubation in an alkaline
phosphatase-conjugated goat anti-mouse serum at 1:1000 (36).
Sequencing of Khc Alleles--
DNA was isolated from
Khcm/Df(2R)Jp6 pre-lethal larvae
using the QIAmp Tissue Kit. Overlapping ~300-base pair fragments of genomic DNA covering the entire coding sequence of Khc were
amplified separately using the polymerase chain reaction. The
polymerase chain reaction products were then purified using the
Qiaquick gel extraction kit. DNA was sequenced using a Thermo
Sequenase sequencing kit, and the reactions were run on an ABI
automated sequencer. Both sense and antisense strands were sequenced
and in areas that had changes both strands were sequenced at least twice.
Expression and Purification of K401-BIO for Motility--
The
expression plasmid pEY4, used for motility assays, contains a
Drosophila Khc cDNA that encodes the
NH2-terminal 401 residues of Khc fused to a
cDNA that encodes the COOH-terminal 87 residues of
Escherichia coli Biotin Carboxyl Carrier Protein. This
construct was generously provided by Dr. Jeff Gelles (39). The
mutations tested were inserted by restriction digest at 2 unique sites
(NruI and BssHII) in wild-type Khc.
Mutant Khc inserts were amplified from mutant genomic
DNA using the polymerase chain reaction. The oligonucleotide primers
used were 5'-GTCAAGGGCGCTACGGAACG-3' and 5'-TGCTTGCCTCCATGAGATCC-3'.
After restriction digestion, the plasmid and amplification
products were ligated using T4 DNA ligase and transformed into E. coli DH5
. Plasmids isolated from single colonies were
sequenced. Those containing the appropriate mutations and no other
changes were subsequently transformed into BL21(DE3)pLysS cells for
protein expression as described in Berlinear et al. (39).
After induction, cells were harvested and subjected to 3 cycles of
freezing (liquid N2) and thawing (37 °C). The cell
extract was then centrifuged and the resulting supernatant
(approximately 4 ml) was dialyzed overnight against 4 liters of storage
buffer (50 mM Tris·Cl, pH 7.5, 1 mM EDTA,
10% sucrose, 10 mM DTT, 1 mM phenylmethylsulfonyl fluoride, 1 µg/ml pepstatin A, 10 µg/ml
N
-p-tosyl-L-arginine
methyl ester, 10 µg/ml N-tosyl-L-phenylalanine chloromethyl ketone, 1 µg/ml leupeptin, 10 µg/ml soybean trypsin inhibitor). The cell extract was not capable of producing
microtubule-based movements in the gliding assay described below. To
enrich for active K401-BIO motors, the clarified dialysate was
incubated for 20 min at room temperature with 7 mM
magnesium/AMP-PNP and 0.4 mg/ml taxol-stabilized microtubules followed
by centrifugation. The resulting pellet was resuspended in a salt wash
(75 mM NaCl + 7 mM Mg/AMP-PNP in extraction
buffer) to remove proteins that were nonspecifically bound to
microtubules. After sedimentation, the resulting pellet was resuspended
in 10 mM MgATP plus 100 mM NaCl in extraction
buffer to release K401-BIO motors. After centrifugation, the
supernatant was stored on ice and used within 24 h for motility assays. These preparations induced microtubule gliding but the gliding
was not smooth, suggesting that either the inactive motors were not
completely eliminated or misorientation of the motor on the glass
prevented efficient motility. The supernatants were also characterized
by SDS-polyacrylamide gel electrophoresis and Western blots. The blots
were probed with either anti-KHC (FLYK-2) or alkaline
phosphatase-conjugated avidin. The KHC bands stained heavily with
avidin, indicating that the motors were indeed biotinylated by the
bacteria (data not shown). A few faint lower molecular weight
polypeptide bands were also observed. Those biotinylated polypeptides
did not cross-react with anti-KHC. Similar low molecular weight
biotinylated proteins produced by this expression system have been
previously reported (39).
Expression and Purification of K401 for Kinetic
Analysis--
The motors used for kinetic analyses were re-engineered
to eliminate the biotin tag and a new purification scheme was used to
minimize the loss of motor activity. Motor domain mutations were
introduced by site-directed mutagenesis (Chameleon Double-stranded Site-Directed Mutagenesis Kit) into a plasmid, pET5b-K401, that has
been used extensively for previous kinetic analysis (6, 7, 12, 40, 51).
It encodes only the NH2-terminal 401 residues of
Drosophila KHC. The mutagenic primers used were as follows:
K401-4 (5'-CCGTGATTCCAAGCTTATGC-GCATCCTGCAG-3'); K401-23 (5'-GTGTGCACAAGGATAAGAAC-3'); K401-17
(5'-GGTTCCGAGAAGGTTTTCAAGACTGGAGCGG-3'); and K401-37
(5'-CTGCCCTGGCGAACGGAAACAAAACGCAC-3'). The selection primer
(5'-CTAATCCTGTTACTAGTGGCTGC-3') removed a AlwNI site
from the pET5b plasmid. Plasmids isolated from single colonies were sequenced. Those containing only the desired mutations were transformed into BL21(DE3)pLysS cells. Each of the Khc alleles was
expressed as described previously with slight modifications (40). Four 2-liter cultures were incubated at 37 °C until
A600 = 0.5. The cells were then
temperature shifted to 20-22 °C and induced with 0.075 mM isopropyl-
-D-thiogalactopyranoside. Cells
were cultured overnight, harvested by centrifugation at 4 °C, then
stored at
80 °C until purification.
For protein purification, approximately 30 g of cells were diluted
to a final volume of 180 ml (1 g/6 ml) in lysis buffer (10 mM NaPO4 buffer, pH 7.2, 75 mM
NaCl, 2 mM MgCl2, 1 mM EGTA, 1 mM DTT, 2 mM phenylmethylsulfonyl fluoride)
plus lysozyme to 0.1 mg/ml and incubated on ice for 45 min with gentle
stirring. The cells were then lysed by 3 cycles of freezing (liquid
N2) and thawing (37 °C). The cell lysate was clarified
by ultracentrifugation yielding a supernatant of ~140 ml. The
supernatant was then loaded onto a 100-ml S-Sepharose column that was
equilibrated with S-Sepharose column buffer (10 mM
NaPO4 buffer, pH 7.2, 75 mM NaCl, 2 mM MgCl2, 1 mM EGTA, 1 mM DTT, 0.02 mM ATP). The column was eluted
with a 600-ml linear salt gradient (75-600 mM NaCl). The
K401 protein eluted at approximately 100 mM NaCl. Fractions
enriched in K401 were pooled and dialyzed against DEAE buffer (20 mM Tris·HCl, pH 7.8, 50 mM KCl, 5 mM MgCl2, 0.1 mM EGTA, 0.1 mM EDTA, 1 mM DTT, 0.02 mM ATP).
The dialysate was clarified by ultracentrifugation and passed over a
15-ml DEAE-Sephacel column equilibrated with DEAE buffer (20 mM Tris·HCl, pH 7.8, 50 mM KCl, 5 mM MgCl2, 0.1 mM EGTA, 0.1 mM EDTA, 1 mM DTT, 0.02 mM ATP).
The column was eluted with a 200-ml linear salt gradient (50-400
mM KCl). The K401 protein eluted at approximately 80-100
mM KCl. Fractions enriched in K401 were pooled and
concentrated by ultrafiltration (Amicon Centriprep 30) to ~5 ml. The
concentrated K401 was then dialyzed twice against ATPase buffer (20 mM Hepes, 5 mM magnesium acetate, 0.1 mM EGTA, 0.1 mM EDTA, 50 mM
potassium acetate, 1 mM DTT, 5% sucrose adjusted to pH 7.2 with KOH), clarified, and stored at
80 °C. This procedure yielded 4-10 mg of highly purified K401 per 30 g of E. coli.
The protein concentration of the kinesin preparations was determined by
the Bradford method (Bio-Rad Protein Assay with ovalbumin and IgG as
standards). It was also measured spectrophotometrically at
A280 and A259 to
determine the concentration of the stoichiometrically bound ADP (40).
In addition, the concentration of active kinesin was determined using
the creatine kinase-coupled assay described previously (41). The active
site concentration for each preparation varied from 90 to 99% of the
protein concentration estimated by the Bradford method. For the
experiments reported, the concentration of kinesin is based on the
active site concentration of the preparation.
Mammalian Brain Tubulin and Microtubules for Motility and Kinetic
Experiments--
Bovine brain tubulin was prepared as described
previously (40). On the day of each experiment, an aliquot of tubulin
was thawed, cycled, and then stabilized with 20 µM taxol.
Motility Assays--
Microtubule-gliding assays were performed
using K401-BIO preparations as described by Berlinear et al.
(39) except that
-casein was used in all washes instead of bovine
serum albumin. Samples were observed by video-enhanced differential
interference microscopy using an Axioplan microscope (Carl Zeiss, Inc.,
Thornwood, NY) equipped with a 100 × Plan-Neofluar objective, a
Hamamatsu C2400 series video camera, and an Argus-10 image processor
(Hamamatsu Photonics, Hamamatsu City, Japan). Images were recorded on
Maxell S-VHS tapes using Mitsubishi model BV-1000 Professional Video Cassette recorder. Microtubule movements were measured directly from
the video monitor.
ATPase Assays--
ATPase assays were performed at 25 °C in
ATPase buffer at 50 mM potassium acetate by following the
hydrolysis of [
-32P]ATP as described previously (40).
All concentrations are reported as final values after mixing. To
initiate an ATPase reaction, a 5-µl aliquot of MT·K401 complex (0.5 µM K401, 0.25-20.0 µM tubulin, and 20 µM taxol) was mixed with 5 µl of substrate (0.01-2.0
mM MgATP and trace [
-32P]ATP). After
incubation for times varying from 5 to 120 s, the reaction mixture
was quenched by the addition of 10 µl of 4 N HCl followed
by the addition of 20 µl of chloroform, and neutralization with 8.7 µl of 2 M Tris, 3 M NaOH (final pH 7-7.8).
1.5 µl of each quenched reaction was spotted on a
polyethyleneimine-cellulose TLC plate, and then developed in 0.6 M KH2PO4 buffer at pH 3.4. Radiolabeled ATP and ADP were quantitated using a FUJIX Bio-imaging Analyzer Bas 1000 with MacBAS version 2.4 (Fuij Photo Film Co.; Kohshin
Graphic Systems, Inc.). The concentration of product
([
-32P]ADP) was plotted as a function of time, and the
data were fit to a line. The rate of ATP hydrolysis was determined from
the slope and then plotted as a function of either ATP or microtubule concentration. The fit of the data to a hyperbola (KaleidaGraph, Synergy Software, Reading, PA) provided the steady-state parameters: kcat, Km,ATP, and
K0.5,MT.
The concentration of kinesin used in the steady state ATPase assays was
0.5 µM. This concentration was selected to ensure that
kinesin motors were dimeric under the experimental conditions of the
assay (Kd for dimerization ~40 nM
(42)). The data in Fig. 7A were fit to a quadratic equation
because the steady-state ATPase assays as a function of microtubule
concentration were performed with tubulin concentrations that were as
low as the enzyme concentration,
|
(Eq. 1)
|
where E represents the enzyme kinesin;
E0 = 0.5 µM kinesin;
Mt, tubulin; and K0.5,MT is the
concentration of tubulin required to provide one-half the maximal velocity.
 |
RESULTS |
Identification of Mutations in the Coding Sequence of the Motor
Domain of Khc--
To identify amino acid changes that alter the
mechanochemical functions of kinesin in vivo, we screened
for recessive lethal mutations in the Khc gene of
Drosophila. Forty independent mutant lines were established
and changes in their Khc genes were identified through DNA
sequence analysis. It has been shown that the NH2-terminal ~400 amino acids of KHC are sufficient for microtubule-based movement (43, 44). This abbreviated KHC can be truncated further to the
NH2-terminal ~350 amino acids and still function as a
microtubule-activated ATPase and motor although processivity is
compromised and ATPase characteristics are altered (12, 41, 45-47).
Therefore, we searched for missense changes in the
NH2-terminal ~350 codons of the 40 mutant genes. Motor
domain changes were found in 13 of them; 3 are nonsense and 10 are
missense mutations (Table I). To address
the possibility that other lesions in the 13 motor domain alleles
contributed to the lethal phenotypes observed, sequencing was extended
to the 3' ends of their coding regions. One additional missense change
was found in Khc10. Although the sequence
analysis was not complete for all genes, it was extensive enough to
show that the probability of any unidentified changes in a given motor
domain allele is quite small (<0.02).
Stability of Mutant KHC Proteins in Vivo--
The motor domain
mutations were expected to have two different effects: some would
change mechanochemical functions while others would reduce steady-state
levels of KHC protein in vivo. To identify alleles that
reduce steady state levels of protein, adult flies that carried a
mutant Khc allele and a myc-tagged wild-type
Khc allele were tested by Western blotting. The transgenic tagged allele overexpressed a functional KHC fusion protein that electrophoresed more slowly than native KHC, allowing visualization of
the levels of the mutant KHCs (Fig. 2).
The relative stabilities of all 13 of the motor domain alleles are
shown in Table I. The three alleles with nonsense mutations
(Khc24, Khc27, and
Khc8) and one allele with a missense mutation
(Khc18) do not produce detectable KHC. The
remaining 9 missense alleles produce roughly normal levels of KHC
protein, suggesting that the mutant polypeptides can fold and
accumulate in vivo. Therefore, the phenotypes caused by
those 9 missense alleles are probably due to altered mechanochemical
functions.

View larger version (26K):
[in this window]
[in a new window]
|
Fig. 2.
Stability of mutant KHC proteins in
vivo. A Western blot of cytosol preparations from adult
flies of the indicated genotypes was probed with an antibody that binds
to the motor domain of Drosophila KHC (36). Genotypes:
+, wild-type chromosomes; Df, a deletion that
removes Khc from chromosome 2; m-Khc, a fusion
gene on chromosome 3 that expresses a Myc-tagged KHC at high levels;
4, 17, 23, 27, and 37, the respective mutant
Khc alleles. The upper band corresponds to
transgenic Myc·KHC whereas the lower band corresponds to
endogenous wild-type or mutant KHC. The absence of detectable protein
suggests that the nonsense allele Khc27 is a
protein null. The 4 missense alleles that were selected for
mechanochemical characterization (Khc 4, 17, 23, 37) all
produce stable mutant KHCs.
|
|
Selection of Alleles for in Vitro Characterization--
Three
criteria were considered in selecting a subset of the motor domain
alleles for mechanochemical tests: the phenotypic severity caused by
the allele, the evolutionary conservation of the affected residue, and
the location of that residue in three-dimensional structural models of
the KHC motor domain (24, 26, 27). To compare lethal phenotype
severities, animals were generated that carried the mutant allele of
interest on one chromosome and a deletion that removed the
Khc locus (Df(2R)Jp6) on the other chromosome
(36). Motor domain alleles that allowed the emergence of any adult
flies were classified as mild. Alleles that, like nulls, caused at
least 50% lethality in the second larval instar were classified as
severe. Alleles that caused 50% lethality at later stages of
development but produced no adults were classified as moderate. The
severities of the motor domain alleles are reported in Table I, and the
complete lethal profiles of the alleles chosen for mechanochemical
characterization are shown in Fig. 3.

View larger version (20K):
[in this window]
[in a new window]
|
Fig. 3.
Determination of the severities of KHC
mutations in vivo. A graphic representation of
the time course of lethality caused by mutant Khc alleles. The
x axis shows successive stages in the development of
Drosophila. The y axis shows the percent of live
animals remaining at the beginning of each stage. Each line
is labeled with an abbreviated genotype: numbers represent the
different Khc alleles and Df represents a
deletion of the Khc locus. The number of second instar
larvae tested for each genotype were:
Khc27/Df = 25, Khc4/Df = 122, Khc23/Df = 86, Khc17/Df = 86, Khc37/Df = 96, and
Khc23/Khc4 = 209. Note
that the effect of Khc4 is similar to both the
null mutation Khc27 (compare first and second
lines) and the deletion (compare third and fourth lines). Therefore
Khc4 causes a near complete loss of function and
is classified as "severe" in Table I. Khc37
allows the survival of some animals to adulthood and thus is classified
as "mild." Khc23 and
Khc17 are less severe than a null but do not
allow survival of any adults and thus are classified as
"moderate."
|
|
To assess the conservation and positions of the residues affected in
the motor domain alleles, sequence alignments and three-dimensional modeling were performed (Fig. 4 and Table
I). Based on these data, four alleles covering the full range of
in vivo severities were selected for in vitro
characterization: Khc4,
Khc17, Khc23, and
Khc37. Khc4 causes the
most severe phenotype, equivalent to a null. The affected amino acid
(Thr291) is identical in all but one member of the
superfamily and is located in
5 which is thought to be important for
the microtubule-KHC interaction (22-24, 26, 27, 31, 48).
Khc37 causes a mild lethal phenotype. The
affected amino acid (Asp277) is conserved in both the KHC
subfamily and in the superfamily, frequently being substituted by a
glutamic acid. It lies at the boundary of
4 and L12, which is also
thought to be important for the microtubule-KHC interaction (31).
Khc23 is a moderate allele and the affected
residue (Glu164) is identical in the KHC subfamily as well
as conserved in the superfamily. It is located at the boundary of
5a
and L8 (
5a/L8b), which might participate in microtubule binding and
in interactions between dimerized KHC motor domains (24, 31).
Khc17 is another moderate allele and the
affected residue (Ser246) is identical in the KHC subfamily
except for the divergent KHC of Neurospora crassa which has
a reasonably conserved substitution. It is located in L11 which might
link changes in the structures of the ATP and the microtubule-binding
sites (49, 50).

View larger version (65K):
[in this window]
[in a new window]
|
Fig. 4.
Amino acid conservation and location of motor
domain mutations selected for mechanochemical characterization.
A, the amino acid changes caused by the four
Drosophila motor domain alleles selected for mechanochemical
characterization are placed above partial sequence alignments of
Drosophila (Dm), human (Hs), and rat
(Rn) KHCs, which are all members of the KHC subfamily, and
Drosophila NCD, which is a member of the COOH-terminal motor
subfamily (27, 58-61). The corresponding amino acid numbers for the
different motor proteins are included to facilitate location of the
affected amino acids in published motor domain crystal structures.
B, location of the affected amino acids in a crystal
structure model of the rat brain KHC motor domain (27). This model was
rotated to display the locations of four wild-type amino acids that are
changed in the motor domain alleles and the positions of their side
chains. The helices and loops thought to be most directly involved in
microtubule binding are on the left, and the
nucleotide-binding pocket is at the rear near the
top. The ADP in the active site is shaded yellow.
The side chains of the wild-type residues altered in the motor domain
mutations are green except for Khc17.
The location of the residue affected by the
Khc17 mutation cannot be shown accurately
because loop 11 has not been resolved in KHC crystal structures. In the
linear sequence of loop 11, the affected amino acid is 3 residues from
the switch II region and 17 residues from the beginning of 4.
|
|
Microtubule Motility with Mutant KHC Proteins--
To test the
functional integrity of the four selected mutant KHCs in
vitro, we first assayed their abilities to generate
microtubule-based movement. Biotinylated, dimerized KHC motor domains
(designated K401-BIO) were expressed in E. coli (39). To
enrich for active motors, bacterial cytosol was subjected to a cycle of
binding to microtubules in the presence of Mg/AMP-PNP and release with MgATP. The Western blot in Fig. 5 shows
that this approach produced soluble KHC motor domains of the expected
size. Each of the four mutant proteins was tested in parallel with
wild-type K401-BIO at saturating MgATP concentrations (2.5 mM) in a microtubule-gliding assay developed by Berlinear
et al. (39). All 5 types of K401-BIO motors could move
microtubules. However, many microtubules were stationary and those that
moved halted intermittently, even in the wild-type assays. This
suggests that a significant fraction of the motors affixed to the
coverslip were either inactive or in suboptimal orientations for full
activity. Microtubule gliding velocities were measured from the
fraction of microtubules that were motile during periods of smooth
gliding (Table II). While the possibility
of unperceived interruptions and variable drag forces hindered
interpretation of the relative velocities, the fact that the mutant
motors could indeed generate gliding movements indicated that each
retained some mechanochemical capability.

View larger version (10K):
[in this window]
[in a new window]
|
Fig. 5.
The K401-BIO proteins used for motility
assays. Various KHC motor domains fused to a portion of an
E. coli protein that is post-translationally biotinylated
were purified by sedimentation with and release from microtubules using
Mg/AMP-PNP and MgATP, respectively. Equal volumes of the ATP release
supernatant of K401-BIO wild-type (WT), 4, 17, 23, and 37 were run on a 7.5% SDS-polyacrylamide gel
and blotted to nitrocellulose. The blot shown was probed with a
monoclonal anti-Drosophila KHC antibody (FLYK2) (36). The
variability in the amount of KHC in each lane may be due to the effects
of the mutations on microtubule-motor binding. The rates of microtubule
gliding generated by these K401-BIO protein preparations are reported
in Table II.
|
|
Steady-state Kinetic Analysis of Mutant KHC Proteins--
To gain
more critical insights into the effects of the selected motor domain
mutations on the KHC mechanochemical cycle, steady-state ATP turnover
was analyzed. For those studies, we re-engineered motor domains
containing only the NH2-terminal 401 amino acids of KHC
(K401) without the biotin motility anchor. The new construct allowed
purification of milligram amounts of highly active motor domains and
facilitated comparison of our results to extensive previous kinetic
studies of the same molecule (6, 7, 12, 40, 51). Fractions from the
various steps in our purification of K401 and the final purification
products of each mutant K401 are shown in Fig.
6. In each case, the motor domains were
highly purified and
90% of the motor domains were active based on
active site titration. All K401 concentrations and thus the derived
kinetic parameters were calculated based on the concentration of active motors.

View larger version (64K):
[in this window]
[in a new window]
|
Fig. 6.
Expression and purification of K401 proteins
for kinetic analysis. The left panel shows a Coomassie
Blue R-250 stained 8% acrylamide, 2 M urea gel of various
fractions collected during the purification of the K401 proteins that
were used for ATPase assays. The lanes contain from left to
right: molecular weight standards, preinduced cell lysate,
induced cell lysate, low speed supernatant of induced lysate
(LS-S), low speed pellet (LS-P), high speed
supernatant (HS-S), S-Sepharose column eluant, and
DEAE-Sephacel column eluant. The right panel shows a
Coomassie-stained gel of the concentrated, purified protein
preparations that were used in ATPase assays. The lanes contain from
left to right: wild-type K401 and the mutant
proteins K401-4, K401-17, K401-23, and K401-37. The lanes were loaded
with equal volumes from equivalent preparations.
|
|
Two series of steady-state ATPase assays were performed on the purified
K401 proteins. Because KHC is a microtubule-activated ATPase (52), we
first measured the rate of ATP hydrolysis as a function of microtubule
concentration in the presence of saturating levels of MgATP (2 mM MgATP; Fig.
7A). In the second set of
experiments, we measured the rate of ATP hydrolysis as a function of
MgATP concentration in the presence of saturating levels of
microtubules (18 µM tubulin; Fig. 7B). The
mutant kinesins all exhibited Michaelis-Menton kinetics, and the
steady-state kinetic parameters were determined: kcat, Km,ATP,
K0.5,MT,
kcat/Km,ATP, and
kcat/K0.5,MT (Table
III).

View larger version (37K):
[in this window]
[in a new window]
|
Fig. 7.
Steady-state ATPase activity of wild-type and
mutant K401 motors. A, the rate of
[ -32P]ATP hydrolysis was determined for MT·K401
complexes (0.5 µM K401) in the presence of saturating
MgATP (2 mM) as a function of taxol-stabilized microtubule
concentration (0.25-20 µM tubulin). The data were fit to
the quadratic equation as described under "Experimental
Procedures." B, the rate of hydrolysis was determined in
the presence of saturating microtubules (20 µM tubulin)
as a function of MgATP concentration (0.01-2 mM). Each
line is the fit of the data to a hyperbola with the kinetic parameters
for wild-type and mutant kinesins reported in Table III. , K401-WT;
, K401-17; , K401-4; , K401-37; , K401-23.
|
|
View this table:
[in this window]
[in a new window]
|
Table III
Steady state ATPase analysis of Khc mutants
Listed are the mean and S.E. for each of the steady-state parameters,
derived from at least three independent assays.
kcat, Km, and
K0.5,MT values were derived from the best fit of the
data to hyperbolae (shown in Fig. 6).
|
|
The mutation that caused the mildest phenotype in vivo,
Khc37, caused only slight changes in K401
kinetics while the mutations that caused moderate or severe phenotypes
in vivo caused more substantial changes in kinetics. Tests
of K401-37 revealed a kcat of 15 s
1, suggesting that the ATPase cycle is somewhat slower
than wild-type (20 s
1). The
Km,ATP (~60 µM) was
lower than wild-type (96 µM), suggesting somewhat tighter
binding of ATP. The K0.5,MT at 0.7 µM was equivalent to wild-type (0.8 µM),
suggesting normal interactions with microtubules. The
kcat/K0.5,MT at 22 µM
1 s
1 (wild-type = 25 µM
1 s
1) supports this
interpretation. The amino acid substitution in K401-37 (D277N) occurs
at the junction of
4/L12 which we expect to be important in the
mechanochemical cycle. Further insight into the role of
Asp277 will require tests of other amino acid substitutions.
Tests of K401-4, the most severe allele in vivo, revealed
that the Km,ATP was increased 3-fold to
~240 µM while the kcat remained
near wild-type at 17 s
1. These data and the calculated
3-fold decrease in catalytic efficiency (kcat/Km,ATP,
Table III) suggest that the T291M mutation causes a significant
weakening of ATP binding. The T291M mutation also caused an increase in
K0.5,MT from 0.8 to 3.2 µM as well
as a 5-fold decrease in the
kcat/K0.5,MT from 25 µM
1 s
1 to 5.3 µM
1 s
1 (Table III). Both
steady-state parameters are indicative of an altered microtubule-motor
interaction. When free in solution, KHC has ADP bound tightly in the
catalytic pocket (13). Proper interaction with a microtubule causes
release of the ADP which allows ATP access to the binding site (Fig.
1). Therefore, the weakened ATP binding of K401-4 could be a secondary
effect of the altered microtubule-motor interaction. To determine if
the mutation has a primary effect on ATP binding, we measured rates of
steady-state ATP hydrolysis in the absence of microtubules. This
"basal ATPase" rate for K401-4 (0.14 ± 0.005 s
1) was 14-fold greater than for wild-type (0.01 ± 0.002 s
1), suggesting that the T291M mutation does have
an effect on the structure and function of the ATP-binding pocket that
is independent of defects caused by aberrant microtubule binding.
Thr291 is located in
5, which is connected to
4 by
L12, on the microtubule-binding face of the motor domain. Previous work suggests that
5 and L12 are involved directly in microtubule binding
(22, 24, 26, 27, 31, 48). Furthermore, the adjacent
4 via L11 is
thought to be important in transmitting structural changes between the
microtubule and ATP-binding sites, changes that link the ATPase and
microtubule binding cycles (49, 50, 53). In current crystal structure
models of KHC, the side chain of Thr291 extends roughly
parallel to the motor domain surface from
5 toward
4 (Fig.
4B). Substitution by the methionine side chain, which is
longer, more hydrophobic, and lacks hydrogen bonding capacity, probably
shifts the orientations of
5,
4, and L12. Such a structural shift
could raise the basal ATPase rate by partially mimicking a
conformational change that is normally induced by microtubule binding;
a change that facilitates ADP-ATP exchange.
The results of the steady-state analysis of K401-17 indicate a
significantly slowed ATPase cycle with a decrease in
kcat from 20 s
1 to 6 s
1. The K0.5,MT was 1.6 µM, a 2-fold increase but still a fairly tight
microtubule-motor interaction. It is unlikely that weakened microtubule
binding is responsible for the slow ATP turnover because even high
concentrations of microtubules (>15 µM tubulin) did not
increase the turnover rate (Fig. 7A). Furthermore, it is
unlikely that defective ATP binding is responsible for the slow
turnover because neither the Km,ATP nor
the basal ATPase rate (0.01 ± 0.003 s
1) differed
significantly from wild-type. The S246F amino acid change occurs in L11
which connects
4 on the microtubule-binding surface to the switch II
region of the ATP pocket. As mentioned above, it is thought that
L11/
4 could link conformational changes at the microtubule-binding
interface to conformational changes in the catalytic pocket that are
required for efficient turnover. The S246F substitution in K401-17
could slow the ATPase cycle by distorting that linkage.
K401-23 also has significantly slowed ATP turnover as shown by the
2-fold reduction in kcat to 10 s
1.
The K0.5, MT at 0.7 µM was similar to wild-type (0.8 µM), suggesting that microtubule-motor
binding is normal, while the Km,ATP was
reduced 3-fold to ~30 µM, indicating that motor-ATP
binding is abnormally strong. We expect that a change in the nucleotide
pocket that tightens ATP binding also slows product release which in
turn slows ATP turnover, a model consistent with product release
limiting the ATPase cycle (13, 54, 55). This interpretation of the data
suggests a change in the structure of the ATP-binding site, but the
mutation in K401-23 (E164K) occurs at the
5a/L8b junction, which is
remote from the ATP-binding site (Fig. 4B). Current crystal
structures and protease sensitivity studies agree that the 164 position
is solvent-exposed throughout the mechanochemical cycle (24, 26, 27,
56). Thus, it is reasonable to propose that the negatively charged
Glu164 is involved in an electrostatic interaction on the
surface of the motor domain that has long-range effects on the
structure of the nucleotide-binding site.
 |
DISCUSSION |
To probe the mechanochemical mechanisms employed by kinesin we
used random mutagenesis of Drosophila and DNA sequencing to identify amino acid changes in KHC that impair motor domain function in vivo. Of the 40 recessive lethal mutations studied, 10 have missense amino acid changes in the motor domain. Four of those were selected for further characterization. The 4 mutations range from
a severe allele that causes a near complete loss of function to a mild
allele that causes only a partial loss of function, as assessed,
comparison of the lethal phenotypes that they cause with those caused
by a null allele. After expression and purification of the motor
domains fused to a biotin motility anchor, microtubule gliding assays
showed that the mutant motors retained some mechanochemical functions.
However, the relative rates of gliding did not agree well with the
relative severities of the in vivo phenotypes. We suspect
that gliding rates are extremely sensitive to the presence of inactive
motors that may interfere with microtubule gliding as well as the
orientation of the active motors on the slide. Because of the combined
effects of these two phenomena, the rates measured may not reflect
accurately the mechanochemistry of the active majority. Using a
different motor domain construct without the biotin anchor and
optimized for purification of active proteins, steady-state kinetic
analysis of the mutant proteins revealed defects whose relative
severities generally correlated with the relative severities of the
in vivo phenotypes. These results suggest that the changes
in steady-state kinetics of ATP turnover that we measured in
vitro are physiologically relevant.
To interpret the kinetic effects of the mutations, we considered the
evolutionary conservation of the amino acids that were changed and
their positions in the atomic structure of a motor domain dimer. The
allele that was mildest in vivo,
Khc37, has an aspartic acid to asparagine change
at the junction of
4 and L12. Asparagine is less polar than aspartic
acid but their side chains are very similar in size. The steady-state
kinetic analysis showed relatively mild effects, however, a change of the corresponding human KHC residue to alanine (nonpolar and small) caused a 2-fold reduction in K0.5, MT (31).
Combined, these results indicate that both the polarity and the size of
this residue are important for correct microtubule-KHC interaction.
Furthermore, since Khc37 clearly causes axonal
transport defects (not shown) and semilethality, our results suggest
that even slight changes in kinetics can have significant consequences
in vivo.
The next mildest allele, Khc17, changes a serine
to a phenylalanine in L11. Because L11 has not been resolved by
crystallography, the position and orientation of the serine side chain
is difficult to predict. However, one can assume that the change
disrupts any interactions that the serine normally has because the
phenylalanine side chain is dramatically larger and more hydrophobic.
The S246F mutation causes a substantial decrease in
kcat (5.9 versus 20 s
1
for wild-type),
kcat/Km,ATP
(0.065 versus 0.2 µM
1
s
1), and
kcat/K0.5,MT (3.6 versus 25 µM
1 s
1),
yet both the Km,ATP and
K0.5,MT are close to wild-type. These results
suggest that Khc17 binds ATP and the microtubule
lattice relatively normally, yet a key step important for ATP turnover
is defective. This interpretation is consistent with the hypothesis
that L11 acts as a structural link to couple microtubule binding to
activation of the hydrolytic cycle (25, 53).
The most severe motor domain allele, Khc4,
changes a threonine in
5 to a methionine (T291M). The methionine
side chain is larger than that of threonine and more hydrophobic.
Furthermore, the threonine side chain should form a hydrogen bond,
perhaps with an amino acid in
4, and the methionine side chain would not hydrogen bond. Thus, the T291M mutation probably changes the orientations of
5,
4, and L12, which in turn cause shifts in other structural elements. The kinetic changes caused by the mutation suggest that the structures of both the ATP-binding pocket and the
microtubule-binding site are altered to mimic a partially activated
site. Consistent with this interpretation is the observation that there
is a substantial increase in the rate of steady-state ATP turnover in
the absence of microtubules. Our results and the fact that
Thr291 is invariant in the kinesin superfamily suggest that
it has a key role in the transmission of structural changes between the microtubule- and ATP-binding sites.
The Khc23 allele, less severe than
Khc4 and more severe than
Khc17, changes a negatively charged glutamic
acid to a positively charged lysine (E164K) at the
5a/L8b junction.
The glutamic acid side chain is solvent exposed and remote from the
ATP-binding pocket, yet the change to lysine causes tighter ATP binding
and a 2-fold reduction in ATP turnover rate. A change of the
corresponding glutamic acid in human KHC to an uncharged alanine also
causes a 2-fold reduction in ATP turnover rate (31). Thus, it may be the loss of the negative charge in Khc23 rather
than the gain of the positive charge that causes the slow ATP turnover.
Combined, these observations suggest that Glu164 normally
participates in an ionic interaction that influences the structure of
the nucleotide-binding pocket during the ATPase cycle.
Our examination of KHC crystal structures revealed a possible mechanism
for the influence of Glu164 on nucleotide binding. The
elongated, negative Glu164 side chain extends away from
5a/L8b and the dimer interface toward the center of the
microtubule-binding surface. It comes into close proximity with the
elongated, positive side chain of Arg292, which projects
from helix
5 toward
5a/L8b (Fig.
8). Given their proximity and opposite
charges, Glu164 and Arg292 could interact to
form an ionic link between
5 and
5a/L8b. It is worth noting that
in human KHC, replacement of the Arg292 equivalent by an
uncharged alanine (R284A) (31) like our E164K change, causes a 2-fold
reduction in ATP-turnover rate. It is also noteworthy that this
Glu164/Arg292 amino acid pair is highly
conserved in the KHC and several other NH2-terminal kinesin
subfamilies, but is very divergent in the COOH-terminal kinesin
subfamily. We propose that a Glu164-Arg292
ionic bridge coordinates the positions of L8 and
5, and that the
effect of the E164K mutation on ATP binding is due to a misorientation of
5, that as discussed above for T291M, can influence the structure of the nucleotide-binding pocket.

View larger version (62K):
[in this window]
[in a new window]
|
Fig. 8.
Two ionic interactions that may influence
dimeric kinesin structure and function. Shown is part of the
crystal structure model of dimeric rat brain KHC (24). One subunit is
on the left (A) and one is on the
right (B). They are joined by their 7 helices,
which project vertically. A potential ionic contact described by
Kozielski et al. (24) is shown between the
Lys160 side chain (orange) in L8b of subunit A
and the Glu219 side chain (yellow) in L10 of
subunit B. The side chains of Glu164 (green) and
Arg292 (magenta) are highlighted to point out
their proximity and their probable ionic interaction which we propose
as an important link between L8 and 5. Thr291
(green), the amino acid mutated in
Khc4, is also shown to illustrate that changes
in the Glu164-Arg292 link could shift the
positions of a side chain known to influence both nucleotide binding
and microtubule binding.
|
|