Amino Acid Substitution within the S2 and S4 Transmembrane Segments in Shaker Potassium Channel Modulates Channel Gating

2000 ◽  
Vol 275 (3) ◽  
pp. 720-724 ◽  
Author(s):  
Myeong Hyeon Wang ◽  
Uhtaek Oh ◽  
Hae Ik Rhee
Keyword(s):  
Amino Acid ◽  
Potassium Channel ◽  
Amino Acid Substitution ◽  
Channel Gating ◽  
Shaker Potassium Channel ◽  
Transmembrane Segments

scholarly journals Uncharged S4 Residues and Cooperativity in Voltage-dependent Potassium Channel Activation

1998 ◽  
Vol 111 (3) ◽  
pp. 421-439 ◽  
Author(s):  
Catherine J. Smith-Maxwell ◽  
Jennifer L. Ledwell ◽  
Richard W. Aldrich
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Potassium Channel ◽  
Voltage Dependence ◽  
Channel Gating ◽  
Ionic Currents ◽  
Channel Activation ◽  
Functional Changes ◽  
Activation Pathway ◽  
Voltage Dependent

Substitution of the S4 of Shaw into Shaker alters cooperativity in channel activation by slowing a cooperative transition late in the activation pathway. To determine the amino acids responsible for the functional changes in Shaw S4, we created several mutants by substituting amino acids from Shaw S4 into Shaker. The S4 amino acid sequences of Shaker and Shaw S4 differ at 11 positions. Simultaneous substitution of just three noncharged residues from Shaw S4 into Shaker (V369I, I372L, S376T; ILT) reproduces the kinetic and voltage-dependent properties of Shaw S4 channel activation. These substitutions cause very small changes in the structural and chemical properties of the amino acid side chains. In contrast, substituting the positively charged basic residues in the S4 of Shaker with neutral or negative residues from the S4 of Shaw S4 does not reproduce the shallow voltage dependence or other properties of Shaw S4 opening. Macroscopic ionic currents for ILT could be fit by modifying a single set of transitions in a model for Shaker channel gating (Zagotta, W.N., T. Hoshi, and R.W. Aldrich. 1994. J. Gen. Physiol. 103:321–362). Changing the rate and voltage dependence of a final cooperative step in activation successfully reproduces the kinetic, steady state, and voltage-dependent properties of ILT ionic currents. Consistent with the model, ILT gating currents activate at negative voltages where the channel does not open and, at more positive voltages, they precede the ionic currents, confirming the existence of voltage-dependent transitions between closed states in the activation pathway. Of the three substitutions in ILT, the I372L substitution is primarily responsible for the changes in cooperativity and voltage dependence. These results suggest that noncharged residues in the S4 play a crucial role in Shaker potassium channel gating and that small steric changes in these residues can lead to large changes in cooperativity within the channel protein.

Use of voltage clamp fluorimetry in understanding potassium channel gating: a review of Shaker fluorescence data

2009 ◽  
Vol 87 (6) ◽  
pp. 411-418 ◽  
Author(s):  
A.J. Horne ◽  
D. Fedida
Keyword(s):  
Potassium Channels ◽  
Potassium Channel ◽  
Voltage Clamp ◽  
Channel Gating ◽  
Specific Protein ◽  
Channel Activation ◽  
Shaker Potassium Channel ◽  
Inactivation Gating ◽  
Nanosecond Time Resolution ◽  
Shaker Potassium Channels

Voltage clamp fluorimetry (VCF) utilizes fluorescent probes that covalently bind to cysteine residues introduced into proteins and emit light as a function of their environment. Measurement of this emitted light during membrane depolarization reveals changes in the emission level as the environment of the labelled residue changes. This allows for the correlation of channel gating events with movement of specific protein moieties, at nanosecond time resolution. Since the pioneering use of this technique to investigate Shaker potassium channel activation movements, VCF has become an invaluable technique used to understand ion channel gating. This review summarizes the theory and some of the data on the application of the VCF technique. Although its usage has expanded beyond voltage-gated potassium channels and VCF is now used in a number of other voltage- and ligand-gated channels, we will focus on studies conducted in Shaker potassium channels, and what they have told us about channel activation and inactivation gating.

scholarly journals An Amino Acid Substitution in the Pore Region of a Glutamate-gated Chloride Channel Enables the Coupling of Ligand Binding to Channel Gating

1996 ◽  
Vol 271 (27) ◽  
pp. 16035-16039 ◽  
Author(s):  
Adrian Etter ◽  
Doris F. Cully ◽  
James M. Schaeffer ◽  
Ken K. Liu ◽  
Joseph P. Arena
Keyword(s):  
Amino Acid ◽  
Ligand Binding ◽  
Amino Acid Substitution ◽  
Chloride Channel ◽  
Channel Gating ◽  
Pore Region

An Amino-Acid Substitution in the Influenza-B NB Protein Affects Ion-Channel Gating

2004 ◽  
Vol 197 (3) ◽  
pp. 135-143 ◽  
Author(s):  
A. Premkumar ◽  
G. D. Ewart ◽  
G. B. Cox ◽  
P. W. Gage
Keyword(s):  
Amino Acid ◽  
Ion Channel ◽  
Amino Acid Substitution ◽  
Channel Gating ◽  
Influenza B ◽  
Ion Channel Gating

scholarly journals Evidence for Intersubunit Interactions between S4 and S5 Transmembrane Segments of the Shaker Potassium Channel

2003 ◽  
Vol 278 (31) ◽  
pp. 29079-29085 ◽  
Author(s):  
E. J. Neale ◽  
D. J. S. Elliott ◽  
M. Hunter ◽  
A. Sivaprasadarao
Keyword(s):  
Potassium Channel ◽  
Shaker Potassium Channel ◽  
Transmembrane Segments ◽  
Intersubunit Interactions

scholarly journals Evidence for Intersubunit Interactions between S4 and S5 Transmembrane Segments of the Shaker Potassium Channel

2003 ◽  
Vol 278 (31) ◽  
pp. 29079-29085 ◽  
Author(s):  
Edward J. Neale ◽  
David J. S. Elliott ◽  
Malcolm Hunter ◽  
Asipu Sivaprasadarao
Keyword(s):  
Potassium Channel ◽  
Shaker Potassium Channel ◽  
Transmembrane Segments ◽  
Intersubunit Interactions

Hubsm: A Novel Amino Acid Substitution Matrix for Comparing Hub Proteins

2017 ◽  
Vol 7 (8) ◽  
pp. 212
Author(s):  
Renganayaki G. ◽  
Achuthsankar S. Nair
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Low Complexity ◽  
Database Search ◽  
Substitution Matrix ◽  
Compositional Bias ◽  
Sequence Alignments ◽  
Amino Acid Substitution Matrix ◽  
Alignment Algorithms ◽  
Hub Proteins

Sequence alignment algorithms and  database search methods use BLOSUM and PAM substitution matrices constructed from general proteins. These de facto matrices are not optimal to align sequences accurately, for the proteins with markedly different compositional bias in the amino acid.   In this work, a new amino acid substitution matrix is calculated for the disorder and low complexity rich region of Hub proteins, based on residue characteristics. Insights into the amino acid background frequencies and the substitution scores obtained from the Hubsm unveils the  residue substitution patterns which differs from commonly used scoring matrices .When comparing the Hub protein sequences for detecting homologs,  the use of this Hubsm matrix yields better results than PAM and BLOSUM matrices. Usage of Hubsm matrix can be optimal in database search and for the construction of more accurate sequence alignments of Hub proteins.

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