Investigation of Ionization Pattern of the Adjacent Acidic Residues in the DXDXE Motif of GH-18 Chitinases Using Theoretical pKa Calculations

2017 ◽  
Vol 57 (3) ◽  
pp. 572-583 ◽  
Author(s):  
Piyanat Meekrathok ◽  
Predrag Kukic ◽  
Jens Erik Nielsen ◽  
Wipa Suginta
Keyword(s):  
Pka Calculations ◽  
Acidic Residues

scholarly journals The Role of Acidic Residues in the C Terminal Tail of the LHCSR3 Protein of Chlamydomonas reinhardtii in Non-Photochemical Quenching

2021 ◽  
pp. 6895-6900
Author(s):  
Franco V. A. Camargo ◽  
Federico Perozeni ◽  
Gabriel de la Cruz Valbuena ◽  
Luca Zuliani ◽  
Samim Sardar ◽  
...  
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Photochemical Quenching ◽  
Acidic Residues ◽  
Non Photochemical Quenching

scholarly journals The C2A-C2B Linker Defines the High Affinity Ca2+ Binding Mode of Rabphilin-3A

2006 ◽  
Vol 282 (7) ◽  
pp. 5015-5025 ◽  
Author(s):  
Pierre Montaville ◽  
Christine Schlicker ◽  
Andrei Leonov ◽  
Markus Zweckstetter ◽  
George M. Sheldrick ◽  
...  
Keyword(s):  
Binding Mode ◽  
Bound State ◽  
C2 Domain ◽  
Binding Assays ◽  
Host Proteins ◽  
Binding Properties ◽  
C2 Domains ◽  
Phospholipid Binding ◽  
Acidic Residues ◽  
Structural Base

The Ca2+ binding properties of C2 domains are essential for the function of their host proteins. We present here the first crystal structures showing an unexpected Ca2+ binding mode of the C2B domain of rabphilin-3A in atomic detail. Acidic residues from the linker region between the C2A and C2B domains of rabphilin-3A interact with the Ca2+-binding region of the C2B domain. Because of these interactions, the coordination sphere of the two bound Ca2+ ions is almost complete. Mutation of these acidic residues to alanine resulted in a 10-fold decrease in the intrinsic Ca2+ binding affinity of the C2B domain. Using NMR spectroscopy, we show that this interaction occurred only in the Ca2+-bound state of the C2B domain. In addition, this Ca2+ binding mode was maintained in the C2 domain tandem fragment. In NMR-based liposome binding assays, the linker was not released upon phospholipid binding. Therefore, this unprecedented Ca2+ binding mode not only shows how a C2 domain increases its intrinsic Ca2+ affinity, but also provides the structural base for an atypical protein-Ca2+-phospholipid binding mode of rabphilin-3A.

Chemical Modification of the Bovine Mitochondrialbc1Complex Reveals Critical Acidic Residues Involved in the Proton Pumping Activity†

Biochemistry ◽  
1998 ◽  
Vol 37 (7) ◽  
pp. 2037-2043 ◽  
Author(s):  
Tiziana Cocco ◽  
Marco Di Paola ◽  
Sergio Papa ◽  
Michele Lorusso
Keyword(s):  
Chemical Modification ◽  
Proton Pumping ◽  
Acidic Residues ◽  
Pumping Activity

scholarly journals pKa calculations for class A beta-lactamases: methodological and mechanistic implications

1997 ◽  
Vol 73 (5) ◽  
pp. 2416-2426 ◽  
Author(s):  
X. Raquet ◽  
V. Lounnas ◽  
J. Lamotte-Brasseur ◽  
J.M. Frère ◽  
R.C. Wade
Keyword(s):  
Beta Lactamases ◽  
Class A ◽  
Pka Calculations

scholarly journals Mapping the BKCa Channel's “Ca2+ Bowl”

2004 ◽  
Vol 123 (5) ◽  
pp. 475-489 ◽  
Author(s):  
Lin Bao ◽  
Christina Kaldany ◽  
Ericka C. Holmstrand ◽  
Daniel H. Cox
Keyword(s):  
Fusion Protein ◽  
Binding Site ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Membrane Domain ◽  
Intracellular Domain ◽  
High Affinity ◽  
Acidic Residues ◽  
The Relationship

There is controversy over whether Ca2+ binds to the BKCa channel's intracellular domain or its integral-membrane domain and over whether or not mutations that reduce the channel's Ca2+ sensitivity act at the point of Ca2+ coordination. One region in the intracellular domain that has been implicated in Ca2+ sensing is the “Ca2+ bowl”. This region contains many acidic residues, and large Ca2+-bowl mutations eliminate Ca2+ sensing through what appears to be one type of high-affinity Ca2+-binding site. Here, through site-directed mutagenesis we have mapped the residues in the Ca2+ bowl that are most important for Ca2+ sensing. We find acidic residues, D898 and D900, to be essential, and we find them essential as well for Ca2+ binding to a fusion protein that contains a portion of the BKCa channel's intracellular domain. Thus, much of our data supports the conclusion that Ca2+ binds to the BKCa channel's intracellular domain, and they define the Ca2+ bowl's essential Ca2+-sensing motif. Overall, however, we have found that the relationship between mutations that disrupt Ca2+ sensing and those that disrupt Ca2+ binding is not as strong as we had expected, a result that raises the possibility that, when examined by gel-overlay, the Ca2+ bowl may be in a nonnative conformation.

scholarly journals Effects of Amino Acid Substitutions at Conserved and Acidic Residues within Region 1.1 of Escherichia coli ς70

2000 ◽  
Vol 182 (1) ◽  
pp. 221-224 ◽  
Author(s):  
Christina Wilson Bowers ◽  
Andrea McCracken ◽  
Alicia J. Dombroski
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Aspartic Acid ◽  
Transcription Initiation ◽  
Amino Acid Substitutions ◽  
Conserved Residues ◽  
Acidic Residues

ABSTRACT Amino acid substitutions in Escherichia coliς70 were generated and characterized in an analysis of the role of region 1.1 in transcription initiation. Several acidic and conserved residues are tolerant of substitution. However, replacement of aspartic acid 61 with alanine results in inactivity caused by structural and functional thermolability.

Ionization Behavior of Acidic Residues in Calbindin D9k

1999 ◽  
Vol 37 (1) ◽  
pp. 106-115 ◽  
Author(s):  
T�nu Kesvatera ◽  
Bo J�nsson ◽  
Eva Thulin ◽  
Sara Linse
Keyword(s):  
Calbindin D9k ◽  
Acidic Residues ◽  
Ionization Behavior
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