Role of Chain Extension in the Ability of Peptide Oligomers to Damage the Lipid Membrane Studied by the l- to d-Amino Acid Substitutions of hIAPP18–27

2020 ◽  
Vol 124 (45) ◽  
pp. 10147-10156
Author(s):  
Feihong Meng ◽  
Tong Lu ◽  
Yajie Wang ◽  
Yanping Zhao ◽  
Zhengqiang Li ◽  
...  
Keyword(s):  
Amino Acid ◽  
Lipid Membrane ◽  
Chain Extension ◽  
Amino Acid Substitutions

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.

scholarly journals Amino acid substitutions in the FXYD motif enhance phospholemman-induced modulation of cardiac L-type calcium channels

2010 ◽  
Vol 299 (5) ◽  
pp. C1203-C1211 ◽  
Author(s):  
Kai Guo ◽  
Xianming Wang ◽  
Guofeng Gao ◽  
Congxin Huang ◽  
Keith S. Elmslie ◽  
...  
Keyword(s):  
Amino Acid ◽  
Calcium Channels ◽  
Molecular Mechanisms ◽  
Channel Gating ◽  
Fine Tuning ◽  
Amino Acid Substitutions ◽  
Dependent Inactivation ◽  
Voltage Dependent ◽  
Kinetics Of

We have found that phospholemman (PLM) associates with and modulates the gating of cardiac L-type calcium channels (Wang et al., Biophys J 98: 1149–1159, 2010). The short 17 amino acid extracellular NH2-terminal domain of PLM contains a highly conserved PFTYD sequence that defines it as a member of the FXYD family of ion transport regulators. Although we have learned a great deal about PLM-dependent changes in calcium channel gating, little is known regarding the molecular mechanisms underlying the observed changes. Therefore, we investigated the role of the PFTYD segment in the modulation of cardiac calcium channels by individually replacing Pro-8, Phe-9, Thr-10, Tyr-11, and Asp-12 with alanine (P8A, F9A, T10A, Y11A, D12A). In addition, Asp-12 was changed to lysine (D12K) and cysteine (D12C). As expected, wild-type PLM significantly slows channel activation and deactivation and enhances voltage-dependent inactivation (VDI). We were surprised to find that amino acid substitutions at Thr-10 and Asp-12 significantly enhanced the ability of PLM to modulate CaV1.2 gating. T10A exhibited a twofold enhancement of PLM-induced slowing of activation, whereas D12K and D12C dramatically enhanced PLM-induced increase of VDI. The PLM-induced slowing of channel closing was abrogated by D12A and D12C, whereas D12K and T10A failed to impact this effect. These studies demonstrate that the PFXYD motif is not necessary for the association of PLM with CaV1.2. Instead, since altering the chemical and/or physical properties of the PFXYD segment alters the relative magnitudes of opposing PLM-induced effects on CaV1.2 channel gating, PLM appears to play an important role in fine tuning the gating kinetics of cardiac calcium channels and likely plays an important role in shaping the cardiac action potential and regulating Ca2+ dynamics in the heart.

Role of Entropic Interactions in Viral Capsids: Single Amino Acid Substitutions in P22 Bacteriophage Coat Protein Resulting in Loss of Capsid Stability

Biochemistry ◽  
1995 ◽  
Vol 34 (4) ◽  
pp. 1120-1126 ◽  
Author(s):  
Debora Foguel ◽  
Carolyn M. Teschke ◽  
Peter E. Jr. Prevelige ◽  
Jerson L. Silva
Keyword(s):  
Amino Acid ◽  
Coat Protein ◽  
Single Amino Acid ◽  
Amino Acid Substitutions ◽  
Viral Capsids ◽  
Capsid Stability

scholarly journals Functional role of positively selected amino acid substitutions in mammalian rhodopsin evolution

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Miguel A. Fernández-Sampedro ◽  
Brandon M. Invergo ◽  
Eva Ramon ◽  
Jaume Bertranpetit ◽  
Pere Garriga
Keyword(s):  
Amino Acid ◽  
Functional Role ◽  
Amino Acid Substitutions

scholarly journals The amino acids that constitute sequence gamma 268-282 of fibrinogen are not involved in fibrin monomer polymerization.

1993 ◽  
Vol 40 (4) ◽  
pp. 515-520
Author(s):  
A Janiak ◽  
T Plucinski ◽  
G Kupryszewski ◽  
C S Cierniewski
Keyword(s):  
Amino Acid ◽  
Conformational Changes ◽  
Single Amino Acid ◽  
Amino Acid Substitutions ◽  
Peptide Fragment ◽  
Specific Antibodies ◽  
Fibrin Monomer ◽  
Fibrin Monomers ◽  
Peptide Region

Congenitally abnormal fibrinogens with impaired fibrin monomer polymerization have been described to contain single amino-acid substitutions localized in certain positions of the gamma 275-330 peptide region. To evaluate the role of the amino-acid sequence in the vicinity of Arg275 in fibrin monomer polymerization, the peptide fragment corresponding to gamma 268-282 was synthesized and used to obtain peptide-specific antibodies. These antibodies, when purified immunochemically on the immobilized peptide, bound to the intact fibrinogen and fibrin monomers with the same binding affinity. However, they did not recognize the gamma 268-282 epitopes on the denatured and reduced fibrinogen molecules. The lack of influence of antipeptide antibodies on fibrin monomer polymerization indicates that the gamma 268-282 peptide is not directly involved in the structure of the polymerization site in the D domain of fibrinogen. It is suggested that substitution of Arg275 either by His or Cys in abnormal fibrinogens results probably in conformational changes which disturb a proper orientation of the polymerization site and reduce its expression.

scholarly journals Exploring the Role of the Ω-Loop in the Evolution of Ceftazidime Resistance in the PenA β-Lactamase from Burkholderia multivorans, an Important Cystic Fibrosis Pathogen

2016 ◽  
Vol 61 (2) ◽  
Author(s):  
Krisztina M. Papp-Wallace ◽  
Scott A. Becka ◽  
Magdalena A. Taracila ◽  
Elise T. Zeiser ◽  
Julian A. Gatta ◽  
...  
Keyword(s):  
Amino Acid ◽  
Burkholderia Cepacia ◽  
Clinical Isolates ◽  
Dynamics Simulation ◽  
Single Amino Acid ◽  
Amino Acid Substitutions ◽  
Biochemical Basis ◽  
Content Type ◽  
Burkholderia Multivorans

ABSTRACT The unwelcome evolution of resistance to the advanced generation cephalosporin antibiotic, ceftazidime is hindering the effective therapy of Burkholderia cepacia complex (BCC) infections. Regrettably, BCC organisms are highly resistant to most antibiotics, including polymyxins; ceftazidime and trimethoprim-sulfamethoxazole are the most effective treatment options. Unfortunately, resistance to ceftazidime is increasing and posing a health threat to populations susceptible to BCC infection. We found that up to 36% of 146 tested BCC clinical isolates were nonsusceptible to ceftazidime (MICs ≥ 8 μg/ml). To date, the biochemical basis for ceftazidime resistance in BCC is largely undefined. In this study, we investigated the role of the Ω-loop in mediating ceftazidime resistance in the PenA β-lactamase from Burkholderia multivorans, a species within the BCC. Single amino acid substitutions were engineered at selected positions (R164, T167, L169, and D179) in the PenA β-lactamase. Cell-based susceptibility testing revealed that 21 of 75 PenA variants engineered in this study were resistant to ceftazidime, with MICs of >8 μg/ml. Under steady-state conditions, each of the selected variants (R164S, T167G, L169A, and D179N) demonstrated a substrate preference for ceftazidime compared to wild-type PenA (32- to 320-fold difference). Notably, the L169A variant hydrolyzed ceftazidime significantly faster than PenA and possessed an ∼65-fold-lower apparent Ki (Ki app) than that of PenA. To understand why these amino acid substitutions result in enhanced ceftazidime binding and/or turnover, we employed molecular dynamics simulation (MDS). The MDS suggested that the L169A variant starts with the most energetically favorable conformation (−28.1 kcal/mol), whereas PenA possessed the most unfavorable initial conformation (136.07 kcal/mol). In addition, we observed that the spatial arrangement of E166, N170, and the hydrolytic water molecules may be critical for enhanced ceftazidime hydrolysis by the L169A variant. Importantly, we found that two clinical isolates of B. multivorans possessed L169 amino acid substitutions (L169F and L169P) in PenA and were highly resistant to ceftazidime (MICs ≥ 512 μg/ml). In conclusion, substitutions in the Ω-loop alter the positioning of the hydrolytic machinery as well as allow for a larger opening of the active site to accommodate the bulky R1 and R2 side chains of ceftazidime, resulting in resistance. This analysis provides insights into the emerging phenotype of ceftazidime-resistant BCC and explains the evolution of amino acid substitutions in the Ω-loop of PenA of this significant clinical pathogen.

scholarly journals Possible changes in fidelity of DNA polymerase δ in ancestral mammals

2020 ◽  
Author(s):  
Kazutaka Katoh ◽  
Naoyuki Iwabe ◽  
Takashi Miyata
Keyword(s):  
Amino Acid ◽  
Dna Polymerase ◽  
Phylogenetic Analyses ◽  
Amino Acid Level ◽  
Amino Acid Substitutions ◽  
Dna Polymerase Δ ◽  
Time Period ◽  
Mammalian Lineage ◽  
Exonuclease Domain

AbstractDNA polymerase δ (polδ) is one of the major DNA polymerases that replicate chromosomal genomes in eukaryotes. Given the essential role of this protein, its phylogenetic tree was expected to reflect the relationship between taxa, like many other essential proteins. However, the tree of the catalytic subunit of polδ showed an unexpectedly strong heterogeneity among vertebrate lineages in evolutionary rate at the amino acid level, suggesting unusual amino acid substitutions specifically in the ancestral mammalian lineage. Structural and phylogenetic analyses were used to pinpoint where and when these amino acid substitutions occurred: around the 3′-5′ exonuclease domain in later mammal ancestry, after the split between monotremes and therians. The 3′-5′ exonuclease domain of this protein is known to have an impact on the fidelity of replication. Based on these observations, we explored the possibility that the amino acid substitutions we identified in polδ affected the mutation rate of entire chromosomal genomes in this time period.

scholarly journals Exploring the Role of L10 Loop in New Delhi Metallo-β-lactamase (NDM-1): Kinetic and Dynamic Studies

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5489
Author(s):  
Alessandra Piccirilli ◽  
Emanuele Criscuolo ◽  
Fabrizia Brisdelli ◽  
Paola Sandra Mercuri ◽  
Sabrina Cherubini ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Amino Acid ◽  
Double Mutant ◽  
Amino Acid Substitutions ◽  
New Delhi ◽  
Kinetic Behavior ◽  
Dynamic Studies ◽  
The Stability

Four NDM-1 mutants (L218T, L221T, L269H and L221T/Y229W) were generated in order to investigate the role of leucines positioned in L10 loop. A detailed kinetic analysis stated that these amino acid substitutions modified the hydrolytic profile of NDM-1 against some β-lactams. Significant reduction of kcat values of L218T and L221T for carbapenems, cefazolin, cefoxitin and cefepime was observed. The stability of the NDM-1 and its mutants was explored by thermofluor assay in real-time PCR. The determination of TmB and TmD demonstrated that NDM-1 and L218T were the most stable enzymes. Molecular dynamic studies were performed to justify the differences observed in the kinetic behavior of the mutants. In particular, L218T fluctuated more than NDM-1 in L10, whereas L221T would seem to cause a drift between residues 75 and 125. L221T/Y229W double mutant exhibited a decrease in the flexibility with respect to L221T, explaining enzyme activity improvement towards some β-lactams. Distances between Zn1-Zn2 and Zn1-OH- or Zn2-OH- remained unaffected in all systems analysed. Significant changes were found between Zn1/Zn2 and first sphere coordination residues.

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