LTX 109 is a synthetic antimicrobial peptidomimetic (SAMP) currently in clinical phase II trials for topical treatment of infections multiresistant bacterial strains. All possible eight stereoisomers the have been synthesized and tested effect, hemolysis, hydrophobicity, revealing strong unusual dependence on stereochemistry molecule proposed to act general membrane mechanism. The three-dimensional structures were assessed using nuclear magnetic resonance spectroscopy (NMR) molecular...

The role played by entropy for the enormous rate enhancement achieved enzymes has been debated many decades. There are, example, several confirmed cases where activation free energy is reduced around 10 kcal/mol due to entropic effects, corresponding a of ∼107 compared uncatalyzed reaction. However, despite substantial efforts from both experimental and theoretical side, no real consensus reached regarding origin such large contributions enzyme catalysis. Another remarkable instance effects...

Abstract Background Many biologically active compounds bind to plasma transport proteins, and this binding can be either advantageous or disadvantageous from a drug design perspective. Human serum albumin (HSA) is one of the most important proteins in cardiovascular system due its great capacity high physiological concentration. HSA has preference for accommodating neutral lipophilic acidic drug-like ligands, but also surprisingly able positively charged peptides. Understanding how short...

Significance Faced with an exponential decrease in chemical reaction rates as the temperature is lowered, cold-adapted organisms require specialized enzymes to maintain a functional metabolism. Such catalyze their reactions lower activation enthalpies counterbalanced by more negative entropies, yielding higher at low temperatures compared mesophilic enzymes, although room are often similar. The structural mechanisms behind this universal property still remain largely unknown. We attack...

Abstract A systematic study of the linear interaction energy (LIE) method and possible dependence its parameterization on force field system (receptor binding site) is reported. We have calculated free for nine different ligands in complex with P450cam using three fields (Amber95, Gromos87, OPLS‐AA). The results from these LIE calculations our earlier give relative energies that agree remarkably well experimental data. However, absolute are too positive all fields, it clear an additional...

The inherent instability of peptides toward metabolic degradation is an obstacle on the way bringing potential peptide drugs onto market. Truncation can be one to increase proteolytic stability peptides, and in present study susceptibility against trypsin, which major enzymes gastrointestinal tract, was investigated for several short diverse libraries promising cationic antimicrobial tripeptides. Quite surprisingly, trypsin able cleave very small at a substantial rate. Isothermal titration...

The interactions between a range of small cationic antibacterial tripeptides and bovine human serum albumin in buffered aqueous solution at 25 °C have been studied using isothermal titration calorimetry. Results from the binding study indicate single site on with dissociation constant 4.3 22.2 μM for different peptides. In theoretical mouse model, this corresponds to 95% binding. effect interaction capacity peptides against Staphylococcus aureus, strain ATCC 25923 was by including assays...

A major issue for organisms living at extreme temperatures is to preserve both stability and activity of their enzymes. Cold-adapted enzymes generally have a reduced thermal stability, counteract freezing, show lower enthalpy more negative entropy activation compared mesophilic thermophilic homologues. Such balance thermodynamic parameters can make the reaction rate decrease linearly, rather than exponentially, as temperature lowered, but structural basis optimization toward low working...

Life has effectively colonized most of our planet and extremophilic organisms require specialized enzymes to survive under harsh conditions. Cold-loving (psychrophiles) express heat-labile that possess a high specific activity catalytic efficiency at low temperatures. A remarkable universal characteristic cold-active is they show reduction both in activation enthalpy entropy, compared mesophilic orthologs, which makes their reaction rates less sensitive falling temperature. Despite...

Periplasmic chaperone/usher machineries are used for assembly of filamentous adhesion organelles Gram-negative pathogens in a process that has been suggested to be driven by folding energy. Structures mutant chaperone–subunit complexes revealed final transition (condensation the subunit hydrophobic core) on release organelle from pre-assembly complex and incorporation into fibre structure. However, view large interface between chaperone reported stability this complex, it is difficult...

ABSTRACT Metallo-β-lactamase (MBL) genes confer resistance to virtually all β-lactam antibiotics and are rapidly disseminated by mobile genetic elements in Gram-negative bacteria. MBLs belong three different subgroups, B1, B2, B3, with the largely confined subgroup B1. The B3 a divergent of predominantly chromosomally encoded enzymes. AIM-1 ( A delaide IM ipenmase 1) from Pseudomonas aeruginosa was first MBL be identified on readily element. Here we present crystal structure use silico...

Abstract The variation in inhibitor specificity for five different amine inhibitors bound to CST, BT, and the cold‐adapted AST has been studied by use of association constant measurements, structural analysis high‐resolution crystal structures, LIE method. Experimental data show that binds 1BZA 2BEA 0.8 0.5 kcal/mole more strongly than BT. However, interactions orientations within S1 site have found be virtually identical three enzymes studied. For example, four water molecules...

Uracil DNA glycosylase (UDG) is a repair enzyme in the base excision pathway and removes uracil from strand. Atlantic cod UDG (cUDG), which cold-adapted enzyme, has been found to be up 10 times more catalytically active temperature range 15-37 degrees C as compared with warm-active human counterpart. The increased catalytic activity of enzymes their mesophilic homologues are partly believed caused by an increase structural flexibility. However, no direct experimental evidence supports...

A theoretical study of the one-photon absorption five fluorescent proteins (FPs) is presented. The properties are calculated using a polarizable embedding approach combined with density functional theory (PE-DFT) on wild-type green protein (wtGFP) and several its mutants (BFP, eGFP, YFP eCFP). observed trends in excitation energies among FPs reproduced by our when performing calculations directly crystal structures or extracted from molecular dynamics simulations. However, former case, QM/MM...

DYRK1A has emerged as a potential target for therapies of Alzheimer’s disease using small molecules. On the basis observation selective inhibition by firefly d-luciferin, we have explored static and dynamic structural properties fragment sized variants benzothiazole scaffold with respect to X-ray crystallography NMR techniques. The compounds excellent ligand efficiencies show remarkable diversity binding modes in equilibrium. Binding geometries are determined part interactions often...

Predicting the effect of single-point mutations on protein stability or protein-ligand binding is a major challenge in computational biology. Free energy calculations constitute most rigorous approach to this problem, though estimation converged values for amino acid remains challenging. To overcome limitation, we developed tailored protocols calculate free shifts associated with mutations. We herein describe QresFEP protocol, which includes an extension our recent cover all acids mutations,...

Cold-adapted enzymes are characterized both by a higher catalytic activity at low temperatures and having their temperature optimum down-shifted, compared to mesophilic orthologs. In several cases, the does not coincide with onset of protein melting but reflects some other type inactivation. psychrophilic α-amylase from an Antarctic bacterium, inactivation is thought originate specific enzyme-substrate interaction that breaks around room temperature. Here, we report computational redesign...

The incorporation of nongenetically encoded amino acids is a well established strategy to alter the behavior several types promising cationic antimicrobial peptides. Generally, these elements have been improved mimics hydrophobic yielding peptides with increased stability and potency. In this initial study, effect systematic replacement Arg in well-defined moderately tripeptide library described. It shown that arginine analogues need display strong basicity produce active further revealed...

This work describes how the systematic incorporation of a range unnatural amino acid derivatives in P1, P1′, and P2′ positions allows for generation short lactoferricin based cationic antimicrobial peptides with stability toward chymotryptic degradation. The necessary pharmacophore sets up degradation by chymotrypsin, heavily truncated native tripeptide was rapidly digested despite its sequence. Degradation studies indicated that increased half-lives could be obtained altering binding to...