Amino Acid Type (amino + acid_type)

Distribution by Scientific Domains


Selected Abstracts


A model of a gp120 V3 peptide in complex with an HIV-neutralizing antibody based on NMR and mutant cycle-derived constraints

FEBS JOURNAL, Issue 3 2000
Anat Zvi
The 0.5, monoclonal antibody is a very potent strain-specific HIV-neutralizing antibody raised against gp120, the envelope glycoprotein of HIV-1. This antibody recognizes the V3 loop of gp120, which is a major neutralizing determinant of the virus. The antibody,peptide interactions, involving aromatic and negatively charged residues of the antibody 0.5,, were studied by NMR and double-mutant cycles. A deuterated V3 peptide and a Fab containing deuterated aromatic amino acids were used to assign these interactions to specific V3 residues and to the amino acid type and specific chain of the antibody by NOE difference spectroscopy. Electrostatic interactions between negatively charged residues of the antibody Fv and peptide residues were studied by mutagenesis of both antibody and peptide residues and double-mutant cycles. Several interactions could be assigned unambiguously: F96(L) of the antibody interacts with Pro13 of the peptide, H52(H) interacts with Ile7, Ile9 and Gln10 and D56(H) interacts with Arg11. The interactions of the light-chain tyrosines with Pro13 and Gly14 could be assigned to either Y30a(L) and Y32(L), respectively, or Y32(L) and Y49(L), respectively. Three heavy-chain tyrosines interact with Ile7, Ile20 and Phe17. Several combinations of assignments involving Y32(H), Y53(H), Y96(H) and Y100a(H) may satisfy the NMR and mutagenesis constraints, and therefore at this stage the interactions of the heavy-chain tyrosines were not taken into account. The unambiguous assignments [F96(L), H52(H) and D56(H)] and the two possible assignments of the light-chain tyrosines were used to dock the peptide into the antibody-combining site. The peptide converges to a unique position within the binding site, with the RGPG loop pointing into the center of the groove formed by the antibody complementary determining regions while retaining the ,-hairpin conformation and the type-VI RGPG turn [Tugarinov, V., Zvi, A., Levy, R. & Anglister, J. (1999) Nat. Struct. Biol.6, 331,335]. [source]


The mechanism of neutral amino acid decomposition in the gas phase.

INTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 8 2001
N -dimethylglycine, N -dimethylglycine ethyl ester, The elimination kinetics of N, ethyl 1-piperidineacetate
The gas-phase elimination kinetics of the ethyl ester of two ,-amino acid type of molecules have been determined over the temperature range of 360,430°C and pressure range of 26,86 Torr. The reactions, in a static reaction system, are homogeneous and unimolecular and obey a first-order rate law. The rate coefficients are given by the following equations. For N,N-dimethylglycine ethyl ester: log k1(s,1) = (13.01 ± 3.70) , (202.3 ± 0.3)kJ mol,1 (2.303 RT),1 For ethyl 1-piperidineacetate: log k1(s,1) = (12.91 ± 0.31) , (204.4 ± 0.1)kJ mol,1 (2.303 RT),1 The decompositon of these esters leads to the formation of the corresponding ,-amino acid type of compound and ethylene. However, the amino acid intermediate, under the condition of the experiments, undergoes an extremely rapid decarboxylation process. Attempts to pyrolyze pure N,N-dimethylglycine, which is the intermediate of dimethylglycine ethyl ester pyrolysis, was possible at only two temperatures, 300 and 310°C. The products are trimethylamine and CO2. Assuming log A = 13.0 for a five-centered cyclic transition-state type of mechanism in gas-phase reactions, it gives the following expression: log k1(s,1) = (13.0) , (176.6)kJ mol,1 (2.303 RT),1. The mechanism of these ,-amino acids differs from the decarbonylation elimination of 2-substituted halo, hydroxy, alkoxy, phenoxy, and acetoxy carboxylic acids in the gas phase. © 2001 John Wiley & Sons, Inc. Int J Chem Kinet 33:465,471, 2001 [source]


Amino acid interaction preferences in proteins

PROTEIN SCIENCE, Issue 3 2010
Anupam Nath Jha
Abstract Understanding the key factors that influence the interaction preferences of amino acids in the folding of proteins have remained a challenge. Here we present a knowledge-based approach for determining the effective interactions between amino acids based on amino acid type, their secondary structure, and the contact based environment that they find themselves in the native state structure as measured by their number of neighbors. We find that the optimal information is approximately encoded in a 60 × 60 matrix describing the 20 types of amino acids in three distinct secondary structures (helix, beta strand, and loop). We carry out a clustering scheme to understand the similarity between these interactions and to elucidate a nonredundant set. We demonstrate that the inferred energy parameters can be used for assessing the fit of a given sequence into a putative native state structure. [source]


Protocols for the Sequential Solid-State NMR Spectroscopic Assignment of a Uniformly Labeled 25 kDa Protein: HET-s(1-227)

CHEMBIOCHEM, Issue 11 2010
Anne Schuetz
Abstract The sequence-specific resonance assignment of a protein forms the basis for studies of molecular structure and dynamics, as well as to functional assay studies by NMR spectroscopy. Here we present a protocol for the sequential 13C and 15N resonance assignment of uniformly [15N,13C]-labeled proteins, based on a suite of complementary three-dimensional solid-state NMR spectroscopy experiments. It is directed towards the application to proteins with more than about 100 amino acid residues. The assignments rely on a walk along the backbone by using a combination of three experiments that correlate nitrogen and carbon spins, including the well-dispersed C, resonances. Supplementary spectra that correlate further side-chain resonances can be important for identifying the amino acid type, and greatly assist the assignment process. We demonstrate the application of this assignment protocol for a crystalline preparation of the N-terminal globular domain of the HET-s prion, a 227-residue protein. [source]


Peroxidative aggregation of ,-synuclein requires tyrosines

PROTEIN SCIENCE, Issue 11 2004
Alina Olteanu
Abstract ,-Synuclein is the main component of the intracellular protein aggregates in neurons of patients with Parkinson's disease. The occurrence of the disease is associated with oxidative damage. Although it is known that peroxidative chemistry leads to the aggregation of ,-synuclein in vitro, the specific amino acid types of ,-synuclein involved in this type of aggregation have not been identified. We show, using human cytochrome c plus H2O2 as the source oxidative stress, that the tyrosines of ,-synuclein are required for aggregation. The studies reveal the chemical basis for a crucial step in the aggregation process. [source]