Protein, proteins families

Table 8.1 The major proteins/protein families that constitute the cytokine group of regulatory molecules3...

GeneWise [44] allows a nucleic acid sequence to be aligned with a sequence or sequence profile (HMM) associated with a potentially homologous protein or protein family. The protein/protein family information is used to infer a putative intron-exon structure in the nucleic acid sequence. The core of the model is a state model of matches, insertions, and deletions, similar to those used in HMMER and Smith-Waterman algorithms. Two key additions are made to the core. The first addresses frame-shifts. The second is a five-region model for introns. The five regions are... 

An integrated database based on SwissProt, TrEMBL, Pfam, PRINTS and PROSitE, and thus includes data on proteins, protein families, and do-mains/motifs, providing useful information for predicting protein struc-tme and function for sequenced genomes. 

We have previously calculated conformational free energy differences for a well-suited model system, the catalytic subunit of cAMP-dependent protein kinase (cAPK), which is the best characterized member of the protein kinase family. It has been crystallized in three different conformations and our main focus was on how ligand binding shifts the equilibrium among these ([Helms and McCammon 1997]). As an example using state-of-the-art computational techniques, we summarize the main conclusions of this study and discuss a variety of methods that may be used to extend this study into the dynamic regime of protein domain motion. 

Holm L and C Sander 1994. The FSSP Database of Structurally Aligned Protein Fold Families. Ni Acids Research 22 3600-3609. 

G-Protein Coupling. The heterotrimeric guanosine triphosphate (GTP) binding proteins, known as G-proteins, are a principal family of proteins serving to couple membrane receptors of the G-protein family to ionic and biochemical processes. This topic is reviewed in References 63—67. 

ZT Zhang. Relations of the numbers of protein sequences, families and folds. Protein Eng 10 757-761, 1997. 

To gain the most predictive utility as well as conceptual understanding from the sequence and structure data available, careful statistical analysis will be required. The statistical methods needed must be robust to the variation in amounts and quality of data in different protein families and for structural features. They must be updatable as new data become available. And they should help us generate as much understanding of the determinants of protein sequence, structure, dynamics, and functional relationships as possible. 

M Brown, R Hughey, A Krogh, IS Mian, K Sjolander, D Haussler. Using Dirichlet mixture priors to derive hidden Markov models for protein families. Intelligent Systems in Molecular Biology 1 47-55, 1993. 

RL Tatusov, EV Koonin, DJ Lipman. A genomic perspective on protein families. Science 278 631-637, 1997. 

Neer, E.J., et al. The ancient regulatory-protein family of WD-repeat proteins. Nature 371 297-300, 1994. 

Sonnhammer, E.L., Eddy, S.R., Durbin, R. Pfam a comprehensive database of protein domain families based on seed alignments. Proteins 28 405-420, 1997. 

AKAPs are cyclic AMP-dependent protein kinase (PKA)-anchoring proteins, a family of about 30 proteins anchoring PKA at subcellular sites in close vicinity to a certain substrate. 

APP is a type-I transmembrane protein that is part of an evolutionarily conserved protein family, including the amyloid precursor-like proteins 1 (APLP1) and 2 (APLP2). APP and APLPs are functionally redundant and form homo- and hetero-oligomers. The absence of the A 3 sequence in the APLPs underlines the importance of APP that can only give rise to the A 3 species. Decreasing the formation of soluble A 3... 

Two types of calbindins have been described, calbindin D28k and calbindin Dpk- The latter (now renamed as S100G) belongs to the SI00 protein family. 

Today, molecular chaperones are divided into three principle classes, according to their mode of action (Table 1). The one class comprises the chaperonins or HsplOO protein family members. Chaperonins are oligomeric proteins, composed of two rings placed... 

Cytokeratins are members of the intermediate filament class of cytoskeletal proteins. Cytokeratins are a large protein family comprising two subfamilies of polypeptides, i.e. acidic (type I) and basic (type II) ones. Cytokeratin form tetramers, consisting of two type I and two type II polypeptides arranged in pairs of laterally aligned coiled coils. The distribution of the different type I and II cytokeratins in normal epithelia and in carcinomas is differentiation-related and can be used for cell typing and identification. 

The HMG (high mobility group) box is a DNA-binding domain found in several transcription factors, that can in some cases bend DNA. Some members of this protein family recognize a unique DNA sequence, whereas others bind to a common DNA conformation. 

Neurotrophins (NGF brain-derived neurotrophic factor, BDNF neurotrophin-3, NT-3 NT-4 NT-6) are important regulators of neural survival, development, function, and plasticity of the vertebrate nervous system [1]. Neurotrophins generally function as noncovalently associated homodimers. They activate two different classes of receptors, through which signaling pathways can be activated, including those mediated by Ras and members of the cdc42/rac/rho G protein families, MAP kinase, PI-3 kinase, and Jun kinase cascades. 

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